This article isprotected bycopyright. Allrights reserved. Accepted Article

article as doi: 10.1002 / jsfa.7692 differencesbetween version lead to this may been through the copyediting, typesetting, pagination andproofreading process, which This article hasbeen accepted for publication andundergone full peer review but has not a Queensland, Australia c b Hue T.M. Tran Advances ingenomics for theimprovement ofquality in Coffee +61 7 3346 0551, Email: ro Email: 7 33460551, +61 The Innovation (QAAFI), ofQuee University * Western HighlandsAgriculture& ForestryScienceInstitute (WASI), Vietnam Southern CrossUniversity,Australia QueenslandAlliance forAgricultureand F Correspondence to Correspondence ab , L. Slade, L. Lee : RobertHenry, [email protected] [email protected] c , Agnelo Furtado , Agnelo

Queensland Alliance for Agriculture and FoodQueenslandandfor Agriculture Alliance ood Innovation (QAAFI), The University of ood Innovation(QAAFI), nsland, St Lucia nsland, StLucia QLD Tel. 4072, Australia,

and the Versionof Record. Please cite this a , Heather Smyth a , Robert Henry

a* This article isprotected bycopyright. Allrights reserved. Accepted Article sequencing,generation association studies. Key words: explored. sequencing and association genetic analysis qualityare described and thepotential fortheapplication ofnext generation association genetic analysis. The genomic re ( ofarabicacoffee base suggests qualitycan now beidentified byassociat components inthe coffeebeanthat knare species. Genes responsible for control determinants controlling quality in coffee complex arabica coffee ( more genetically the for sequence genome reference a However, development. coffee, for robusta sequence ofagenomic report of analysis coffee newtoolsfor providing is aprimary targetof coffee improvement genetic programs. in Advances aregenomics developing countries.Production ofgenotype isan importantCoffee cropthatprovides Abstract Coffea spp.) mayberequired tofind thephenotypicdiversity requiredfor effective Coffee quality,genetics,genomics, Coffee biochemical next compounds, C. arabica) thatgenomics analysis ofcoffee of thewild relatives will also berequired tofullydefine the molecular of levelsthe of the major biochemical ion analysis. However, thenarrowgenetic quality at the molecular level. Therecent quality themolecular at a livelihood to millions of people livingin ofpeople a livelihood tomillions produced from thishigh quality coffee own to beimportantin determining coffee sources availablefor the sources coffee study of toadvance coffee quality research are s with improved coffee qualityattributesimproved coffee s with Coffea

canephora, is a major a is major

This article isprotected bycopyright. Allrights reserved. Accepted Article Afrocoffea sub-genera, feasible tounderstand the improvement programs. Withadvances in genomic and sequencing technology, itis improving thequalitycommercialof both sp across twogenera Rubiaceae family and the of will also be discussed. In addition, the potential value of the study of genetics of coffee coffee of genetics of study the of value potential Indiscussed. the will alsobe addition, genetics of biochemical compounds likely flavour aretobe playingarolein that coffee Availa by breeding. coffeequality improving for use foundation for as a determinants, quality compounds whichareconsidered This review will discuss current knowledge coffee quality,thereby helping improvethe efficiency ofbreeding programs. Although Coffea productionCommercial coffee isdominated by only twospecies belonging tothe petroleum) providing a livingto petroleum) providing isanCoffee important crop andthe second most tradedcommodity inthe world(after except for coffee). All coffee species are diploid (2n= spontaneous hybridizationbetween eugenioides Coffea genus: and C. arabica (Moens) summarized by Anthony etal. C. arabica maternal(as progenitor) Coffea Psilanthus C. arabica Coffea and is is considered to have bettercuppingquality than whichis tetrap aself-fertile Baracoffea genera has been examinedin several studies and and L. and L.and Coffeeae coffee genomeand the mole C. canephora GENERAL INTRODUCTION INTRODUCTION GENERAL more than 125 million people people 125 million morethan Psilanthus tribe and consists of more than124species ofspread consists tribeand more (J.-F. Leroy) J.-F. Leroy,and Leroy) (J.-F. C. canephora C. canephora 8

9 . regarding the geneticsof thosebiochemical ble genomic resources forthe study of the 2x=22) and generally self-incompatible,2x=22) andgenerally (thelatter generallyreferred to as robusta Hook.f, each ofHook.f, each oftwowhich inturnconsist ecies remains a targetfor most coffee loid (2n=4x=44) derived from a loid (2n=4x=44) (as paternal progenitor) 2 respectively.The grouping cular inheritance underlying 1 . Coffee belongs to the. Coffee belongs Psilanthus C. canephora, 3

4

5

and

6 and

7 . C. This article isprotected bycopyright. Allrights reserved. Accepted Article (total chlorogenic acids, aliphatic acids and quinic acid) quinic acids and chlorogenicacids, aliphatic (total (coffeeoil, diterpeneesters), minerals (potassium andphosphorus), acids and esters of tasters preference the and acidity tongue), on the richness organolepticwhile quality reflects aroma, taste, defects (e.g. sticks, stones, damaged beans and and the organoleptic propertiesof the coffee. beans of the coffee attributes bothphysical the by evaluating isassessed quality Coffee considered. next sequencing generation quality using compounds are considered to play lignin), nitrogenous lignin), compounds (protein, free include carbohydrates andfibre (sucrose, re bean ofthe components and volatile components. Important non-volatile non-volatile Biochemical compounds influencing theorgano cup. compounds in coffee beans are important contributors to the quality ofthe coffeein the Chlorogenic acids (CGAs)andcaffeine, responsiblebitterness arefor aromaprecursors. produce to sugars reducing with react example, for acids, beans compounds that contribute to the flavour of components, sucrose, caffeine, trigonelline, lipids andCGAs are majorbiochemical volatiles detected so far detected in greencoffee bean volatiles coffee cup quality(often referred to simply as ‘cup’).There aboutarethree hundred cup quality, caffeine and subsome classes of 11 . While sucrose, trigonelline and lipid ha trigonelline and . While sucrose, BIOCHEMICAL CONTROL OF COFFEE QUALITY AND ITSVARIATION BIOCHEMICALCONTROL OFCOFFEE QUALITYAND a role inroasting chemistry and association genetic analysis will be will genetic analysis association and Physical quality reflects moisture content, ducing sugars, wall cell polysaccharides, the beverage after the roasting of the CGAs have correlationa with CGAs negative amino acids, caffeine, trigonelline), lipids lipids trigonelline), caffeine, aminoacids, 14 flavour, body (afeeling of the heaviness or black beans), black bean size and bean colour; of which twenty one volatiles, ofwhichtwentyonevolatiles, lepticquality ofcoffeebeans include ve ave positive correlation with coffee 11 . Allbiochemical ofthese 10 . A range of biochemical 12 . Proteins and amino . Proteins 13 . Among these This article isprotected bycopyright. Allrights reserved. Accepted Article Grosch the concentrat a in but by shift odorants, new profile odour. aroma changein phenolic This Severalnotes in roasted coffee become more intensive in thebrew such as caramel and properties andthe compositionof coffeehas been thoroughlyreviewed by Flament volatile compounds contribute tocoffee coffee flavour and its constituents have been reported. How the volatile and non- isextremel itsformation and flavour Coffee However, the change in bean composition, under coffee roastingunder coffee conditions beanroasted is complicated and not allformation pathways arefully understood and morerecentlybySunarharum et al. compound-groups are more than a thousand volatiles which been identified as for keycompounds coffee cup including 3-isobutyl-2-methoxypyrazine and 2-methoxy-3,5-dimethylpyrazine, have coffee aroma andits mechanisms have been reviewed byBuffo &Cardelli-Freire superior beverage quality quality characteristics is feasible andit is possible to select varietiescoffee with the identifica functionalapproaches, genomic thatis,ascribinglinkstocoff composition, more directly affected by genetics. This is roastedbean and brewis ofcustomer's interest, while the green bean attributes are therefore should of coffee quality genetics 16 . 15 . The aromaof the brew. is different fromthatof roasted coffee. 20 . 19 . The use of green bean bean or The use of . green 17 quality andrelationships betweensensory . The reactionsinvolved in the formation of a challenge inthe study ofbeangenetics of can be grouped into twentykey aroma ee quality. However,ee withtheprogressin be considered carefully since aromain especially especially in aroma profile,from green to ycomplex; however, numerous studieson of coffee is not caused by the formation of of by theformation notcaused is of coffee ions of existing ones as summarised byonessummarised as ions ofexisting tionof coffee ofmolecular determinants 14 . In the roasted coffee bean, there roasted bean roasted in thestudy 18 . 12

This article isprotected bycopyright. Allrights reserved. Accepted Article factors such as thecultivation conditions (soi the cup depends notonly ongenetic factors varieties) (species, but alsoon non-genetic The composition of the beans that determines genotype Liberica yields coffee that is bitter and without finesse finesse without and is bitter that coffee yields Liberica genotype genotypes Blue Mountain and Bourbon produceCatimor, finercoffeesthan while brewthanKent, a SL28produces milder genotype Forexample, profiles. flavour specific with associated be can varieties different coffees, arabica the Within bitterness. and body acidity, aroma, preference, for Guinean), and (Congolese studied groups genetic main on the variation in the biochemical composit on thevariationinbiochemical 21-24 different between species and toa lesserextend within species Thebean chemical composition and organoleptic characteristics are significantly Similarly, Tessema et al. Fatty acidand CGAswereused as indica biochemical constituents (sucrose, fat, crude arabica germplasm collections from Ethiopia and lipids areata higher concentration in correlation a positive have that compounds in quality traits ofvariation study coffees, Moschetto coffee are more aromaticwithmore perceptible aciditybut less body. Withinthe robusta Robusta coffeebeans have a bitter, full bodied reported. been also have types coffee different between flavour in differences Significant other . Coffea species. et al

28 27 found important differences in cup quality between the two the between quality cup in differences important found also found thatfound thequalitytraits also (organoleptic quality) and C. arabica tors todifferentiat C. arabica with quality such as sucrose, trigonelline such assucrose, with quality . Thisisan encour ion of the bean are summarised in Table 1 in Table of thebean are ion summarised protein and minerals)were inthe diverse l, air temperature, al taste, but low acidity while of those arabica for association mapping.In general, the properties andquality ofcoffeein than in e arabicavarieties C. canephora 29 aging resultforthe aging . 10 titude, sunexposure . A number. ofstudies and some 25

26 . This article isprotected bycopyright. Allrights reserved. Accepted Article a single allopolyploidization event allopolyploidization a single diploid ancestors, by formed an allotetraploid species Being phenolic compounds) in somatic embryo regulation in arabica coffee species relation to size andshapeofthetree epigenetics andcoffee quality.Only a very few studies have reported on epigenetics in been several on studies onfactors affectingcoffeequality, not therehas beenresearch Epigenetics is extremely complex andisnot yetfully understood. therehave Although This change thatis due control tofactors each howandwhen gene is expressed. positive correlationto coffee composit general, volcanic soils, low temperature,altitude high and growing under shade have In methods. processing and and harvest and irrigation) fertilisation management, and rainfall),plant condition (plant age, be been manyreports presentedindetail ontheseissues interaction would help withrea defining duplicated genes (homoelogues).Proteins wi for sequence divergence resulting in development of functional variations between most recentof reviews Joetet al. influence on coffeequality a strong have also beverage ofthe preparation the and roasting techniques, harvest chemical composition and environmental effects, or Santos et al. Another factorthat mayinfluence coffee qua and preparation toaromamethods profile, modified gene modified gene expressionnotcaused byalteration inthe gene sequence orDNAcode. impacts onimpacts beanquality, orSunarharum al. et C. canephora 30

35 . Understanding the influence ofeach factor andtheir and 39 44 onthe relationshipscoffee bean between quality, , arabica mayhave genetic redundancyallowing C. eugenioides 41 ions which relates to coffee quality ions whichto coffeequality relates , and epigeneticin (especially mechanisms listic breeding strategies. Since there have have Since there strategies. breeding listic a recent naturalhybridization between two an maturity), cultivatan maturity), they are notreviewedin thispaper. th different properties may be encoded lity isepigeneticeffe 17 on the impacts of processing, roasting processing, of the impacts on , and whichmayhave gone through 26

