Identification Genes Controlling Capsaicinoid Content in Capsicum

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Identification Genes Controlling Capsaicinoid Content in Capsicum 1/25/2019 Summary of C. annuum ‘Dempsey’ sequencing A B Identification Genes Controlling Capsaicinoid Content in Capsicum spp. Dempsey Dempsey January 13, 2019 Seoul National University Byoung-Cheorl Kang PGAv.1.6. UCD10X 1 Horticultural Crops Breeding and Genetics Lab 4 Horticultural Crops Breeding and Genetics Lab Capsicum (hot and sweet peppers) Variation of pungency in Capsicum spp. Scoville heat units . The most important vegetable crop in Asian countries (SHU) Examples (The 3rd most important vegetable crop in the world) 15,000,000 Pure Capsaicin 2,000,000-5,300,000 . Consists of approximately 22 wild species and five domesticated species Carolina Reaper, Pepper X (C. annuum, C. chinense, C. frutescens, C. pubescens, C. baccatum) 1,500,000–2,000,000 Trinidad Moruga Scorpion . Use: spices, vegetables, ornamental, pharmaceutical and industrial 855,000–1,463,700 applications Infinity Chilli, Bhut Jolokia chili pepper Genes 350,000–580,000 . A member of the family Solanaceae that includes tomato, potato, Red Savina habanero controlling eggplant, tobacco, and petunia 100,000–350,000 Habanero, Scotch bonnet pepper, Datil pepper capsaicinoid content . Genome size: about 3.0 - 3.5 Gb (x=12) 50,000–100,000 Bird's eye chili (Thai Chili), Malagueta pepper are largely . Molecular markers are available for major traits 30,000–50,000 Cayenne pepper, Tabasco pepper, Cumari pepper unknown! Serrano pepper, Peter pepper, Aleppo pepper . Genome sequence and high density maps are available 10,000–23,000 Espelette pepper, Jalapeño pepper, Chipotle 3,500–8,000 Anaheim pepper, Poblano pepper, Rocotillo pepper 1,000–2,500 Pimento, Banana pepper 100–900 Bell pepper (Early Calwonder: ECW) , Aji Dulce No significant heat (wikipedia.org/wiki/Scoville_scale) Horticultural Crops Breeding and Genetics Lab 5 Horticultural Crops Breeding and Genetics Lab Capsicum spp. reference genomes Capsaicinoid Capsicum annuum ‘CM334’ (Nature Genetics, 2014) • Pungency causing substance in pepper (Capsicum spp.) • Resistant to P. capsici • Unique characteristic only in the genus Capsicum • Resistant to nematode (Me7) • Pharmacological effects • Resistant potyviruses (Pvr4), CMV, PVX – Anticancer, antioxidant, pain relief, and obesity control Capsicum annuum ‘Zunla-1’ (PNAS, 2014) Capsicum annuum ‘Chitepin’ Capsicum chinence ‘PI159236’ (Genome Biology, 2017) • Resistant to viruses Capsicum baccatum ‘PBC81’ • Resistant to anthrancnose Capsicum annuum ‘CM334’ (Hortic Research, 2018) Capsaicin Dihydrocapsaicin Capsicum annuum ‘Dempsey’ (Poster#PE946) Nordihydrocapsaicin n-vanillylnonanamide Horticultural Crops Breeding and Genetics Lab 6 Horticultural Crops Breeding and Genetics Lab 1 1/25/2019 Accumulation of capsaicinoid Overview of our approaches • Capsaicinoid is accumulated in placenta and interlocular septum Pungency in placenta Pungency in pericarp • Two RIL populations • Two F2 populations • Genotyping • Genotyping and expression - whole genome resequencing - genotype-by-sequencing - genotype-by-sequencing - transcriptome sequencing • Phenotyping • Phenotyping - multi-year & multi location - multi-year & multi location - Placenta tissues - Pericarp