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

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.

Deciphering the Genetic Architecture of Cooked Rice Texture

“…Among the implemented ML-GWAS methods, pLARmEB and ISIS EM-BLASSO detected the higher number of significant QTNs. The same observation was made in the recent study (Sant'ana et al, 2018 ), who reported a high number of trait-associated SNPs using two methods. On the other hand (Ma et al, 2018 ), acknowledge the robustness of ISIS EM-BLASSO than the other three methods (FASTmrEMMA, pLARmEB, mrMLM).…”

“…Indeed, although, no SNP significantly associated QTNs were identified for cohesiveness using SL-GWAS and mrMLM methods, we detected putative genomic regions underlying COH using three other ML-GWAS methods. Multi-locus GWAS has gained popularity with a growing number of studies reporting the use of this approach (Misra et al, 2017 ; Ma et al, 2018 ; Sant'ana et al, 2018 ; Zhang et al, 2018 ) to perform marker-trait association. Some of the distinct advantages of multi-locus GWAS over single-locus GWAS are their power, accuracy in QTN effect estimation, reduced rate of false positives (Wang et al, 2016 ; Tamba et al, 2017 ; Ma et al, 2018 ).…”

Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.

“…With its relatively small, diploid, sequenced and annotated genome, Coffea canephora is highly compliant with genomic‐based breeding approaches using Genome Wide Association Studies (GWAS). Thanks to the rapid development of genomic resources and the publication of the reference genome (Denoeud et al ., ), third‐generation markers based on single‐nucleotide polymorphisms (SNPs) have gradually been identified and assayed in Coffea , particularly in C. arabica (Sant'Ana et al ., ; Tran et al ., ).…”

Hello darkness, my old friend: 3-Ketoacyl-Coenzyme A Synthase4 is a branch point in the regulation of triacylglycerol synthesis inArabidopsis thaliana

“…primary and secondary metabolites and enzyme activities) (Wu et al, 2018(Wu et al, , 2016Fusari et al, 2017). Regarding lipid metabolism, a number of GWAS have been reported, for instance in Arabidopsis, maize, coffee, and canola, resulting in the identification of new enzymes and regulators (Riedelsheimer et al, 2013;Li et al, 2019;Sant'Ana et al, 2018;Gacek et al, 2017). These studies focused on lipid levels under optimal growth conditions.…”