33

29

36

37 ion practices (shade

40 38 cts. Epigeneticsis on climatechange

20 , especially the 30-34 42 . Post-

43 . This article isprotected bycopyright. Allrights reserved. Accepted Article environmental variations with those ofcompare itsprogenitors a gene expression in mayresultingenes phenotypicnovelty with with yield in with yieldin were not significant, indicati determinantsand cuptasting components measured intwo groups of association genetics incoffee. diversity for different traits, buton the otherhanddifficult makeit to conduct source ofgeneticdiversity. Thisonone hand elimination and conversion appeartohaveoccurred in rearrangements involving homoeologous epigeneticin alternationsembryoge somatic epigenome instability. However, epigenome Vidal etal. instability. embryogenesis while embryogenic suspensions have a high risk of genome and always equally expressed arealso homoelogues subject toextensive by homoelogues leading tonew genetic di between SequenceExpressed Tags (ESTs)and gene differential expressionfor arabica using Si by Montagnon Montagnon by targ isthe and quality both yield Improving GENETICS OF BIOCHEMICAL COMPOUNDS COMPOUNDS OFBIOCHEMICAL GENETICS C. arabica C. canephora et al C. arabica and and

48 , genetic correlations betweencoffeeyieldquality and C. canephora 47 45 . Understanding the genetic inheritance thegenetic ofquality. Understanding traitscan . Recently, Lashermes et al. . Landey et al. Landey etal. . ng that the coffee quality is not negatively associated associated negatively not is quality coffee the that ng grown in twocontrastedwas also conditions usedto . Thedivergence offunctionin homoeologous nd to itsability examine toadapt exchangesaswell as silencing, gene expressionfrom transcript redundancy ngle Nucleotide Polymorphisms (SNPs) from (SNPs) Polymorphisms Nucleotide ngle 43 versity in breeding populations. However, et for coffee breeding programs.etfor coffeebreedingIna study epigenetic control and are therefore not confirmed theverylimited geneticand QUALITY 46 usefulagronomic traits. Homoeologous nesis-derived plants during coffee somatic willmakea potentnew source ofgenetic foundhomoeologous displaying genes KNOWN TOBE RELATED TOCOFFEE 44 C. arabica confirmed that the genomic that the genomic confirmed and toa bemajor C. canephora This article isprotected bycopyright. Allrights reserved. Accepted Article studies using intraspecific hybrids Male/femalein additive inheritancesucros was mentionedwas byBertrandet al. improvement tointroduce thedisease resist inheritance of qualitycharacters inintrog breeding (e.g. parent for selection) robusta coffee quality improvement. The gene effectsappear tobe involved inthe variationof caffeine content in the seeds hybrids are detailed in Table 2 in Table detailed are hybrids biochemical compounds determining coffee quality inintraspecific andinterspecific beverage quality. Known inheritance mode bioc key theof geneticunderstanding control benefit breedingprograms, butthere appears little research hasthat focussed on quality at the interspecific level is not not is level interspecific the at quality relating to thevariability ofquality componen during fixation their to relation in species hybrids due to the differences among intraspecific of that from different was hybrids The inheritance of coffee cup quality was also reported by Leroy reported quality also was cup of coffee The inheritance complexitytrait.implying the ofthis combination offat and sucrose content fat content and sucrose contentindicates that care should be taken in selectingfor a these traits canbe improved at theintraspecific level. The negative correlationbetween of heritability caffeine narrow-sense andfat acidity,only amale additive effect was observed robusta coffee,female additiof bitterness 48-56 58 51, 56 .

31 similar to that in intraspecific hybrids similar tothat inintraspecific and alsoreviewed by Leroy etal. . The heritability. measured ininterspecific evolution ofspecificallelesof some genes 48 ressed lines, which resulted during arabica arabica during resulted which lines, ressed . Both. majorandminor genes withadditive ve effects were predominant, while for while werepredominant, ve effects e and trigonelline was contrasted in two and heritabilityof thekey values content inintraspecific hybridsimplies that content ts. As a result, the genetic variation in in variation genetic the a result, As ts. ant genes fromant genes Timor hybridto arabica, hemical compounds thatrelateto coffee 51 . This will information assist the et al

51 where for 10 10 . . The high high . The 57

This article isprotected bycopyright. Allrights reserved. Accepted Article from Timor hybrid arabica. The focusofarabica improvement is the improvementcanephoraquality of dueitsknownlowerquality compared to on focused has research recent the of and past most improvement, genetic For coffee MAS.trait-linked in markers for use development coupled withtrait phenotyping,it shouldpossible be to easily identify excellent reviews byLeroy etal. are there breeding, improvement arabica and of canephora strategies and trend the Fresh brewing ispopular for necessary be would trigonelline, CGAs like lower heritability or effectively by crossing between parents ofdi In summary,highly heritable traits like fa lyophilisation (i.e. coffeeprocessing (i.e. instant lyophilisation polysaccharides) whichinfluencetheextr reduction, the beancomposition ofgalactomannans arabica andcanephora. between the same mean thatarabica quality improvement isunnecessary. Qualitydeterminants arenot second priority in arabica as its qualityits is secondas priorityinarabica quality factors as well as to qua for speciality coffee has intensified research may beapplied to arabicainthe future. Fo 10 4 orclimatechangeadaptation . Withoftheadvancesin se

arabica, ratherthaninstantco ntify these features organoleptic 10 and Vossen etal. t or caffeine content could be improved improved be could content t orcaffeine considered superior.Ho action during theindustrialaction processof sucrose, Marker Assisted Selection (MAS) Marker Assisted sucrose, r arabica, the increasing consumer demand demand consumer increasing the arabica, r Forcanephora, apartfromcaffeine ) isprobably the most important target. aimed at pinpointingsmall differences in fferent favourablevalues. For traitswith moreon transferof disease resistance quencing technology andmarker 59 20 ; quality ; quality improvementis the 60 . or other compounds (other other compounds or ffee processing – although it – although ffee processing 61 wever,this doesnot . Formore detail on This article isprotected bycopyright. Allrights reserved. Accepted Article different regions (Brazil, Yemen,Indian, marker systems(RAPD, AFLP,SRAP,from and coffeecollected TRAP) SSR, ISSR, studies show a very low variation genetic amongst arabica cultivarsusing different accessions/introgression/hybrids; and spontaneous/sub-spontaneous) almost all differing results. In general, amongthree main types ofmaterial (cultivar/varieties; numberA ofworksassessment onthe of arabica diversityhave beenwith done reproduction methodand dissemination may expect to seethemostdiversity, hasdiversity ranging from low variation, more diverse inintrogressed the lines (accessions/introgress group The second moderate moderate Coffee genetic diversity Coffee genetic in in somestudies In contrast to In contrast population structureand its genetic diversity. association mapping is verycritical. Ther breeding improvement, and thus the selection of appropriate germplasm for programs. This alsofor isproblematic diversity tomato)indicating cultivated foundin the 800aforementioned in diversity found found thatcultivated coffee varietiesco geneticdiversityleast ofthis speciescompared to othermajor also crops.Thisstudy arabica fromthearabica coffee accessions the World CoffeeResearch annualreport 77 tohigh C. arabica 77-79 but not in the others 78 . The correlationof genetics withgeography/origin clearlyshows , C. canephora C. arabica COFFEE GENOMIC RESOURCES and associationmapping workfor inarabica possess a high genetic due to diversity origin, its ntain approximately 45%of the genetic Australia and Vietnam, Tanzania, Hawaii) Australia andVietnam,Tanzania, efore itefore is essentialto understand the ion/hybrids) significant lowion/hybrids) shows to 80 59 75 C. canephora , and it is structured in two main groups collection atCATIE,Costa Rica showsthe accessions (while only 2% of tomato 2% tomato (whileonly of accessions , genetic diversity 800 , genetic assessment of

72

70 thelimitation variabilityfor breeding of . Inthemost recent work presented in 70

27

71-74

. The last group, in which one 75

72

76 to 62-69 . This article isprotected bycopyright. Allrights reserved. Accepted Article for almost half (49.2%) of the reference ofthege (49.2%) half for almost transfers wastransfers alsoanalysed withatypica arabica applying association within studies The genome size of coffee has been estimated to be 1.3 Gb for for Gb 1.3 be to estimated been has of coffee size genome The Coffee whole genome andsynteny for anytraits in coffee. diversity ofthe twodominant speciesis cr of robusta coffee has just been completedand reported in2014 elements (TEs)in the orderconservative chromosomalgene am among which139werean both anchored covering approximately Mb 364 ahigh-d Using 3). (Table of568.6Mb length of 25, resulting consists genome assembly usedtocorrect also Mb),was (710 genome In addition, Illumina sequence data, correspo BAC-end reads were used, repr genome sequenceof (Guinean and Congolese) with six subgroups for other diploid coffee species varied from 0.96 pg (469 Mb) ( Mb) (469 pg 0.96 from varied species coffee diploid other canephora and 1.2 Gb) to (equivalent pg 2.47 in Mb) ( C. canephora C. canephora C. humilis due to itsparental relationship to this species ) breeding populationswas variable, indicatingthe possibility of 87 86

88 . Using flow cytometry, the DNA content of arabica was estimated as estimated was of arabica content DNA the cytometry, flow Using . . Despite its economic importance, the first high-quality draft genome genome draft high-quality the first importance, . Despiteits economic C. canephora C. canephora esenting 29.5X coverage of esenting 29.5Xcoverage were anchored to the11 , andmate-pairreadsSanger Roche 454single genome were identified genome were and classifiedaccounting C. canephora lamount ofchloroplast-derived fragments d oriented. Coffee displays themost displays d oriented.Coffee 216 contigs and 13,345 scaffolds with atotal 13,345 scaffolds and 216 contigs itical for any genetic improvement scheme scheme improvement any genetic for itical ong asteridangiosperms.Transposable nome length. Organelletonuclear genome sequencing errors and fill fill gaps. The errorsand sequencing ensity genetic map, a total of 349 scaffolds scaffolds of 349 ensity geneticmap,atotal as 1.43 pg (equivalent to 700 to Mb),while pg (equivalent as 1.43 81-83 nding to 60X ofnding to60X coverageCoffee ofthe species and usingit to improve . Thelinkage disequilibrium assessed 84 . Understanding the genetic C. mauritiana C. canephora the genome size the genome size (710 Mb). C. arabica 86 . To generate a whole whole a . generate To ) to 1.84 pg (900 pg (900 ) to1.84

85 chromosomes, chromosomes, and 710Mb and C. This article isprotected bycopyright. Allrights reserved. Accepted Article using differentmaterials and biological sequencing platforms et al. of sequence genome whole chloroplast The Several studies studies Several coffee species, resource is extremely important for the studyof questionable. Several research groups are working on an an on working are groups research Several questionable. of the members among phylogeny the up build helps and Hub familiesgene andmetabolic pathwaysare the genomicsdata, data of transciptomic most valuable genomics resource for further involvedin enzymes andflavonoid alkaloid N-methyltransfer as were examinedsuch and aroma were coffee flavour whichin several functionsinvolved gene in secondarycompound biosynthesis and from otherIntotal,25,574pr plant genomes. more fragment mitochondrion-derived 750kb accounting0.16% insertions, of (2,014 for show one-to-threecorresponden ploidyin their changing interveningsepa one correspondences with grape chromosomes, provingthe lackof any events most recent reportedthatstudy coffee C. arabica coffee Among comparisonspecies, of genomesshowed ahigh gene between synteny 89 90 . (Table 3) (Table andthisalsoprovides anim (EaEaCaCa) and (EaEaCaCa) C. arabica. 95-97 have compared genomes between coffee and other crops. The

C. canephora characterized. Species-specif ce with the tomatoce with genome chromosomal regions showed unique one-to- (CC) and rate histories. Coffee and grape genomes genomes and grape Coffee rate histories. , SNP polymorphisms, SNPand genotyping data, ases (NMTs), genes,and ases defence-related the draft genome) and an unusually large and anunusuallylarge thedraft genome) Coffea arabica publicity available via the publicity Coffeeavailable Genome portant reference for studying other species species other studying for reference portant secondary compound synthesis. This is the genomicsespeciallycoffee, studyin as all otein-coding gene models were obtained than 100 Kb longer than those known thanthose Kb longer than100 genetics and genomics of the high quality C. arabica Coffeeae L. was first reported by Samson Samson by reported first L. was C. arabica (EaEaCaCa), C. (EaEaCaCa), ic gene family expansions 91 86