tissues - HPLC - HPLC (Park et al., TAG, 2018) Trinidad Moruga Scorpion Trinidad Scorpion Bhut Jolokia (Han et al., Plant Biotech J, 2018) Super-hot peppers Pungency in whole fruit • GWAS population • Genotyping - genotype-by-sequencing • Phenotyping (Aza-Gonza´lez et al, 2011; Mazourek et al, 2009; Bosland et al, 2015) - Whole fruits - HPLC 7 Horticultural Crops Breeding and Genetics Lab 10 Horticultural Crops Breeding and Genetics Lab Structural genes controlling pungency KR • Mutations in the Pun1 gene (capsaicin synthase) result in nonpungency IDENTIFICATION OF QTL CONTROLLING PUNGENCY IN CAPSICUM p-amt • Mutations in the p-AMT gene greatly reduce pungency level The positive correlation of expression of structural genes and the level of pungency regulated and (Stewart & Kang 2005, Aza-Gonza´lez et al, 2011; coordinated at by transcription factors. Stellari et al, 2010) 8 Horticultural Crops Breeding and Genetics Lab Horticultural Crops Breeding and Genetics Lab QTL studies for capsaicinoid content QTL mapping in Capsicum Population Cross (Species) No. of QTL QTL location Marker type R2 (%) Reference (No. of plants) Maor (C. annuum) F Blum et al, 2 1 Chr. 7 400 RAPD 34-38 × BG 2816 (C. frutescens) (242) 2003 Biparental pop Genotype CIM, MIM NuMex RNaky (C. annuum) F Ben-Chaim et al, Proper sequencing 3 6 Chr. 3, 4, 7 728 SSR, AFLP, and RFLP 9-25 × BG2814-6 (C. frutescens) (234) 2006 method for pepper Association Validation Experimental mapping NuMex RNaky (C. annuum) RIL Chr. 3, 4, 5, 6, 7, Yarnes et al, GBS Using bi-parental 12 16,188 unigenes 9-26 population × BG2814-6 (C. frutescens) (105) 10, 11 2013 Diverse model approach population and previous researches Phenotype NB1 (C. annuum) F 234 HRM, SSR, CAPS, and Lee et al, 2 4 Chr. 2, 3, 6 9-19 Interesting traits useful General Linear Model (GLM) (175) gene-based markers 2016 Core collection × Bhut Jolokia (C. chinense) for breeding Mixed Linear Model (MLM) Plant architecture • Improving capsaicinoid content in pepper varieties is very challenging Pungency Fruit color • Comparison of QTLs from different studies was difficult Plant disease Limitations • Markers were far from QTLs due to low-density genetic map • No candidate genes under QTLs are known. 12 9 Horticultural Crops Breeding and Genetics Lab Horticultural Crops Breeding and Genetics Lab 2 1/25/2019 RIL populations Methods for genotyping Cross combination Generation # of lines Trait • Whole-genome re-sequencing of ‘PD RIL’ (Kim et al, 2014) C. annuum ‘Long sweet’ Vit C and E F 207 x C. annuum ‘AC2212’ 6-7 Fruit color Sequencing 18× for parents and 1× for RILs C. annuum ‘35001’ • Genotyping-by-sequencing of ‘TH RIL’ F 176 Carotenoid content x C. annuum ‘35009’ 7-9 PstI/MseI double digestion with SBG v.2.0 kit (Keygene, Netherlands) C. annuum ‘Perennial’ Pungency F 166 x C. annuum ‘Dempsey’ 6-11 Morphological traits • SNP calling C. annuum ‘TF68’ Pungency Genotyping C. annuum ‘CM334’ reference genome v.1.6 F 92 x C. chinense ‘Habanero’ 10-11 Yield BWA-mem, SAMtools, Picard, and GATK UnifiedGenotyper Pungency SNPs with minimum QUAL 30 and depth 3 C. annuum ‘YCM334’ F 176 x C. annuum ‘Tean’ 9-11 Phytophthora resistance C. annuum ‘CM334’ • Sliding window approach F6-7 250 Disease resistance x C. annuum ‘ECW30R’ Bin map Imputation of missing data Window length: physical length (PD RIL) or SNP