SNP in the Coffea arabica genome associated with coffee quality

Abstract

Association analysis was performed at the whole genome level to identify loci affecting the caffeine and trigonelline content of Coffea arabica beans. DNA extracted from extreme phenotypes was bulked (high and low caffeine, and high and low trigonelline) based on biochemical analysis of the germplasm collection. Sequencing and mapping using the combined reference genomes of C. canephora and C. eugenioides (CC and CE) identified 1351 non-synonymous SNPs that distinguished the lowand high-caffeine bulks. Gene annotation analysis with Blast2GO revealed that these SNPs corresponding to 908 genes with 56 unique KEGG pathways and 49 unique enzymes. Based on KEGG pathway-based analysis, 40 caffeine-associated SNPs were discovered, among which nine SNPs were tightly associated with genes encoding enzymes involved in the conversion of substrates (i.e. SAM, xanthine and IMP) which participate in the caffeine biosynthesic pathways. Likewise, 1060 nonsynonymous SNPs were found to distinguish the low-and high-trigonelline bulks. They were associated with 719 genes involved in 61 unique KEGG pathways and 51 unique enzymes. The KEGG pathway-based analysis revealed 24 trigonelline-associated SNPs tightly linked to genes encoding enzymes involved in the conversion of substrates (i.e. SAM, L-tryptophan) which participate in the trigonelline biosynthesis pathways. These SNPs could be useful targets for further functional validation and subsequent application in arabica quality breeding. Keywords Caffeine. Trigonelline. Association mapping. Extreme phenotypes. TAVs Key message Forty caffeine-associated SNPs and 24 trigonellineassociated SNPs tightly linked to genes encoding enzymes involved in the conversion of substrates which participate in the caffeine and trigonelline biosynthesic pathways were Communicated by V. Decroocq

Comprehensive analysis of quality characteristics in main commercial coffee varieties and wild Arabica in Kenya

“…This finding is consistent with a previous report ( Ky et al, 2001 ). Increased sucrose and trigonelline contents along with decreased caffeine and CGA contents are associated with high beverage quality ( Tran et al, 2018 , Richard et al, 2007 ). Variation in non-volatile contents is affected by coffee variety ( Perrois et al, 2015 , Vidal et al, 2010 , Yapo et al, 2003 ).…”

An extreme-phenotype genome‐wide association study identifies candidate cannabinoid pathway genes in Cannabis

“…This could be addressed by sequencing individuals within pools or by sequencing a physical random pool to check for spurious associations 52 . However, both approaches would negate to some extent the lower costs associated with sequencing a maximum of two phenotypically extreme DNA pools 52 , 56 . One approach that could be assessed is to apply a Chi-squared test to the read counts for the pools surrounding intervals, in order to reject the null hypothesis that the phenotype and AFe are not correlated.…”

“…XP-GWAS has resolved QTL for kernel row number in Zea mays (maize) 52 and has also been successfully applied to inbred lines of Beta vulgaris (sugar beet) 51 and its crop wild relatives 55 to identify trait-associated variants. More recently, this analysis has identified variants associated with caffeine and trigonelline content in the self-fertilising species Coffea arabica (Arabian coffee) 56 . However, few studies have evaluated the utility of XP-GWAS in obligate outcrossing and highly heterozygote plants such as Cannabis .…”

Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes

“…In addition, no major introgressions could be verified (Scalabrin et al 2020). To understand how genetic diversity impacts the coffee economy several initiatives to investigate this allopolyploidy genome -and relative species genomes -are undergoing to better understand its organization and underlying regulatory networks (Lashermes et al 2016;Tran et al 2018aTran et al , 2018bMekbib et al 2022;Cenci et al 2012;Denoeud et al 2014).…”