. 92 tribe which is still still is which tribe

93 genome sequence sequence genome

94 . This genomic . Thisgenomic eugenioides

This article isprotected bycopyright. Allrights reserved. Accepted Article genome genome captureand next-generationstrategies sequencing, andwere evaluatedon 72 arabica assisted Re in coffee breeding. selection be validated in other genotypes for consiste for caffeine, eight forCGAs and one for caffeine and CGAs markers associated with quality traitsidenti population between Polymorphism) andSSR weremarkersused to construct a geneticmap ofanF2 using parallel between different usinggenotypes direct sequencing. Thevari diversitythe nucleotide offouridentify sucrose in metabolismenzymes from and SNPs, INDELs(insertions deletion infancyand thereforelimited.Pot in its still evaluation theuse cost.However, of DNA technology incoffeequality improvement is wouldhelp reduce the length ofbreeding selection cyclesand thus phenotypic As forother crops, determination ofmole (EE) and Molecular markers markers Molecular Other genomicresources was in with the agreement ancestra that important resourcefor the and differences, obtainingsequence thusawhole-genome sequence wouldbe an detected C. eugenioides and 87,271 SNPs specific to SNPsspecific and 87,271 C. liberica 98 . The two sub-genomes of of twosub-genomes The . in silico (LL) Coffea was more closely related to C. arabica analysisof ESTresources 98-100 species toallowtheidentificati allotetraploid genomeof , but, numerous chromosomal rearrangements were and and C. canephora l historyof theallotetraploid C. canephora C. arabica cently, a total of 33,239 SNPs specific to specific 33,239 SNPs of cently, atotal cular predictors for coffee quality traits s) ands) SSRs(Simple Sequence Repeats) to ation of these was alsogenes analysed et al. fied was nineteen for sugar content, eightfiedwasnineteenfor sugar content, ncy beforethey can beused in marker 101 C. arabica (Ca and Ea)indicated sufficient

101 (artificial tetraploid). (artificial . AFLP (Amplified Fragment Length Length Fragment (Amplified . AFLP weredeveloped using targeted used polymorphisms generated generated polymorphisms used C. arabica. C. arabica. on of more polymorphic sites on of morepolymorphicsites than to to than 102 . These markers needto Results also revealed revealed also Results C. arabica C. liberica

The number of C. canephora

100 , which . . C. This article isprotected bycopyright. Allrights reserved. Accepted Article discovery have used theavailable resource of ESTs for further research such as microsatellite marker these all resources are publishedoravailable and leaf rust resistant manage genetic diversity in coffee species species coffee in diversity genetic manage a for genome support samples from relation to metabolismsucrose Three BAC libraries were developed for each ofspecies (BAC)libraries. chromosome Bacterial artificial A total of 246,500 ESTs have been reported with 69,801 for reportedwith ESTs havebeen of 246,500 A total summarised in Table 5. fruits and roots) at different stag different at roots) and fruits arabica with the expression ofqualitya with the expression transcriptome analysis and theidentification ES biochemicalpathways. essential through potential genes contributing toqualitytrai developmentThe oflargeEST sequencing proj Expressed sequence tags (ESTs) andregulatoryelements of genes controllingimportantidentification traits in coffee. important resource to support genomic studi biosynthesis pathways of lipids and main storage proteins proteins main storage and oflipids pathways biosynthesis reductase gene (CaM6PR) resources availableresources in coffee ha and 10,566 for and 10,566 116 , analysis of transcriptome divergence and analysis of genes involved in the C. canephora 106 ssemblies, accelerate breeding accelerate ssemblies, interested of traits as well as C. racemosa , bean size and cup quality quality and cup size , bean 108 and 72 from (Table 4). These available BAC libraries of libraries BAC available These 4). (Table es of development and maturation maturation and ofdevelopment es nd the genes within these pathways ve been reviewed byKochko 104 , genome compositionand, genome evolution using different organs of the plant (leaves, flower, flower, of (leaves, plant the organs different using C. arabica ts and their interplay with other genes other genes with interplay andtheir ts 103 es such as comparative genomics and the which limitstheir use. ofA number studies Ts facilitateTs the development of whole ofbiosyntheticthe pathways associated . ects has thesupported identificationof 107 . These genomicresources will and mannose-6-phosphate C. canephora 117 C. canephora , gene structure prediction prediction structure , gene et al. 109-115

85 andare 10 Coffea and . The EST , 166,133 , 166,133 for . However,. not 105 C. arabica , nematode are an are C. in This article isprotected bycopyright. Allrights reserved. Accepted Article arabica diploid different coffee populations different coffee QTLs QTLs relating to organoleptic traits a mapping of quantitative trait loci (QTLs) complex traits(yieldcomponents, quality The construction of ge and QTL identification genetic mapping research on coffee quality improvement. increase and quality improvement quality increase and for framework isolation of candidate genes to coffeequalitywerenoted Co-location ofsome QTLs and genes involved may determine the allelic variation of variation may determine coffeequality theallelic and functional annotation withthede annotation functional and performed on been have and cup compounds toquality relating analyses ofQTLs number a date, To markersas well as genomic resources of DNA collection large of a the absence and andgermplasm), cultivars Ethiopian of due toits long life cycle, lowpolymorphism (inof the case than in annualcrops andcost more effort requires in general in coffee mapping Linkage the QTLs. directly usedin MASwithouttheneedunderstanding of functionality gene underlying 300 pathways in pathways 300 C as indicated in Table 7 inTable asindicated . canephora C. canephora C. canephora by Paillard et al. al. et by Paillard netic maps is often the first st netic maps is often 51, 56, 96, 102, 120-129 102, 96, 56, 51, andother species, but nonehas been reportedfor

51 118 . Using such . Using candidateinmapping genesassociation 50, 51, 56, 131, 132 131, 56, 50, 51, . This genomic resource will be very important for further further for important very be will resource genomic . This 119 120 nd genes associating withcaffeine orCGA tection of tection a totalof 345 in pathways 119 . In many cases, markers linked to QTLs are followed by several others constructed for for constructed others several by followed . The first genetic maps were constructed in the in constructed were maps firstgenetic . The controlling these traits and thus provide a and mapsenable disease).Genetic the

130 followedby manipulationof genes foryield

in different metabolic pathways related metabolic pathwaysrelated in different (Table 6). ep for of molecular dissection 133 . The co-localisation between between co-localisation . The C.

arabica – withtheexception C. arabica C. and This article isprotected bycopyright. Allrights reserved. Accepted Article transcriptional regulations during seed development development seed during regulations transcriptional coffee species.Currently there are works ontranscriptomics tounderstand the resourcefor bevaluable mole This will a expression. their for examined were andfruitripening metabolism to sugar related involved in the flavour and sensory involved intheflavourandsensory quali arabica bitterness in the coffeecup bitterness in biosynthesis mayexplainthe factthat both CGA and caffeineinvolved are inconferring caffeine accumulation 131, 134-141 131, quality processes. These genes whare candidate genes community, especially those on genes encoding the enzymes of keymetabolic have been cloned andcharacterised. These resultsuseful are tothe coffee genetics them of some and identified been have genes candidate coffee of a number genomics, coffee research groups around theworld.Th relatingidentification ofgenes toThe quality identification Gene However, sequences from the genes thatare knowncan serve as useful references in low andhighlevelsofthekey biochemical trigonelline synthesis and no studies on alle have been identifiedin Although severalgenes encoding the biosynth bean qualityand ultimatelybe useful in breeding programs forcoffeequality. facilitate the development of robust geno 10 ’s . fr Recently, 36,935 unigenes . Genes regulating the main chemical themain . Genes regulating

ancestors, were identified by Yuyama et al. 143 C. arabica andchlorogenic acids 51 . and om leaves and fruits of and fruits om leaves C. canephora cular and genetics studies ofcommercial tyof coffee are listed inTable 8 mics/metabolomics fingerprints of coffee coffee of fingerprints mics/metabolomics compoundswhich canbe utilised in MAS. lic variation (e.g., SNPs) associated with associated (e.g.,SNPs) lic variation anks tothe concertedoncoffee efforts is one of the objectives main of several esis ofbiochemical compounds in coffee components that are thought to be ich may control the variability of coffee ich maycontrolthevariability 144 orgalactomannan , there are no genes identified for 39 142

13 . Asub-set ofthesegenes or more specifically for C. eugenioides, C. eugenioides, 60 . These could could . These 13,86, 51, 104, 117, one of one C. This article isprotected bycopyright. Allrights reserved. Accepted Article thought tobe involved inflavourquality, theand sensory it should be possible to apply are that sequences) gene reference their (and compounds ofbiochemical knowledge on perennialcrops and forestrytrees (pine, and successfully applied invarious crops including annuals (rice,maize, soybean,wheat) or quality amongcoffee species,quality in especially drought tolerance, cold hardiness and timing of bud set summarised by Sexton et al. al. et Sexton by summarised set bud of timing and hardiness cold tolerance, drought candidateofgenes/QTLs traits complex such as detect to approaches genetic these used have (NGS) sequencing generation next ofA number previous studies involving geno populations except bi-parental mapping of QTLs for trigonelline and CGA contents. there hasbeenno research focusing on al facilitate further studies onbean composit have also been identified.These studiesprovided via gene sequences ESTsthat will relating to the synthesis of sucrose, caffei considerablegeneti showed Previous studies coffee than arabica coffeedue the limitationsof thetechnology used.More studieshave been conducted forrobusta regionsgrowing being developing countries– contribution.The reasons couldpossibly be comparedrelatively limited toothercrops Researchon genetics and genomics forcoffee, especially in relation toqualityis biochemical compounds in re-sequencing todetectpolymorphisms ASSOCIATION GENOMICS APPROACHUSINGNEXTASSOCIATION GENERATION (NGS) SEQUENCING AND PERSPECTIVES FORTHESTUDYOFGENETICSOF QUALITY AND PERSPECTIVES COFFEE C. arabica to itslowerploidylevel an . cottonwood) summarised by Hall et al. for genetic mapping of the control of the control of mapping for genetic ne, several sub-groups of CGAs and lipidsCGAs and ne,of severalsub-groups lelic ofthesegenesin variation natural diploids. In diploids. addition, anumber ofgenes ion relating torelating ion coffee quality. However, me-wide association studies (GWAS) using using associationme-wide (GWAS) studies andthus belies itspotentialand economic dueto thelackof funding –most coffee c variationc in compo physical woodresistant physical properties,genes, thethe quality complexityof traitsand d greater genetic diversity. diversity. d genetic greater unds defining coffee 146 . Based . Based 145

This article isprotected bycopyright. Allrights reserved. Accepted Article by several authors have beendescribeda PacBio) preparation) aswelldifferent sequen library ligation, of DNA, (shearing in the The NGS level. genome involved strategies whole steps amountof datain a single sequencing run, ma number ofauthors studi plant genomics in NGS Application of from naturalpopulations foruse in breedingwith coffeevarieties better quality. haplotypes valuable to mapping detect QTL withbi-parental GWAS combined and NGS DNA tobeDNA sequenced per sample. Forthis method, inregions ofinterest the genome enrichment allowsfor larger DNAinsertsi regions or genes enriched inthe library from genomic DNA.However,target se toquite similar amplicon enrichment is has already known genomesequence map for that species; and (2) re-sequencing oftoby theuse bioinformaticstools asse data, followed sequence pre-existing have do not that species for applied - sequencing ofwholeincluding genomesequencing(1) canused methods be Two targeted sequencing. identify the available variation in these genes exploited in a population ofof amplicons setscand PCR Sequencing highwith a depth ofcoverage to identify commonand rare sequence variations. and pairs base of hundreds of lengths with of the genome regions selected and small enrichment.Amplicon sequencing will sequence amplified(PCR regions amplicons) of Targeted sequencing includes two approaches, amplicon sequencing and target 151, 152 151, 147-150 . beusedNGS viaancan or approach ofwhole sequencing genome . NGS lowers the cost of sequencing and generates a large a large generates and of sequencing cost the lowers . NGS nd their advantages and disadvantages have been reviewed beenreviewed have and disadvantages nd their advantages 152 . mble the sequences and obtain the genomic zes and enableszes and a greater amount oftotal quencing termsin only of using selected idate genes from DNA bulks will help to will help bulks fromDNA genes idate es hases been extensively reviewed bya cing platforms (Illumina, cing platforms performed onindividualsthat ofa species king itking feasible at genetics the to study Life Technologies, Technologies, Life de novo 148 . Target . Target This article isprotected bycopyright. Allrights reserved. Accepted Article mapping. to data generate adenseSN can beused on the chromosome. Inaddition,whole-genome re-sequencingand SNP genotyping from NGS to data reads sequence assemble published ESTgenes. and BACsequencesca sequencesSNPmarkersidentify andmost genes includingto genefor novel and progenitors of of sequence genomic of sequence genomic is available, a obtain thegenomic sequenceof mapping resolutionthat is achieved andthenumbersof markerscovered Inorganismgenome-wideof interest. st the inthe ofone ofmostcritical (LD) factorsistheextent linkage disequilibrium Whenmaking decisions ontheapproachesof candidateor gene of whole-genome, as afollow-up analysis toGWAS becan targeted, making it an ideal approach well-understood, candidate well-understood,isgene selection candidate causal genenotmutations previously identified typically limited to the field of known gene canephora NGS technology hasbeenused toas selection ofcandidate genes the to support used be must information phenotypic and physiological biochemical,

