Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken

Abstract

Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.

Research progress and applications of genome‐wide association study in farm animals

“…Additionally, the polygenic effect of economic traits in farm animals accentuates the difficulty in investigating causal variants [81]. Multiple peaks related to body weight, shank length, semi-eviscerated weight, and some meat quality and carcass traits have been detected [82][83][84]. Advances in techniques for fine-mapping and prioritizing variants have been developed through functional annotation [26], Bayesian approaches [85], and sequencing technology [86].…”

“…Over a decade of improvements in sequencing technology, whole-genome sequencing and modified reduced genome sequencing (e.g., RAD, RRGS, and GBS) have occurred and SNPs are the most common markers in recent studies [89][90][91]. Currently, multiple genomic variant types, including copy number variations (CNVs) [92][93][94], insertion-deletion (InDel) [84,95], structure variations (SV) [96][97][98], haplotype [99], presence/absence variations (PAVs) based on pan-genome [100], and even epigenomic markers [101] have gained increasing attention through GWAS. Multiple variant profiles have been generated for multiple breeds [102,103].…”

“…In cattle, Li et al identified the candidate SNPs associated with betaine, L-Lactic acid, and L-Alanine and the range of the proportion of SNP additive variance was from 0.62% to 4.21% [121]. In chickens, Yuan et al identified 253 candidate SNPs and 248 InDels associated with various muscular aldehydes [84], and Wang et al found that SLC16A7 expression was highly correlated with serum triglyceride levels [109]. Animal health status could be reflected directly by the alteration of metabolite profiles in serum or certain tissues [122,123], and mGWAS is a potential approach to investigate the molecular mechanism underlying disease resistance and precise nutrition.…”

“…In chickens, Yuan et al. identified 253 candidate SNPs and 248 InDels associated with various muscular aldehydes [84], and Wang et al. found that SLC16A7 expression was highly correlated with serum triglyceride levels [109].…”

Detection of genomic variations and selection signatures in Wagyu using whole‐genome sequencing data

“…It is noteworthy that there are 97 candidate regions containing 27 genes that were detected by all four methods (Table 1; Table S6). Among them, LRP2BP took part in the regulation of lipid metabolism (May et al, 2007); GAA was associated with the regulation of adipose tissues (Zhu et al, 2018); CACNG6 and CXADR were related to feed efficiency (de Oliveira et al, 2014; Olivieri et al, 2016); and GPCPD1 was a fatty acid metabolism‐related gene in chicken (Yuan et al, 2022). A haplotype comparison analysis of LRP2BP and GAA indicated an obvious differentiation between Wagyu and Chinese indigenous breeds (Figure 1d).…”