Advances in genomics for the improvement of quality in Coffee Hue T.M. Tranab, L. Slade Leec, Agnelo Furtadoa, Heather Smytha, Robert Henrya* a Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Australia b Western Highlands Agriculture & Forestry Science Institute (WASI), Vietnam c Southern Cross University, Australia * Correspondence to: Robert Henry, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia QLD 4072, Australia, Tel. +61 7 3346 0551, Email: [email protected] Accepted Article This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/ jsfa.7692 This article is protected by copyright. All rights reserved. Abstract Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programs. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. Key words: Coffee quality, genetics, genomics, biochemical compounds, next generation sequencing, association studies. Accepted Article This article is protected by copyright. All rights reserved. GENERAL INTRODUCTION Coffee is an important crop and the second most traded commodity in the world (after petroleum) providing a living to more than 125 million people 1. Coffee belongs to the Rubiaceae family and the Coffeeae tribe and consists of more than 124 species spread across two genera Coffea L. and Psilanthus Hook.f, each of which in turn consist of two sub-genera, Coffea and Baracoffea (J.-F. Leroy) J.-F. Leroy, and Psilanthus and Afrocoffea (Moens) summarized by Anthony et al. 2 respectively. The grouping of Coffea and Psilanthus genera has been examined in several studies 3 4 5 6 7. Commercial coffee production is dominated by only two species belonging to the Coffea genus: C. arabica and C. canephora (the latter generally referred to as robusta coffee). All coffee species are diploid (2n=2x=22) and generally self-incompatible, except for C. arabica which is a self-fertile tetraploid (2n=4x=44) derived from a spontaneous hybridization between C. canephora (as paternal progenitor) and C. eugenioides (as maternal progenitor) 8 9. Although C. arabica is considered to have better cupping quality than C. canephora, improving the quality of both commercial species remains a target for most coffee improvement programs. With advances in genomic and sequencing technology, it is feasible to understand the coffee genome and the molecular inheritance underlying coffee quality, thereby helping improve the efficiency of breeding programs. This review will discuss current knowledge regarding the genetics of those biochemical compounds which are considered quality determinants, for use as a foundation for Accepted Article improving coffee quality by breeding. Available genomic resources for the study of the genetics of biochemical compounds that are likely to be playing a role in coffee flavour will also be discussed. In addition, the potential value of the study of genetics of coffee This article is protected by copyright. All rights reserved. quality using next generation sequencing and association genetic analysis will be considered. BIOCHEMICAL CONTROL OF COFFEE QUALITY AND ITS VARIATION Coffee quality is assessed by evaluating both the physical attributes of the coffee beans and the organoleptic properties of the coffee. Physical quality reflects moisture content, defects (e.g. sticks, stones, damaged beans and black beans ), bean size and bean colour; while organoleptic quality reflects aroma, taste, flavour, body (a feeling of the heaviness or richness on the tongue), acidity and the preference of tasters 10. A range of biochemical compounds in coffee beans are important contributors to the quality of the coffee in the cup. Biochemical compounds influencing the organoleptic quality of coffee beans include non-volatile and volatile components. Important non-volatile components of the bean include carbohydrates and fibre (sucrose, reducing sugars, cell wall polysaccharides, lignin), nitrogenous compounds (protein, free amino acids, caffeine, trigonelline), lipids (coffee oil, diterpene esters), minerals (potassium and phosphorus), acids and esters (total chlorogenic acids, aliphatic acids and quinic acid) 11. All of these biochemical compounds are considered to play a role in roasting chemistry 12. Proteins and amino acids, for example, react with reducing sugars to produce aroma precursors. Chlorogenic acids (CGAs) and caffeine, are responsible for bitterness 13. Among these components, sucrose, caffeine, trigonelline, lipids and CGAs are major biochemical compounds that contribute to the flavour of the beverage after the roasting of the Accepted Article beans 11. While sucrose, trigonelline and lipid have a positive correlation with coffee cup quality, caffeine and some sub classes of CGAs have a negative correlation with coffee cup quality (often referred to simply as ‘cup’). There are about three hundred volatiles detected so far in green coffee bean 14 of which twenty one volatiles, This article is protected by copyright. All rights reserved. including 3-isobutyl-2-methoxypyrazine and 2-methoxy-3,5-dimethylpyrazine, have been identified as key compounds for coffee cup 14. In the roasted coffee bean, there are more than a thousand volatiles which can be grouped into twenty key aroma compound-groups 15. The aroma of the brew is different from that of roasted coffee. Several notes in roasted coffee become more intensive in the brew such as caramel and phenolic odour. This change in aroma profile of coffee is not caused by the formation of new odorants, but by a shift in the concentrations of existing ones as summarised by Grosch 16. Coffee flavour and its formation is extremely complex; however, numerous studies on coffee flavour and its constituents have been reported. How the volatile and non- volatile compounds contribute to coffee quality and relationships between sensory properties and the composition of coffee has been thoroughly reviewed by Flament 12 and more recently by Sunarharum et al.17. The reactions involved in the formation of coffee aroma and its mechanisms have been reviewed by Buffo & Cardelli-Freire 18. However, the change in bean composition, especially in aroma profile, from green to roasted bean is complicated and not all formation pathways are fully understood under coffee roasting conditions 19. The use of green bean or roasted bean in the study of coffee quality genetics therefore should be considered carefully since aroma in roasted bean and brew is of customer's interest, while the green bean attributes are more directly affected by genetics. This is a challenge in the study of genetics of bean composition, that is, ascribing links to coffee quality. However, with the progress in Accepted Article functional genomic approaches, the identification of molecular determinants of coffee quality characteristics is feasible and it is possible to select coffee varieties with superior beverage quality 20. This article is protected by copyright. All rights reserved. The bean chemical composition and organoleptic characteristics are significantly different between species and to a lesser extend within species 10. A number of studies on the variation in the biochemical composition of the bean are summarised in Table 1 21-24. Fatty acid and CGAs were used as indicators to differentiate arabica varieties 25 26. Similarly, Tessema et al. 27 also found that the quality traits (organoleptic quality) and biochemical constituents (sucrose, fat, crude protein and minerals) were diverse in the arabica germplasm collections from Ethiopia. This is an encouraging result for the study of variation of quality traits in C. arabica for association mapping. In general, compounds that have a positive correlation with quality such as sucrose, trigonelline and lipids are at a higher concentration in C. arabica than in C. canephora and some other Coffea species. Significant differences in flavour between different coffee types have also been reported. Robusta coffee beans have a bitter, full bodied taste, but low acidity while those of arabica coffee are more aromatic