86 and to examinegenetic change in allopolyploidisationof arabica de novo novo de C. arabica C. canephora C. arabica approach can be applied. other approachThe for obtaining the . The whole genome sequence willbe akey resourceof data 155 . Where a. Where developmental or biochemical pathway is is whole genome re-sequencing as the available draft 153 C. arabica can beuseditisreference of one as since . semble thewhole genomesequence of udies, the extent ofLD determines the P geneticmap of the population for QTL , as ofonly thedraft genome s, which presents the riskof overlooking n be used as reference sequences to identify genes/alleles and their positions positions identify genes/allelesandtheir for examiningspecific gene pathways, or straightforward; but the researcher is researcher but the straightforward; 146

C. canephora 154 C. . Genetic, 44 . To

This article isprotected bycopyright. Allrights reserved. Accepted Article difficult for perennial crops difficult controlled crossing(like conventional ge selection trials. Thisapproach does not require populationsspecific created by because they can be carried outon pre-ex may besuitab Association studies understood. relationships betweenphenotypictraitsan plants dissecting for method popular a very become disequilibrium dueto disequilibrium ofgenerations recombination from geneticallydiverse populations that contain short of linkage stretches Association fromstudies differ quantitative the traits ofinterest.between SNPsand via NGS to detect SNPs, then using an association genomics approach to detect the link belonging tothelipid group, the approach tousecould be whole genome sequencing identified orveryfew identified, for useful for breeding. those compoundsforwhich For candidate genes havenever been confirm orvalidatethecandidate th genes from subgroups caffeine andseveral of sucrose, genes association study of th quality traits, since Amplicon sequencing in a larger set of samples and SNPs variationand SNPs areavailable, association flavin coffee role a be playing to likely traditional method of parent-hybrid map construction construction map parent-hybrid of method traditional toanalysecomplex tr study of and association NGStechnologies Theintegration coffee quality. genes associating 146 . For the . studyonvolatile and non-vola aits will be apowerful strategy complementingthe 155 . Association orlinkagedisequilibrium. mapping has example trigonelline and example trigonelline some compounds our, once the data on oncethedata biochemical compounds our, e biosynthesis pathways, QTLs e biosynthesisand QTLs pathways, candidate netic mapping approaches) which is very whichis approaches) netic mapping isting populations, in collections orin incollections populations, isting d underlying DNA sequen trait trait locus mapping byutilisingsamples could be an appropriate togenetic beanapproach appropriate could genomics will be applied to identify key key to identify applied be will genomics e literature e literature and identify thegeneticbasis ofcomplex traitsin ofCGAsareknown. This will helpto le forperennial speciessuch as coffee tile compounds in coffee and that are that and in coffee compounds tile 145 152 . Such studies thus enable . the alleles thatare the alleles ce variation tobe This article isprotected bycopyright. Allrights reserved. Accepted Article regulatory elements controlling important traits regulatoryelements controllingimportant inbeneficial are libraries comparative genomics, the identification of genes and useful reference points as the genomicapproachisdeveloped. Existing coffee BAC aimed at improvementgenetic ofcoffeequality, but importantly,theywill provide sugar content,caffeinesugar and CGAsin been made with AFLPand SSRmarkers associ While whole technologygenome willprovid aspects of the plant’s biology. of the plant’s aspects understanding of the genetic basisof coffee of wholeavailability genome will sequences genome re-sequencing invariant discovery respectively. There is no doubt that the complementary use ofthe two approachesof targeted re-sequencing andwhole for sequence genome a ofreference development Ethiopia, from aforementioned difficulties canbe overcomebythe use ofwildarabica accessions the andfor specific valida traits of analysis reference isapolyploid(4n)a genome, an using this approach for when taken be should caution quality improvement via breeding programs. However, the traits of between SNPsand link the detect to sequencing targeted and sequencing genome whole both using approach it is resources, genetic and available quality biochemical compounds that govern coffee beancomposition thatrelatestobeverage in validating new C. arabica C. arabica genomic data asgenomic itdata emerges. Withthe current of knowledge quality determinants from natural populations forin use determinants quality since this species has a narrow genetic base, lacks lacks base, genetic has anarrow species this since C. arabica CONCLUSIONS possible to apply an association genomics genomics association an apply to possible provide the greatest stimulus yet to to the yet stimulus thegreatest provide fromd lacks populations controlledcrosses tion ofmarkersor ge quality traits, and indeedof many other e apowerful resource, a good start has ated withqualitytraits identifiedfor . These are already helpful in studies alreadyhelpfulinstudies are . These in coffee, and in coffee, playand animportant will role nes once detected. The The detected. once nes C. arabica , and the the , and This article isprotected bycopyright. Allrights reserved. Accepted Article 4. Davis AP, Chester M, Maurin O and Fay MF, Searching for the relatives of for therelatives MF,Maurin OandFay Searching ChesterM,of DavisAP, Ixoroideae) (Rubiaceae, Coffea 4. sequences. plastid and on nuclear DNA MF, and Fay ChesterM,MvungiY EF,Jaufeerally-Fakim MaurinO,DavisAP, coffea for (rubiaceae) Towards aphylogeny 3. P, B, Etienne HandLashermes F, Anthony Bertrand Resources andBreeding Genomic Relatives: Wild Crop 2. 2011/12,Ed(2013). Review Annual ICO,ICO 1. research. this of support their ongoing for and QAAFI/UQ We number (project acknowledg LP130100376). wasThis research supported under Australian ResearchCouncil's 5. Tosh Tosh J, Davis Dessein S,BlockPD, AP, Huysmans MF, S, Fay Smets Eand of E, Phylogeny Robbrecht 5. (2007). genera based onplastidDNA data morphology. and on plastid data sequence 7. Davis AP, Tosh J, Ruch N and Fay MF,Growingcoffee: N andFay ToshJ,Ruch DavisAP, 7. and Evolution in radiation P,Adaptive Lashermes M-Cand Combes F, DinizLEC, Anthony Coffea 6. Missouri Botanical Garden Molecular Genetics and Genomics Genetics and Molecular P, P, Combes A,Anthony M-C, RobertJ,Trouslot D'Hont F and Lashermes the of and origin characterisation A,Molecular Charrier 9. (2004). and Researchers in ofCoffee, Genetics and Botany AB, and Eskes A Charrier Traders, for Growers, Processors, Production -AGuidebook Processing, Sustainable 8. Linnean Society ofhistory evolutionary and distribution morphology, molecularmorpsubsumedof thebasis on and subgenus subgenus 285 167 , Ed by Wintgens JN. WILEY-VCH Verlag GmbH & Co. KCaA &Co.KCaA Verlag GmbH WILEY-VCH JN. Wintgens , Edby Coffea :51–64 (2010). :357-377 (2011).:357-377 L.( 96 Rubiaceae Tricalysia (Rubiaceae) Tricalysia :194-213 (2009). :194-213 : The circumscription and phylogeny of circumscriptionand phylogeny : The ACKNOWLEDGEMENTS : Resurrection ofthe: Genus 261 REFERENCES :259-266 (1999). 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This article isprotected bycopyright. Allrights reserved. Accepted Article Arabica coffee bean as well as coffee beverage quality. quality. coffee beverage well as as bean coffee Arabica F, Descroix L,F Berthiot and Joet Ribeyre S, R, Dussert B,Boulanger Bertrand T, Climaticfactors impact directly thevo 31. of GreenCoffee,in the Factors influencing Quality JN, Wintgens Processing,Growing, Sustainable Producti 29. 31 (1996). 26. Villarreal D, Laffargue A, Posada H, Bertrand B, Lashermes P and Dussert S, VillarrealH, Bertrand B, PandDussert PosadaS, Laffargue A, D, Lashermes environmental and effectsGenotypic on coffee( 26. Agriculture Agriculture Moschetto B, Montagnon D, TStudies C, Guyot JJ,Leroy Perriot and EskesA, of cup quality on theeffect ofgenotype on 28. Brazil. andAlves AA MaltaMR,Alvarenga MÂ, Cirillo Borém FM, BarbosaJN, wi and itsinteractions Coffeequality HMR, 33. 701 (2010). coffee beans. Arabica composition ofgreen the biochemical and B, kochkoAd Bertrand S, Descroix Doulbeau A, JoëtT,Laffargue F, InfluenceDussert S, environmental of factor 32. (2012). America. Central trad with origins Sudanese-Ethiopian involving P, F and Charmetant H, Davrieux Etienne E, Alpizar Vaast P, B, Bertrand compositi biochemical of bean Comparison 30. (2012). KCaA Traders, andTraders, Researchers Southwestern Ethiopia. Southwestern for analysis diversity W,Genetic Garedew KufaTand Alamerew S, A, Tessema attributesquality ofsome promissing 27. andFoodChemistry Agricultural profile: and origindetermination. impactchemometric on variety chemometric discriminationcoffee of ( LaffargueA,Posada Lashermes H, VillarrealD, PandDussert S, B, Bertrand acid offatty effectiveness the of Comparison 25. Agricultural andFoodchemistry Agricultural Costa Rica, Orosi and Santa Mar´ andSanta Orosi Costa Rica, C, Cilas B and Guyot C,Davrieux F, JC,Fonseca B, Araya Barboza J, Avelino altitudeEffects of slopeexposure, and yiel 36. methods. andFarahA, Pereira AA DuarteGS, coffeeswet post-harvesting and semi-dry processed inBrazilianby compounds 35. ina Muschler RG, of sub-optimal Shade coffeecoffee-zone improves quality Rica. Costa 34. Journal of Agricultural Science of Agricultural Journal Food Chemistry Chemistry Food 85 Agroforestry systems :1869–1876 (2005). :1869–1876 Tree Physiology Physiology Tree Journal of Biological Sciences Sciences Journal ofBiological 118 , Ed by Wintgens JN. WILEY-VCH Verlag GmbH &Co. :851-855 (2010). :851-855 56 51 57 26 :2273–2280 (2008). :2273–2280 :131-139 (2001). :11321-11327 (2009). :11321-11327 ı :1239-1248 (2006). a de Dota. Dota. a de Coffea arabica arabica Coffea 4 (2012). latile organic compound fingerprint in green latilecompound organicfingerprintin green d on coffee quality in two oncoffeequality d altitude terroirs of Coffea arabica on - A Guidebook on for Gr - AGuidebook on and beverage quality of Arabica hybrids ofArabicahybrids quality and beverage on Coffea canephora s, wet processing and their interactions on andtheirinteractionss, wetprocessing on th environmental factors in Minas Gerais, Gerais, in Minas factors environmental th s, chlorogenicacids, and elements for the Chlorogenic acids and other relevant relevant andother Chlorogenicacids itional varieties at various elevations in itional elevations varieties atvarious Journal of the Science of Food and and of Food Journal oftheScience Coffea arabica arabica Coffea L.) varieties and growing origins. origins. L.) varietiesandgrowing 11 Food Chemistry Food Chemistry :236-244 (2011). (2011). :236-244 germplasm germplasm collections in Food Chemistry Food Chemistry . Tropical Science L.) bean fatty acid owers, Processors, Processors, owers, 135 Journal of Journal of :2575-2583 :2575-2583 118 Coffee: 36 :693- :18 ‐ This article isprotected bycopyright. Allrights reserved. Accepted Article 68 of C,Quality Cilas and C Pineda JJ, B,Perriot Guyot J, Avelino F, Decazy environments. toseveral coffees indifferent Honduran relation 37. and sensory quality ofcoffees,in natural and sensory quality Borém FM, RibeiroFerrazJHS, PradoMVB, Taveira DR, V,TostaLuz MF, andenvironmen Genotype RM, MPS andCortez 38. 41. Lecolier A, Verdeil J-L, Escoute J, Ch J, Escoute J-L, A, Verdeil Lecolier affected 41. Agric on JC,Perspectives andRamalho AE,PaisIP, LidonFC Leitão SantosCAFd, climate impactsof the potential change 40. science 2014 oncoffeeand conference ASIC International seed coffee on effects in perspective, Environmental S, agenomic attributes: Dussert and and quality B T, Bertrand composition Joët biochemical 39. 2014 ASIC and science stability in in stability G, E,Herrera Dechamp BertrandB,Camayo A,GeorgetF, RB,Cenci Landey epigenetic Highgenetic JandEtienneand H, Simpson JC, SantoniS,Lashermes P, 43. Springer(2014).Casas-Mollano. inplants chromatin remodelling and applications transcriptionalregulation and agronomic importance:Fundamentals Somatic on Advances Epigenetic 6: Chapter Important Agronomicaland CDl, of Crops,in Pena Embryogenesis and GI Nic-Can 42. 23 speciation in coffee. in speciation Genome A, and Dereeper SeveracD HueberY, M-C, Combes P, Lashermes allopolyploidy following recombination from homoeologous derived rearrangements 44. ONE variation rate. and the AFLP,MSAP asrevealed phenotypic by embryogenesis mining of single nucleotide polymorphisms in ofsinglenucleotidemining polymorphisms LF, Pereira AC, Andrade D, AmbrosioAB, Pot MondegoJM, RO, Vidal data A high-throughput GA, Pereira and MF Carazzolle LG, Vieira CA, Colombo 46. (2014). Casas-Mollano.Springer and J Peña CDl,Armando Venegas R, plants andchromatinremodelling in regulation transcriptional Bottley cropspecies,in A, EpigeneticChapter 3:polyploidy amongst variation applications and importance: Fundamentals inplantsofagronomic Epigenetics 45. allopolyploid of subgenomesContribution to the transcript P, Lashermes and B Bertrand D, A,Severac Dereeper M-C, Combes 47. Plant Physiol allotetraploid inthe expression gene homeologous differential suggests 200 :2356-2361 (2003).:2356-2361 :1043–1051 (2009). :1043–1051 :251–260 (2013). :251–260 8 27 (2013). :152-163 (2015). (2015). :152-163 Coffea arabica Coffea Coffea arabica 154 Coffea arabica Coffea :1053-1066 (2010). :1053-1066 The Plant Journal , Ed, Colombia (2014). , Ed,Colombia tree size and shape mainly throughinternodetree shapedwarfism. size and plants derived from embryogenic suspensions and secondary plants from suspensions andsecondary embryogenic derived grown atcontrasted temperatures. grown , ed. by Alvarez-Venegas R, Peña CDl, Armando J and and J Armando Peña CDl, R, Alvarez-Venegas by ed. , 78 s on coffee plant and bean quality. beanquality. and plant coffee s on :674–685 (2014). :674–685 The 25th International conference on coffee oncoffee conference 25th International The ome and their intertwined regulation in the in the intertwined regulationtheir and ome restin H and Noirot M, Laurina mutation mutation M, Laurina andNoirot H restin Coffea species expressed sequence tags tags sequence expressed species Coffea t Interaction in chemical composition chemical composition in t Interaction , Ed, Colombia (2014b). , Ed,Colombia Epigenetics in Epigenetics plants of Journal of Food Science FoodScience Journal of , ed. by by Alvarez- , ed. New phytologist New phytologist Coffea arabica Emir J Food The 25th The 25th PLOS PLOS Trees . This article isprotected bycopyright. Allrights reserved. Accepted Article & Genomes & Genomes T, Leroy Bellis LegnateF, Hand Kananura E,Improving the quality of African robustas: and for QTLs yield- quality-related traits in 51. and Theoretical Applied Genetics C-L, Ky GuyotB,Louarn J, and Hamon S Noirot M,in Trigonelline inheritance the interspecific 50. Coffea pseudozanguebariae Relations andNoirotM, H Charrier A,Hamon GuyotB, C-L,Louarn J, Ky cross between in an chlorogenic acidinheritance of and interspecific contents between 49. 578 (1998). 59. WCR, Assessment of Genetic Diversity WCR, in CoffeaAssessment ofGenetic arabica. Diversity 59. 107 species M,Inheritance S andNoirot A,Hamon S,LouarnJ,Charrier P, Akaffou Barre coffee cultivated a between cross interspecific an in contents heteroside and of caffeine 53. pseudozanguebariae coffee of content caffeine seed low for Breeding A, Carvalho Pand Mazzafera (Coffea 52. Applied Genetics quality traits in an interspecific cross between cross between anin interspecific traits quality S, C,Hamon H, Hamon AkaffouDS, Keli P,J,Campa S, Doulbeau Legnate Inheritanceand andZoroBIA, agronomic and relationshipKochko A key between 54. C. canephora 58. Bertrand B, Guyot B, Anthony F and Lashermes P, Impact of the F andthe P, Impact B, Guyot of Lashermes Anthony B, Bertrand canephora 58. 504 (2008). Research 2014 Annual Report Research 2014 T,GeneticLeroy parametersand B,CilasGuyot ofseveral C C, Montagnon fromcoffee, biochemical compounds green 48. 