title: Advances in genomics for the improvement of quality in coffee.
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 programmes. 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. © 2016 Society of Chemical Industry.
authors.affiliation: Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia.|Western Highlands Agriculture & Forestry Science Institute (WASI), Daklak, Vietnam.
authors.forename: Hue Tm
authors.initials: HT
authors.lastname: Tran
authors.affiliation: Southern Cross University, East Lismore, NSW 2480, Australia.
authors.forename: L Slade
authors.initials: LS
authors.lastname: Lee
authors.affiliation: Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Agnelo
authors.initials: A
authors.lastname: Furtado
authors.affiliation: Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Heather
authors.initials: H
authors.lastname: Smyth
authors.affiliation: Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Henry
mesh_terms: D000470:Alkaloids / Q000032:analysis; D002110:Caffeine / Q000032:analysis; D040503:Coffea / Q000737:chemistry / Q000235:genetics*; D003069:Coffee / Q000737:chemistry; D063427:Food Quality; D015723:Gene Library; D017343:Genes, Plant; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008055:Lipids / Q000032:analysis; D040641:Quantitative Trait Loci; D012639:Seeds / Q000737:chemistry / Q000235:genetics; D017421:Sequence Analysis / Q000379:methods; D013395:Sucrose / Q000032:analysis
chemical_list: D000470:Alkaloids; D003069:Coffee; D008055:Lipids; D002110:Caffeine; C009560:trigonelline; D013395:Sucrose
keywords: association studies; biochemical compounds; coffee quality; genetics; genomics; next generation sequencing