number (TH RIL) • Composite interval mapping QTL analysis WinQTL Cartographer Horticultural Crops Breeding and Genetics Lab 16 Horticultural Crops Breeding and Genetics Lab Core collection Bin map of ‘PD RIL’ • Whole-genome re-sequencing of 120 RILs C. annuum accessions with one B C. galapagoense mostly from Europe countries C. annuum 218 C. baccatum 47 C. galapagoense C. chinense 46 C. frutescens 25 A others 5 C Total 351 Physical length of bin (Mb) Genetic distance of bin (cM) Chr. Number of SNPs Number of bins Mean Total Mean Total Most C. baccatum, and C. frutescens accessions 1 82,966 390 0.7 272.6 0.5 210.9 C. baccatum, C. frutescens, C. pubescens, 2 80,141 207 0.8 171.1 0.5 108 C. cardenasii, C. chacoense, C. eximium, 3 87,793 279 0.9 257.9 0.4 118 C. praetermissum, C. tovarii accessions mostly 4 54,657 224 1.0 222.5 0.5 117.2 from South America and Europe countries 5 82,413 201 1.2 233.4 0.5 100.2 E Most C. chinense accessions 6 107,015 234 1.0 236.9 0.4 102.2 7 84,339 180 1.3 231.9 0.5 86.3 8 24,383 224 0.6 144.8 0.7 145.6 9 275,842 179 1.4 252.7 0.5 89.7 D 10 230,360 160 1.5 233.6 0.6 102.1 C. annuum accessions mostly from Asia countries 11 252,765 202 1.3 259.7 0.4 83.8 12 68,540 233 1.0 235.7 0.4 94.9 (BMC Genetics, Lee et al, 2016) Total 1,431,214 2,713 1.0 2,752.8 0.5 1,358.9 (DNA Research, Han et al., 2016) 14 Horticultural Crops Breeding and Genetics Lab 17 Horticultural Crops Breeding and Genetics Lab Phenotype evaluation Major QTLs detected from both RILs • Plant growth - more than two environments • Comparison of physical location of QTLs for capsaicinoid content Anseong • Five QTLs on chromosome 1, 2, 3, 4, and 10 were detected commonly Geological Population Year No. of RILs Cultivation location PD RIL 2011 170 Anseong Ground 2012a 162 Anseong Ground 2012b 162 Suwon Pot Suwon TH RIL 2013 102 Anseong Ground 2014 104 Anseong Ground GWAS 2016 351 Jeonjoo Ground 2017 351 Jeonjoo Ground • Evaluation of capsaicinoid content – Dissection of placenta (or whole fruits) from 5 fruits per each RIL – Measurement of capsaicin and dihydrocapsaicin contents by HPLC (Han et al., Plant Biotech J 2018) 15 Horticultural Crops Breeding and Genetics Lab 18 Horticultural Crops Breeding and Genetics Lab 3 1/25/2019 GWAS of capsaicinoid Summary of part 1 • 109,610 SNPs detected from GBS of PstI/MseI and EcoRI/MseI • High-density bin maps were constructed by WGS and GBS of RILs . Capsaicin (99 SNPs) • Five common QTLs were detected on chromosome 1, 2, 3, 4, and 10 • By comparison with GWAS results, 5 candidate genes in capsaicinoid biosynthetic pathway were identified • Candidate genes and associated SNPs can be used for molecular breeding of . Dihydrocapsaicin highly pungent pepper cultivars (Han et al., Plant Biotech J 2018) 19 Horticultural Crops Breeding and Genetics Lab 22 Horticultural Crops Breeding and Genetics Lab Manhattan plot from GWAS and co-located QTLs IDENTIFICATION OF A NOVEL PUNGGENCY CONTROLLING LOCUS (PUN3) IN CAPSICUM pAMT, putative aminotransferase; CSE, caffeoyl shikimate esterase; 4CL, 4-coumaroyl-CoA ligase; C4H, cinnamate 4-hydroxylase; FatA, acyl-ACP thioesterase 20 Horticultural Crops Breeding and Genetics Lab Horticultural Crops Breeding and Genetics Lab Candidate genes for capsaicinoid QTL Non-pungent accession ‘YCM334’ • C.
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