56. Mérot-L’Anthoëne V, Mangin B, Lefebvre-Pautigny F, Jasson S, Rigoreau F,JassonM, Lefebvre-Pautigny S,Rigoreau Mangin B, Mérot-L’Anthoëne V, D,Comp Crouzillat J, LambotCand Husson 56. pseudozanguebariae liberica× Coffea dewevrei CL,Doulbeau Akkaffou Ky S,CharrierS, A,Hamon S,LouarnJand M, Noirot Inheritancecoffee ofbean sucrose content intheinterspecific cross 55. Coffea canephora Coffea in characters andyield sensory, biochemical, 57. Priolli RHM, Paulo, Siqueira WJ, Möller M, Zucchi MI, Ramos LCS, Gallo PB Gallo MI,Ramos PB LCS, WJ,Möller M, Zucchi PriolliRHM, Siqueira Paulo, inheritanceCA, CaffeineColombo of in interspecificand hybrids 57. Genomes :387–394 (2003). :387–394 L.) by interspecificby L.) hybridization. Coffea liberica vardewevrei liberica Coffea (2014). (2014). gene introgression on beverage quality of quality introgression onbeverage gene 7 Pierre. :781-798 (2011). :781-798 (2011). 98 (Gentianales, Rubiaceae). Rubiaceae). (Gentianales, Coffea pseudozanguebariae pseudozanguebariae Coffea :628-637 (1999).:628-637 . Tree Genetics &Genomes Tree Genetics Theoretical and Applied Genetics AppliedGenetics and Theoretical and (2014). 102 Coffea liberica var ‘dewevrei’ liberica Coffea :630–634 (2001). :630–634 (2001). Euphytica and a wild species caffeine-free caffeine-free species awild and Coffea canephora Coffea Genetics Genetics and MolecularBiology arison of three QTL de three QTL arison of Coffea pseudozanguebariae pseudozanguebariae Coffea . 8 Plant Breeding × :1149-1162 (2012). Coffea canephora C. liberica var. dewevrei var. dewevrei C.liberica 59 Coffea canephora Coffea :55–60 (1992). 96 C. arabica :306-311 (1998). :306-311 . Plant Breeding 119 . . :165-168 (2000b). :165-168 . Theor Appl Genet ApplGenet Theor tection models on Tree Genetics & Genetics Tree Coffea arabica Coffea Theoretical and and Theoretical . World Coffee Tree Genetics Tree Genetics Bridson and and Bridson 117 31 Coffea Coffea Coffea cross. cross. :576- :498- x C. This article isprotected bycopyright. Allrights reserved. Accepted Article 71. Teressa A, Crouzillat Petiard Vand A, D, Teressa coffee ( 71. (2008b). arabica coffee analysis genotypes. Ethiopian among AFLP MT, Y, Herselman Dessalegnand Labuschagne L 72. Simple Sequence Repeat Markers. Repeat Simple Sequence 70. Geleta M, Herrera I, Monzon A A Monzon Herrera I, Geleta M, ( coffee of arabica diversity Genetic 70. Genet 69. Steiger DL, Nagai C, Morden PHMCW, Osgood RV and Ming R, AFLP OsgoodRVandMingR,AFLP C, MordenPHMCW, Nagai Steiger DL, analysis of genetic diversity within andamong 69. markers. systems. marker LM M, Ruggiero Silvestrini MalufMP, and SSR RAPD, AFLP by assessed inbred lines coffea arabica of cultivated diversity 67. (2005). in arabica L.) accessions coffee (Coffea incultivated Genetic TranHT, variation S SouthWales, Ed. Australia, northern New 66. varieties. CarvalhoandVosman EVD, MGG,EsselinkB, VieiraVon ESN, Pinho DG Brazilian markers foridentifying microsatellite of Development 65. 68. Masumbuko LI, Bryngelsson T, Mneney EE and Salomon B, Genetic diversity diversity B, Genetic EEandSalomon T,Mneney LI, Bryngelsson Masumbuko in TanzanianArabicacoffee using Rand 68. molecular markers. markers. molecular MH, Yashodha PR, Soumya SS, Kumar N, Suresh N, MK, Sandhyarani Mishra via determined cultivars coffee among Indian diversity Jayarama, Genetic and A Bhat 64. Food, Agriculture & Environment Food, Agriculture& Environment 63. Al-Murish TM, Elshafei AA, Al-Doss AA and Barakat MN, Genetic diversity of Genetic diversity andBarakat MN, Al-MurishTM,ElshafeiAl-DossAA, AA coffee ( 63. (2014). SSR andISSR markers. MottaSoares TCB, FerrãoMAG, LB, ofarabic characterization Molecular JDdS, 62. 2014 ASIC coffee andscience produced from different regions in Brazil, in Effect of TG, LC,Leal CandKieckbusch the DiasEC,Paiva RS,Pimenta androastingconditionson processing 61. Experimental Botany DescroixF,Bertrand S, B,Lashermes A,Salmona J,Doulbeau JoëtT,Laffargue incoffeeseeds. biosynthesis galactomannan Regulationof S, andDussert P 60. 105 Coffea arabica Coffea Coffea arabicaCoffea Hereditas Hereditas Genetics andMolecular Biology :209–215 (2002). :209–215 Sci Agric(Piracicaba,Braz) Sci 139 Journal of Crop ImprovementCrop Journal of 65 L.) collections. L.) collections. L.) in Yemen via SRAP, TRAP and SSR markers.and SSR TRAP Yemen viaSRAP, L.) in :56–63 (2003). :56–63 :323–337 (2014a). :323–337 (2014a). Brazilian archives technology of and biology , Ed, Colombia (2014). , Ed,Colombia (2014). 11 The Scientific World Journal Journal The ScientificWorld :411-416 (2013). Coffea arabica African Journal of BiotechnologyJournal African EJAST 33 om Amplified Polymorphic DNA (RAPD) quality and of quality chemicalcoffee composition and Bryngelsson TV, Article ID 939820, 939820, ArticleID TV, Bryngelsson and a and conilon coffee plants genotypes by by genotypes coffee plants conilon aand :507-U120 (2010). :507-U120 outhern Cross University, NSW, Australia University, Cross outhern 62 1 dC, Filho OG and Colombo CA, Genetic andCA, Colombo dC, FilhoOG Brouhan P, Genetic diversity of Arabica diversity P,Genetic Brouhan :63-79 (2010). :63-79 (2010). Caixeta RMandNeto ET, Lorenzoni :366-373 (2005). The 25th International conference on conference The 25th International Coffea arabica 26 :727–750 (2012b). :727–750 L.) in Nicaragua as estimated by by estimated as L.) in Nicaragua 2012 cultivars. cultivars. (2012). (2012). Coffea arabica arabica Coffea 7 Theor Appl Theor :3193-3199 :3193-3199 57 Journal of Journal of Journal of :728-735 :728-735 This article isprotected bycopyright. Allrights reserved. Accepted Article establishing geneticestablishing relationships in L and Zambolim CD, Cruz EM, SouzaFdF,Zambolim ET, Caixeta FerraoLFV, Sakiyama NS,Comparative of differe study 80. markers. of MDP, Analysis G,Cortina H,McCouch SR and Moncada López-Gartner SSR fluorescent L.)using arabica (Coffea coffee of sample a in structure genetic 79. diversity of the coffee ofthe diversity and Cubry RGL Solorzano A, P,Kalonji Musoli H, Legnate FD, T,Bellis Leroy P, coreDeveloping collections optimizeand management to the the exploitation of 81. (2013). Crop Evol genomics genomics of groups patterns in P, deBellis Cubry F,Avia K,Bouc LD trees: incoffee (LD) disequilibrium linkage of assessment T,Aninitial Leroy 84. of diversity , D. P, Bleysse FD, Bellis M, C,Dufour Billot P, P,Aluka Cubry Musoli P, populations: and cultivated ofwild differentiation T, Genetic and Leroy Charrier A 83. 501 (2013a). fromimpacts climatic andmigration effects.refuges of and T, MusoliLeroy BellisP Global analysis D, Pot P, Cubry FD, canephora 82. 77. Aga E, Bryngelsson T, Bekele E and Bekele E T, AgaE,Bryngelsson coffee arabica ( 77. Evolutionary Applications arabica Coffea B, Muys Vandepitte K, G,Gijbels HunderaK,Glabeke SV, AertsR,Berecha P, and Roldan-Ruiz I GeneticO, Honnay and variation risks ofintrogression in the wild 76. markers. Bertrand Anthony F, B,Quiros O, Jand Wilches P, A,Lashermes Berthaud of wild diversity Genetic A, Charrier 75. ( LashermesP, Andrzejewski S, Bertra Trouslot P F,and Anthony Molecular ofintrogressive breedingin analysis coffee 74. Polymorphic DNA (RAPD) analysis. (RAPD)analysis. DNA Polymorphic and Brazilian and Brazilian MalufMP, Favarin SilvestriniM,JunqueiraMG, AC,Guerreiro-Filho O, andSilvarolla MBand structureColombo CA,Geneticdiversity ofEthiopian, Yemen 78. Plant Soil AFLP and of SSR M,Comparison Labuschagne L and Y, Herselman Dessalegn genotypes. coffee arabica Ethiopian of assessment diversity for genetic analysis 73. Coffea arabica arabica Coffea Tree Genetics & Genomes &Genomes Tree Genetics Euphytica 14 26 54 Pierre ex Froehner (Rubiaceae) Pierre Froehner fro ex Coffea canephora :10 (2013b). :119-125 (2009). :119-125 :1367–1379 (2007). :1367–1379 Coffea arabica L.). gene pool in South-Western Ethiopian montane rainforests. rainforests. montane in South-WesternEthiopian pool gene Coffea arabica 118 Theor Appl Genet Coffea canephora :53–65 (2001). :53–65 Coffea canephora canephora Coffea :243-252 (2012). L. accessions microsatellitesusing markers. Pierre in Uganda. Pierrein Uganda. L.) in Ethiopia as revealed by Random Amplified Random Amplified by revealed as in Ethiopia L.) 5 :435-446 (2009). :435-446 (2009). Hereditas Hereditas Coffea canephora 100 . Genetica coffee (Coffea arabica L.) using molecularcoffee arabica(Coffea L.)using :139–146 (2000). :139–146 Pierre using microsatellite analysis. analysis. microsatellite Pierre using nd B, Combes MC, Dussert S, Graziosi G, S, G, Graziosi Dussert MC, nd B,Combes het S, Pot D, Dufour M, Legnate H and and Legnate H D, S,Pot M, Dufour het ntmolecular markers for classifying and m the Guineo-Congolese region reveals reveals region Guineo-Congolese mthe Salomon B,Geneticdiversity offorest 138 Genome 142 :36–46 (2003). Genet Resour Crop Evol :185–199 (2014).:185–199 . 52 Plant Syst Evol Plant SystEvol :634-646 (2009).:634-646 Genet Resour Genet Resour 299 :225–238 :225–238 60 S Afr J Coffea Coffea :483– BMC This article isprotected bycopyright. Allrights reserved. Accepted Article 87. Noirot M, Poncet V, Barre P, Hamon P, Hamon S and Kochko AD, Genome Genome AD, Kochko and S Hamon P, Hamon Barre P, V, NoirotM,Poncet African size indiploid variations 87. 345 Carretero-Paulet Denoeud DereeperF, Thecoffee and Droc genome L, G, A ofcaffeine biosynthesis. insightevolution provides into theconvergent 86. Coffea Genomics Coffea Genomics KochkoAD,Akaffou S, Andrade AC,Campa Guyot R,Hamon C,CrouzillatD, S, Advancesin and Hamon C R, Tranchant-Dubreuil MingMueller LA,Poncet V, P, 85. 88. Razafinarivo NJ, Rakotomalala J-J, Br J-J, NJ,Rakotomalala Razafinarivo 88. for coffeegenomes. C, S,Tranchant-Dubreuil Ravel Guignon V, A, BocsS,RouardM, Dereeper hub: aresource genome and DrocG,Thecoffee P O,Lashermes Garsmeur Poncet V, 89. Indian Oceanislands. gradients inthe sizevariation of genome wild coffee trees (Coffea) to native Africa and Hamon P,Geographical and GuyotR E, Couturon C, Dubreuil-Tranchant Poncet V, angiosperms. angiosperms. forbiotechnology and implications Samson Bausher and N, Jansen The MG, LeeRK complete Daniell H, S-B, coffee ( the of sequence nucleotide 90. Towards ofthe a betterunderstanding CrouzillatD, and RigoreauM M, Lepelley A, kochko S, Tranchant C,De Hamon Mueller L,Strickler S, SominguesD, R, Wai J, Albert V, Giuliano G, Descombes P,Moine D, Guyot R, Poncet V, Hamon P, 91. arabica of theallotetraploid assembly and theProgress reportsequencing Valle G, on JurmanI, D, CattonaroMagni F, F, S, ScalabrinScaglione MorganteM, Terra L, Navarini Liverani FS, M, Cerutti 92. science 2014 oncoffeeand conference ASIC International 95. Mahe L, Combes MC and Lashermes P, Comparison between a coffee single single coffee a between Comparison P, Lashermes and MC Combes Mahe L, level high evidenced chromosomal andArabidopsisduplicatedcounterparts region copy 95. eugenioides allotetraploid forthe reads long PacBio using assemblies genome reference high quality Building H, RiveraMA, CE, A,CristanchoLF,CorreaJC, Maldonado YepesM,Gaitan H,Zimin Mockaitis YorkeJA, Posada KandAldwinckle A, CE,VillegasAM, Gongora 94. Genomes XXIII Dihaploid and Albert VA, Sankoff D, C J,ChinZheng Korlach Paschoal A,KuhnG, DS, ApreaG, R,WaiFiore A, Ming Giuliano G, M, P, Pietrella J,Domingues Marraccini E, Descombes Luiz-Filipe, P,Couturon MoineD,MuellerAndrade A, L,StricklerSR, Crouzillat KochkoAd, Rigoreau M, D, P,Hamon S, C,Hamon Tranchant-Dubreuil R,Poncet V, Guyot C, Vandecasteele VM, 93. (2015). :1181-1184 (2014).:1181-1184 var. Bourbon genome, in genome, Bourbon var. Coffea arabica , in Plant Biotechnology Journal Plant Biotechnology Coffea arabica arabica Coffea , Ed,(2015).San Diego, CA Plant and Animal Genome XXIV AnimalGenome and Plant Advances in Botanical Research Research inBotanical Advances Nucleic Acids Research Research Acids Nucleic Tree Genetics & Genomes & Genomes Genetics Tree genomesequencing and in assembly, and its diploid ancestral maternal ancestral species and its diploid Coffea Plant andAnimalGenome Plant XXIII Coffea arabica species. Coffea arabica and phylogenetic amongst relationships 5 LD, Pellegrino G, Graziosi G, Vitulo N and GraziosiG, VituloG, N LD, Pellegrino :339–353 (2007). (2007). :339–353 (2014). (2014). Pereira L,Andrade A, Marraccini P, Ming own SC, Bourge M, Hamon S, Kochko A, KochkoA, Hamon S, own SC,BourgeM, , Ed, San Diego, CA (2016). , Ed,SanDiego, Annals ofBotany 8 Lepelley M, Bellanger L, l'Anthoene M,Bellanger L,l'Anthoene Lepelley L.) chloroplast genome: organization organization genome: L.)chloroplast :1345-1358 (2012). 53 :23-63 (2010). genome structure, in , Ed, Colombia (2014). , Ed,Colombia 92 , Ed, San Diego, CA , Ed,SanDiego,CA Plant andAnimal :709-714 (2003). The 25th Science Coffea Coffea Coffea This article isprotected bycopyright. Allrights reserved. Accepted Article sequences analysis provides insightssequencesanalysis into first coffee ( Dereeper A,GuyotR, Cand Tranchant-Dubreuil Anthony Fo, BAC-end 105. 1041 (2005). Evidence of intergenomic relationships in triploid hybrids of coffee( of hybrids triploid in relationships intergenomic of Evidence H-A, andCortina C-M G-C,Caetano Camayo HerreraJ-C,Romero J-V, 100. composition and evolution. andcomposition canephora metabolism. involved genes Towa in sucrose Musoli LGE,Ferreira LP, Vieira P,Legnate PotD, S,Marraccini Bouchet P, Jourdan Debellis I,Pereira F,Cubry LFP, P, 101. 5 insitu hybridization. meioticand revealed by behaviorgenomic organization of sucrose biosynthesis genes. genes. ofsucrose biosynthesis organization Construction and characterization ofa Piffanelli and P,LG Vieira Glaszmann AC, JC, Andrade I,PotD, Jourdan Ferreira LP, Sabau X, Lashermes P, C, Montagnon M, Dufour P, T, Marraccini Leroy 104. CA (2016). San Diego, Neves High-throughput LG, targeted of genotyping Alkimin Resende ER M, Caixeta E, 103. ASIC2008 Science, for and quality relatedits usefulness traits, in interspecificpopulationon an F2 based between map a genetic M,Construction of Moller D and Pot PriolliRamosLCS, RHG, 102. in sucrose variability controlling scienceASIC - segments. 9 Cenci A, Combes M-C and LashermesP,Genomein and evolution diploid tetraploid 99. allotetraploid coffee species ( coffeespecies allotetraploid ofreceptor cultivatedand an ethylene gene inof the vicinity diploid evolution genome Dubreuil- Langston BJ, RN-P, A, rez Byers Ad, Kochko R, Guyot and YuQ, Micro-collinearity R, and Ming C Nagai Poncet Vr, AH, Paterson C, Tranchant 98. Sp.) androsid( Sp.) between distantly-related plant species from the asterid ( asterid the from species plant distantly-related between Tranch F, R,Lefebvre-Pautigny Guyot shared synteny Ancestral A, de Crouzillatand Kochko V, D T,HamonS,Poncet Leroy 97. genomes. and tomato coffee the between maps direct comparisons allowing resolution synteny ZouineWu F,PhilippotM, RigoreauPriyono,F, M, Lefebvre-Pautigny M, P,Bouzayen BrounP,andCrouzillat Frasse Pétiard D, V,SD High Tanksley 96. Biology Molecular between coffee the andthegenome synteny ancestral Arabidopsis genome. :207-217 (2012). Tree Genetics & Genomes & Genetics Genomes Tree Plant Molecular Biology Biology Molecular Plant Coffea using next generation sequencing, in usingnextsequencing, generation , Ed, Montpellier, Ed, France(2007). , Vitis vinifera species as revealed by comparative analysis of orthologous genome of orthologousgenome comparativeanalysis revealed by speciesas 64 , Ed, Campinas, SP, Brazil, pp 882-890(2009). Brazil, pp Campinas, SP, , Ed, :699-711 (2007). :699-711 Plant Molecular PlantBiology Molecular ) clades. ) clades. Coffea Coffea 78 ). 6 BMC Genomics BMC Genomics The Plant Journal The Plant :565-577 (2010). :565-577 (2010). :135–145 (2012). :135–145 (2012). Coffea canephora Coffea sp., in Theoretical and Applied Genetics Applied Genetics and Theoretical , Sousa TV, Resende ChamalaMDV, Sand H and Leroy T, Nucleotide diversity of of diversity T, Nucleotide HandLeroy rds the identification of candidates genes ofcandidatesgenes rds the identification 22nd International Conference on Coffee 22nd InternationalConferenceCoffee on ant-Dubreuil C, Rigoreau M, Hamon P, P, Hamon M, Rigoreau C, ant-Dubreuil Plant and Animal Genome XXIV Genome Animal Plant and arabica Coffea International International conference oncoffee 83 13 :177-189 (2013). :103 (2012). Coffea canephora 67 Coffea canephora Coffea Coffea arabica Coffea :305–317 (2011). BAC library to study the study to BAClibrary and Tropical Plant Biology TropicalBiology Plant Coffea canephora Coffea and and and and P.) genome P.)genome 111 Solanum sp.) as as sp.) Coffea :1032- Plant , Ed,

