Genome-Wide Association Study on the Content of Nucleotide-Related Compounds in Korean Native Chicken Breast Meat

Abstract

Meat flavor is an important factor that influences the palatability of chicken meat. Inosine 5′-monophosphate (IMP), inosine, and hypoxanthine are nucleic acids that serve as taste-active compounds, mainly enhancing flavor in muscle tissue. For this study, we performed a genome-wide association study (GWAS) using a mixed linear model to identify single-nucleotide polymorphisms (SNPs) that are significantly associated with changes in the contents of the nucleotide-related compounds of breast meat in the Korean native chicken (KNC) population. The genomic region on chicken chromosome 5 containing an SNP (rs316338889) was significantly (p < 0.05) associated with all three traits. The trait-related candidate genes located in this significant genomic region were investigated through performing a functional enrichment analysis and protein–protein interaction (PPI) database search. We found six candidate genes related to the function that possibly affected the content of nucleotide-related compounds in the muscle, namely, the TNNT3 and TNNT2 genes that regulate muscle contractions; the INS, IGF2, and DUSP8 genes associated with insulin sensitivity; and the C5NT1AL gene that is presumably related to the nucleotide metabolism process. This study is the first of its kind to find candidate genes associated with the content of all three types of nucleotide-related compounds in chicken meat using GWAS. The candidate genes identified in this study can be used for genomic selection to breed better-quality chickens in the future.

Genome-wide association studies of the fatty acid composition of Korean native chicken breast meat

“…Genetic methods such as genome-wide association studies (GWAS) are very effective for finding genomic regions and potential candidate genes for traits of interest [12]. For example, GWAS were used to identify the candidate genes for growth traits, disease resistance, and other important traits in chickens [13]. However, the GWAS of the fatty acid composition in chicken meat are very scarce.…”

“…We chose chickens from 2 generations as shown in Table 1, each generation was 52 weeks. Housing, hatching, management, feeding, slaughtering, and carcass storage conditions are described in our previous study [13]. We collected blood samples from 382 KNC-R chickens and stored at −20 •C until DNA extraction.…”

Explorations on Key Module and Hub Genes Affecting IMP Content of Chicken Pectoralis Major Muscle Based on WGCNA

“…Two non-synonymous SNPs (c.1318C > T and c.1475 T > A) in the ecto-5 ′ -nucleotidase (NT5E) gene (located near the significant region on BTA 9) have been found to influence the content of IMP and its degradation products in beef by regulating the enzymatic activity of NT5E [20]. The SNP (rs316338889) located in the genomic region on chicken chromosome 5 was significantly associated with IMP, inosine, and hypoxanthine traits of breast meat in the Korean native chicken (KNC) population (p < 0.05) [21]. In addition, the results of another study suggest that SNP 6805A/G of adenosine monophosphate deaminase 1 (AMPD1) gene can be used as a possible candidate marker of IMP content in chicken [22].…”

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

“…By selecting for characteristics such as rapid growth/development, feed efficiency, and high yield/quality of breast meat, it is possible to enhance the genetic potential of broiler chickens further [31,38]. This can be achieved through studies of association between candidate genes and phenotypic traits in commercial broiler (breeder) populations [39][40][41][42][43][44][45][46]. Quantitative genetics, computer science, and DNA chip technologies are used in broiler breeding operations to select breeding birds.…”