Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Bruna S R Da Silva,Romain Guyot,Fernanda F De Oliveira,Suzana T Ivamoto,Rafaelle V Ferreira,Maria B S Scholz,Natalia F Pagiatto,Thierry Leroy,Gustavo C Sant’Ana,Douglas S Domingues,Cintia S G Kitzberger,Lívia M Nogueira,Jean-Pierre Labouisse,Pierre Charmetant,Lilian Padilha,Gustavo H Sera,David Pot,Luiz F P Pereira

doi:10.1038/s41598-017-18800-1

Abstract

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.

Highlights

Coffee beverage popularity is related to its unique aroma and flavor as well as its stimulant properties
C. arabica breeding programs suffered from this lack of diversity, which hampered the development of molecular tools whose efficiency is recognized as maximizing the genetic gains per unit of time
Our objectives were to (i) identify single nucleotide polymorphisms (SNPs) within C. arabica genotypes based on GBS analyses; (ii) analyze the population structure of the IAPAR collection of C. arabica genotypes encompassing wild accessions; (iii) perform a Genome-wide association studies (GWAS) to decipher the genetic basis of lipid and diterpene contents within the broad-based Ethiopian collection; and (iv) draw consequences for coffee collections and C. arabica breeding programs

Summary

Introduction

Coffee beverage popularity is related to its unique aroma and flavor as well as its stimulant properties. The precursors of aroma and flavor, which characterize the beverage, correspond to the chemical compounds of green coffee beans[1] The concentrations of those components, such as sucrose, caffeine, chlorogenic acids and lipids, are genetically controlled and can be selected to improve beverage quality[2]. Previous studies of CAF and KAH diterpenes in Coffea arabica L. suggested a strong genetic control of their biosynthesis[2,7]. Despite their importance, as far as we know, there is no study trying to correlate the variability of these biochemical compounds among accessions with nucleotide diversity that would be of key interest to optimize coffee breeding strategies. Because of its relative simplicity and robustness, the genotyping-by-sequencing (GBS) strategies have been extensively used[21,22]

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Conclusion