This article isprotected bycopyright. Allrights reserved. Accepted Article CIFC 832/2. CIFC fromthe library a BAC of characterization and andVieiraLGE,Construction Domingues DS CacaoSMB,Silva NV, 108. (2006). (ASIC) Science on Coffee Conference International 21st in genome., of an allotetraploid dissection molecular for library coffee BAC an arabica Skelton A, Q, JonesMR,Byers RL, Yu 107. Molecular Genetics and Genomics Genetics and Molecular ( the expressedduringinfectionrust fungus by early L.) genes Petitoand A,Coffee ( BonM Agostini SantosP, C, FernandezD, 109. cherry transcripts. transcripts. cherry shareas tomato gene common repertoires and Coffee S, Tanksley and PétiardJM, CrouzillatV D, Carthy LA, C, Mueller Lin 110. Biology approaches. RT-PCR real-time and cDNA array combined using govern that networks transcriptional Deciphering Salmona J,Dussert S, Descroix F, 115. markers for the EST–SSRsas useof potential tree ESTdatabases: miningcoffee in SSR Hamon P, and A deKochko S, A, Hamon C, Cayrel Tranchant V, RondeauM, Poncet 114. Genome species ( coffee allotetraploid the of analysis forgenome library a BAC of characterisation and Construction B, and Chalhoub P Lashermes S,Combes M-C, Noir Patheyron S, 106. Coffea arabica Coffea of responses MartellossiC,Differential and L Terra R,Del Dreos DeNardiB, 113. Science(ASIC) onCoffee Conference International analysis from leaves, flowers and fruits of fruits and flowers leaves, from analysis Cristancho Vuong H, G, Montoya 112. EST-based genomic resource. an CA, Braziliancoffeegenome VieiraLGE,Andrade ACandColombo project: 111. arabica featuresof expression identifies gene new genesdistinctive and reveals analysis EST-based An EK, Tokuda and VidalRO, CarazzolleMF MondegoJM, 118. agronomic and quality traits. traits. quality and agronomic first 15K coffee microarray, a new toolcoffeemicroarray, anew fo 15K first the Project: CAFE' 'PUCE The Severac D, and PrivatAB Bardil I, A,Gomez 117. Genetics species. and related ofcoffee analyses forgenome markers utilizat and characterization Identification, SinghL, P,KrishnakumarVand Varshney R, Bhat AggarwalR,HendreP, 116. and 66 Coffea arabica Coffea 49 114 :105-124 (2008). :105-124 :1594–1605 (2006). :1594–1605 (2006). Coffea canephora Coffea Genetica :359–372 (2007). :359–372 (2007). L. leaves L.leaves androots to chemically Coffea Coffea Theoretical and Applied Genetics Theoretical Applied Genetics and 141 genus. genus. L.). :217–226 (2013). Theoretical and Applied Genetics Genetics Theoretical Applied and BMC Genomics BMC Genomics Molecular Genetics and Genomics Molecular Genetics and Brazilian Journal of Plant Physiology Physiology Brazilian JournalofPlant . BMC PlantBiology 5 :527–536 (2004). r discovering candidate ion of EST-derived genetic microsatelliteionof EST-derivedgenetic de Kochko A, Bertrand B and Joet T, JoetT, and BertrandA, B deKochko M, Moncada P and YepesM,Sequence 12 Coffea arabica revealed by deep sequencing of seed and and of seed sequencing deep by revealed Nagai C and Moore PH, Construction of Construction of C andMoorePH, Nagai :5 (2011). Coffea arabica induced systemic acquired resistance. , Ed, Montpellier, France(2006). , Ed,Montpellier, 11 112 Coffea arabica :30 (2011). :30 (2011). :114-130 (2005). :114-130 , Ed, Montpellier,49 , Ed, France,p genotype Timor Hybrid Timor Hybrid genotype 109 Theoretical and Applied Applied and Theoretical var. Caturra, in var.Caturra, 436–449 (2006). 436–449 :225-230 (2004). Hemileia vastatrix genes correlated genes to 18 seed development development seed Plant Molecular Molecular Plant :95-108 (2006). :95-108 Coffea arabica Coffea Coffea 21st ).

This article isprotected bycopyright. Allrights reserved. Accepted Article Geneticmap linkage of Trouslot Mand P, CombesMC,PrakashNS, Charrier Lashermes P,Lorieux A, 123. (2007). Conference Science 21st onCoffee International characterization of a true F2 population for geneticmapping and QTL in Arabica, in and R, Development AE, DJandMing NagaiAdamski MR,Byers C,Jones 122. for map arabica coffee. genetic a R, Construction of D, OsgoodandMing R Steiger Moore P, C, Pearl Nagai H, 121. incoffee. map molecular a P andPétiardV,Constructionlinkage of Lashermes PaillardM, 120. interspecific backcross progeny [( interspecific progeny backcross Minier M polymorphism andand HamonP, J,Dufour a Coffea AFLP SSR in C, Lorieux Carasco-Lacombe V, M, Noirot M,Poncet Coulibaly I, B, Revol 124. Single-locusinheritance andpartial linkagemap of Teixeira-Cabral Zambolim TA,SakiyamaAA andL, Pereira NS, I, Schuster 129. (2013). meioses. male rate andfemale in of recombination in breeding, VegaFE,Ebert AWandMingR,Coffeegermplasm resources, and genomics, 119. de Kochko A, Genetic mapping of a caffeoyl-coenzyme A 3-0-methyltransferase gene de Genetic mapping A, Kochko of agene A 3-0-methyltransferase caffeoyl-coenzyme and S Hamon Chrestin H, C, Ky M, M,Pervent M,Bourgeois C, Noirot Campa 131. Ed, Colombia(2014). and beansize, in mapgenetic oflinkage of coffee ( A S, J and McCouch Spindel A, JC,Gonzalez Montoya Tovar E, P, Moncada 130. coffee.of population testcross interspecific pseudo diploid map of an Moncada Agenetic and MDP, SR McCouch GartnerGAL, 128. 676 (2000). conversiongenetic incoffee(Coffeasp.). Hamon SandNoirot M, Interspecific segregationdistortionmap, genetic linkage and C-L, Barre Ky P,Lorieux M, LouarnTrouslotS, P,Akaffou J,Charrier A, 127. interspecific cross. differentiation between ofspecies basis Genetic P, andValérie N, SergeH Michel Amidou ND, 126. 2004) (ASIC on CoffeeScience Conference forofQTL, the in markers detection microsatellite RFLP and using and I J,S,Zaenudin McCarthy Tanksley Syahrudi, Mawardi D, Rigoreau S, CrouzillatPriyono P, M,BellangerL, 125. and Theoretical Applied Genetics and Applied Biotechnology and Applied Plant BreedingReviews Theoretical andAppliedGenetics The 25th International conference oncoffeeThe conference 25th International andscience ASIC 2014 Genetic Resources and Crop Evolution ResourcesandCropEvolution Genetic Coffea liberica Hiern and C. canephora Pierre: Analysis of CoffeaPierre: Analysis C. canephora and liberica an Hiern Coffea canephora 4 :416-421 (2004).:416-421 Theoretical and Applied Genetics andApplied Genetics Theoretical 107 Coffea arabica arabica Coffea C. heterocalyx , Ed by Janick J. John Wiley & Sons, JanickInc. (2008). John Wiley&Sons, Ed by J. , :1148-1155 (2003). Pétiard V, A Robusta consensus genetic map map genetic Robustaconsensus V, A Pétiard : effect of segregation distortion and analysis and analysis distortion segregation : effectof , Ed, Bangalore, India, pp 546-553 (2005). pp546-553 India, , Ed,Bangalore, Theoretical andApplied Genetics 93 × Ed, Montpellier, France, pp 771-777 Genome Genome L) and QTL for yield, plant height plant height QTL foryield, and L) :41-47 (1996). :41-47 (1996). Coffea arabica Coffea C. canephora 54 44 :1011-1021 (2007).:1011-1021 :589-595 (2001). :589-595 (2001). Euphytica Euphytica 108 ) × L. :829-835 (2004). :829-835 20th International International 20th C. canephora Crop Breeding 192 101 :305-323 :305-323 :669- ]. ]. , This article isprotected bycopyright. Allrights reserved. Accepted Article physiology of five oleosinand indeveloping coffee genes germinating grain. J,McCarthy Oleosin of gene family SimkinS and Qian AJ, T, Caillet F,BenAmor V,Michoux M,LinC,Tanksley 137. L.). from coffee( caffeine to of 7-methylxanthine for enzyme the conversion an encoding gene caffeine synthase dual-functional a new Isolation Fujimura T, of and Ashihara H H, Tanaka N, YoneyamaM, Kato A, Okuda MizunoK, 136. (2008). of caffeoyl quinic acids. quinic of caffeoyl accumulation the in involvement (CcPAL1)and its gene ammonia-lyase phenylalanine mapping of aCoffeacanephora and genetic C,Isolation M andCampa Noirot JJ, MaheshV,Rakotomalala Le Gal L,Vigne H, Hamon A, De Kochko S, 138. through geneand enzyme expression activity analysis. belonged to motif B' methyltransferase family inmotif family to belonged B' methyltransferase N-methyltransferase by iscatalyzed trigonelline acid to ofnicotinic Conversion Kato M, and Y T, Yoshizawa Tokiwano S, Kanazawa M, Matsuzaki MizunoK, 141. (Robusta). regulation of caffeine metabolism in PerroisC, Strickler S, GM,ML, L JH,L B, M, M and S P, Differential I. 140. Planta in PAL genes of threehomologous expression Characterization, C, andCampa A de Kochko M, Mahesh Lepelley McCarthy J,V, D, Chabrillange Rigoreau M,Crouzillat N, 139. in metabolism C, SandFoyer C, Tanksley Privat I,Foucrier S,PrinsA,Epalle 135. Experimental Botany and Biophysical Research Communications acid betweenchlorogenic in aninterspecific cross relationship Barre and C-L, caffeine on Ky PNoirot the and M,Genetic investigations 132. 107 content. acid onchlorogenic Impact in coffeetrees. sucrose metabolismsucrose duringcoffee( of analysis andgenomic Biochemical T, PMaP, Marraccini and Leroy Vieira LGE D, Pot CavalariAA, GuerreiroPereira FerreiraSMC, LFP, Geromel LP, C, 134. (2007). 399–434 inCrops Applications Genomics genetic improvement of coffee,in markers: for application DevelopmentRK, DNA and and Aggarwal HendrePS 133. :751–756 (2003). :751–756 C. pseudozanguebariae FEBS letters letters FEBS 236 :313-326 (2012). Planta 163 :691-708 (2006). Coffea arabica 534 (2014). (2014). :75-81 (2003b). :75-81 57 :3243–3258 (2006). :3243–3258 Plant cell reports . Tree Genetics & Genomes & Genomes Genetics Tree Differential regulation ofgr (Arabica) and , Ed by Varshney RK and Tuberosa R. Springer, pp pp R. Springer, andTuberosa RK Varshney by , Ed Coffea canephora Coffea arabica Genomics AssistedCrop Improvement: Vol 2: Coffea arabica 452 25 :1060–1066 (2014). :1060–1066 T, Eychenne M, Kandalaft L, Caillet V, Lin M, Lin Kandalaft L, CailletV, T, Eychenne :986-992 (2006). :986-992 high-resolution mapping high-resolution and differential Coffea canephora Coffea canephora Coffea canephora Coffea arabicaCoffea Theoretical and Applied Genetics Genetics Applied and Theoretical (Arabica)and ) fruit development.) fruit : Quantitative expression analysis analysis expression : Quantitative 9 :1043-1049 (2013). :1043-1049 New Phytologist Phytologist New ain ain sucrose accumulation and Coffea liberica dewevre Coffea liberica (Robusta)revealed Pierre (Rubiaceae). . Coffea canephora Coffea Biochemical and Biochemical Journal of plant Journal of plant Coffea arabica 178 Journal of Journal of :781-797 :781-797 i

This article isprotected bycopyright. Allrights reserved. Accepted Article analysis of leaves and fruits of of andfruits ofleaves analysis LM, RuizM, T, Leroy Charmetant P, Domingues DS and Pereira LFP, Transcriptome Sakuray GAG, Pereira ReisJúniorO, MF, Carazzolle PM,Ivamoto ST, Yuyama 142. properties pilularis. ofEucalyptus wood solid influence genes Methylesterase M,Pectin Shepherd Henson Mand C, McManusDS, LJ, Raymond CE, RJ, Harwood Thomas Henry SextonTR, 145. arabica in metabolism ofcaffeine L,Differential regulation J andMueller Husson S, M, Bedon L,Michaux Lepelley Strickler PrivatSR, I, Perrois C,MathieuG, 143. 2014 ASIC on coffee science and the genetic basis of complex traits in plants. plants. traits in complex basis of the genetic Hall Ingvarsson D,Tegstrom Cand PK, Using mapping todissect association 146. &environment cell modules ofco and transcripts trait thequantitative identify to variation a of source as environment growing the of DussertS,Use and F Descroix A, J, Laffargue T, Salmona Joët 144. science ASIC 2014

Trends inPlantScience Trends Neale DB and Savolainen O, Association of genetics complex traits in conifers. 155. pp123-139(2003).NJ, Totowa, Humana Press, domestication. RJ, Next-generation sequencing Henry forunderstanding crop and accelerating 147. (2010). function, in ES, natu IVUsing Whitt SRandBuckler 154. (2013). Illumina,technology. Anintroduction toNext-generation sequencing 153. integrative biology plant Breeding.in Molecular Technologies Plant Sequencing throughput Using RecentProgress High LiW, GaoQ,YueWang Y, XuJ and Yin G, J, 152. MarkersPlants in in Marker Discovery, for M, Whole-GenomeSequencing Edwards 151. sequencingand its applications. through next-generation discovery S, SNP Cloutier and Kumar S,BanksTW 150. biology to Breeding. Technologies Crop Sequencing Genome Applying Genomics: Fruits of the Promising Harvesting and McCouchSR, R Terauchi RK, Varshney 149. plants. marker to in CJ and J,Application discovery oflarge-scalesequencing Pattemore RJ,Edwards M, Henry WatersMasouleh BundockP,Sexton DL, TR, AK,Nock 148. Journal ofbiosciences 12 and and (2014). Plant Functional Genomics: Methods andProtocols Methods Plant Functional Genomics: Coffea canephora Coffea ‐ Briefings inBriefings functional genomics expressed genes that determine chlorogenicgenes thatacid determine accumulation.expressed , Ed by Henry RJ. Wiley-Blackwell (2013). RJ. (2013). Wiley-Blackwell Henry , Edby , Ed, Colombia (2014). (2014). Colombia , Ed, 33 :1220-1233 (2010b). (2010b). :1220-1233 9 54 :325-330 (2004). :215-227 (2012).:215-227 37 Coffea eugenioides , in International journal of plant genomics genomics International journal of plant :829-841 (2012).:829-841 , Ed, Colombia (2014). , Ed,Colombia (2014). Plant Physiology Plant Physiology The 25th International conference on coffee and on and coffee conference The International 25th Briefings in functional genomics in genomics functional Briefings 11 , in :51-56 (2011). :51-56 (2011). ral allelic diversity to evaluate gene toevaluategene allelicral diversity 158 The 25th International conferenceThe International 25th :531–541 (2012). :531–541 , ed. by ed. by GrotewoldE. , 2012 Journal of Journal of (2012). Molecular Molecular 9 :157-165 :157-165 Coffea Plant, PLOS PLOS ‐ This article isprotected bycopyright. Allrights reserved. Accepted Article Source: (15-18) Table 1.Variation ofthemain biochemica rgnlieLws 08 .50.39 0.75 0.88 Trigonelline Lowest Compound Level afieLws 09 15 0.00 1.51 0.96 Caffeine Lowest urs oet .0 .5 3.80 4.05 7.40 Sucrose Lowest Lipids Ave. 15 10 8-30 8-30 10 15 Lipids Ave. CGAs Lowest 4.34 7 0.8 0.8 7 CGAs Lowest 4.34 Highest 4.80 14.4 11.9 11.9 14.4 4.80 Highest 1.77 1.24 2.64 Highest 2.90 3.30 10.70 Highest 1.62 7.05 11.10 Highest (dmb –g kg C. arabica C. arabica l compoundsquality determining in coffee -1 ) (dmb – g kg C. canephora -1 )

Other species (dmb –g kg -1 )

This article isprotected bycopyright. Allrights reserved. Accepted Article Source: (41-49) heritability broad-sense BSH= heritability; narrow-sense = NSH NSH CGAs 0.74 NSH= Fat content = Male &female additive and 0.36 Trigonelline Caffeine Additive inheritance Polygenic inheritance contentSucrose Trait mode andTable 2:Inheritance heritab

Intraspecific hybrids Female additive effectsFemale Male additive 0.38 NSH = dominant effects additive effectsFemale 0.80 NSH = 0.33; NSH = dominant effects Male & female additive & 0.11 NSH = BSH =0.76 BSH ility of coffee quality determinants

Interspecific hybrids major gene gene major 3-FQA isomer controlledby one inheritance Nuclear heritability inheritance maternalNot additive, High BSH (caf1) No caffeine = recessive gene One major gene withtwoalleles &Polygenic additiveinheritance Higher heritability value &Polygenic additiveinheritance = 0.71 =0.71

This article isprotected bycopyright. Allrights reserved. Accepted Article Genome Chloroplastsequence genome of Genome Whole genome sequence of species Table 3.Genomesequence dataavailabl size (bp) 155,189 25,943 130 79 29 4 18 18 4 29 79 130 25,943 155,189 Est. 710 30 x 25,216 13,345 25,574 92 2,573 2,573 92 25,574 13,345 25,216 30x Est. 710 (Mb) size Coverage Coverage IRs No IRs of

contigs genes No of C. canephora C. scaffolds protein genes No of C. arabica e for thee two main domesticated coffee

genes genes No of No of tRNA Coding region precursors MicroRNA genes rRNA nuclear genome genes containing containing genes Organellar-to- transfers transfers introns This article isprotected bycopyright. Allrights reserved. Accepted Article Noir et al.,2004 8x al., 2006 Joneset x 4 Dereeperet2013 al., 130 6.3x Dereeperet2013 al., 80,813 al., 2005 Leroyet 94 8.6x 10.6x 121 HybridCIFC832/2 Timor 52,416 166 36,864 135 Catimor) x Hybrid (Mokka 36,864 IAPAR 59 55,296 C. arabica DH IF 200 DH IF 200 IF 126 C. canephora coffee species oftwomain Chromosome 4:Bacterial Artificiallibraries Table Genotypes No of

56,832 118 5-6 x Cacao et al., 2013 2013 Cacaoetal., x 5-6 118 56,832 clones Ave. size of Ave. size clones (kb) Coverage Authors Authors Coverage This article isprotected bycopyright. Allrights reserved. Accepted Article amn ta.(0) ed 26 62,508 10,566 69,801 166,133 266 (246,500) Total seeds etal.(104) Salmona Poncet etal. (103) French IRD De Nardi et al. Montoya et al. (101) CENICAFE Vieira et al. (100) Brazilian Genome et al. (99) Lin Uni Nestle and Cornell Fernandez et al. organisation Project/ species coffee main three fromthe Tags Sequence 5:Expressed Table

(102) (98)

Tissues leaf, flower leaf, leaves and leaves and leaves and leaves and fruit evs57 527 leaves seeds fruits fruits roots

arabica C. ESTs ofspecies 130,792 12,381 10,566 33,000 33,000 10,566 12,381 130,792 291 10,799 32,961 ,8 1,587 4,0 13,175 47,000

canephora C. 0405,534 10,420 Unigenes/

racemosa C.

genes This article isprotected bycopyright. Allrights reserved. Accepted Article RFLP and SSR doubled haploid and 1,041 11 segregation (112) (112) segregation 11 1,041 doubled and haploid RFLP andSSR RAPD RFLP and C. canephora F2and F3 ofCaturra SSR F2of (Mundo Novx RAPD F2of AFLP andSSR F2of TallMokka and AFLP AFLP pseudo-F2 C. arabica maps ofcoffeelinkage 6.GeneticTable Markers Population used Length

(IF200) (IF200) doubled haploid x CCC1046 Hybrido de Timor Hybrido de xTimor) Catimor Catimor) (Mokka x hybrid population canephora C. arabica C. arabica

x C. 1,042.4 40 cupping quality cupping 40 1,042.4 (110) traits source-sink 31 1,802.8 540.6 8 8 540.6 Partial linkage ,0 5QLaayi (109) QTLanalysis 15 1,402 1,011 37 1,011 quality and 3800 22 3800 (cM) linkage groups No of size andheight fruit plant yield, and morphology map map productivity purpose Traits/ (119) (119) (111) (118) (118) (92) (92) Authors This article isprotected bycopyright. Allrights reserved. Accepted Article SSR RFLP AFLP and Other species 2populations of SSR SSR pseudo-backcross (COS) (114) of Ortholog Set and vigour yield Conserved 11 ISSR 1,258 AFLP and BP409 x Q121 RFLP andSSR ( RFLP andSSR eugenioides C. liberica DEW dewevrei x pseudozanguebariae ( of hybrid intraspecific C. canephora of Intraspecific hybrid (C.canephora TC (IF200 x DH) distortion distortion DH) TC (IF200x canephora liberica) liberica) canephora C. C. heterocaly C. liberica C. liberica C. canephora C. canephora x (DEW)) x(DEW)) C.liberica x ) x

C. var. var.

C. x x x C.

C.

798.68 11 798.68 QTL (117) analysis 1,144 14 1,144 biochemical (44) and quality yield 11 1,290 1,201 11 1,201 yield and quality (49) 11 1,331 synteny maps 1,502 16 1,502 morphological ,6 5QLaayi (113) QTLanalysis 15 1,360 CGAs, sucrose) sucrose) CGAs, traits (caffeine, and tomato between coffee traits (116) (116) (86) (86) (115) (115) This article isprotected bycopyright. Allrights reserved. Accepted Article 1QTL/A QTL/G 1 14QTLs/A, B,E, D,G, H,I J, K E, F,I, D, B, 23QTLs/A, 7QTLs/B, C, E, G, I 2QTLs/A,G 49,120,121) 44, Source: (43, K G,I, 5QTLs/F, I,K C, E, 14QTLs/A, Cupquality Noof QTLs and LGs 9 QTLs/A, E, I, J CGAs Lipids Trigonelline Caffeine Sucrose Traits Table 7:QuantitativeTrait Loci and Groups Linkage in coffee C. canephora Other species This article isprotected bycopyright. Allrights reserved. Accepted Article 120, 123-130) 44,79, 93,106, Source: (7, canephora C. CaSUS1 & C. arabica Species controllingTable 8:Genes biochemical comp

genes & 8 new CcSUS2 CcSUS1, CaInv3 CaSUS2, Sucrose

CaDXMT1-2 CaDXMT1-2 CaMXMT1-2, and

catalytic alkaloid relating to 23 genes CCS1 & CTS2, CmXRS1, CCS1, CTS2 CmXRS1, Caffeine CaXMT1-2,

, ounds determiningounds quality in traits coffee CTgS2 CTgS2 & CTgS1 N/A Trigonelline

DGAT OLE2, Fatty acids genes & 15other CcSTO1 CcOLE1-5,

F5H1 F5H1 4CL8 pathway -noid phenylpropa involved in Many genes CGAs ,

& HQT POD ,