Genome-Wide Association Study Identifies Loci and Candidate Genes for Body Composition and Meat Quality Traits in Beijing-You Chickens

Abstract

Body composition and meat quality traits are important economic traits of chickens. The development of high-throughput genotyping platforms and relevant statistical methods have enabled genome-wide association studies in chickens. In order to identify molecular markers and candidate genes associated with body composition and meat quality traits, genome-wide association studies were conducted using the Illumina 60 K SNP Beadchip to genotype 724 Beijing-You chickens. For each bird, a total of 16 traits were measured, including carcass weight (CW), eviscerated weight (EW), dressing percentage, breast muscle weight (BrW) and percentage (BrP), thigh muscle weight and percentage, abdominal fat weight and percentage, dry matter and intramuscular fat contents of breast and thigh muscle, ultimate pH, and shear force of the pectoralis major muscle at 100 d of age. The SNPs that were significantly associated with the phenotypic traits were identified using both simple (GLM) and compressed mixed linear (MLM) models. For nine of ten body composition traits studied, SNPs showing genome wide significance (P<2.59E−6) have been identified. A consistent region on chicken (Gallus gallus) chromosome 4 (GGA4), including seven significant SNPs and four candidate genes (LCORL, LAP3, LDB2, TAPT1), were found to be associated with CW and EW. Another 0.65 Mb region on GGA3 for BrW and BrP was identified. After measuring the mRNA content in beast muscle for five genes located in this region, the changes in GJA1 expression were found to be consistent with that of breast muscle weight across development. It is highly possible that GJA1 is a functional gene for breast muscle development in chickens. For meat quality traits, several SNPs reaching suggestive association were identified and possible candidate genes with their functions were discussed.

Single nucleotide polymorphisms associated with growth traits in Jinghai yellow chickens

“…In chickens, many genome-wide association studies (GWAS) were conducted using the Illumina 60K SNP Beadchip. Using this method, major loci associated with growth (Gu et al, 2011;Xie et al, 2012), egg production Wolc et al, 2012), rumpless and ear-tufted traits (Noorai et al, 2012), body composition and meat quality (Liu et al, 2013), resistance to Marek's disease (Li et al, 2013), and immune responses to Newcastle disease virus (Luo et al, 2013) were identified.…”

Genome-wide association study of growth traits in the Jinghai Yellow chicken

“…Such studies have been used to comprehensively analyze complex, economically important traits using technical statistical tools (Fan et al, 2011;Liu et al, 2011;Onteru et al, 2012;Liu et al, 2013;Wolc et al, 2014). Thus, GWAS have been one of the most effective approaches for identifying related QTLs and functional genes (Xu et al, 2013).…”

“…Thus, GWAS have been one of the most effective approaches for identifying related QTLs and functional genes (Xu et al, 2013). In chickens, Sun et al (2013) identified 14 new genes related to meat quality traits in chicken using a GWAS. Liu et al (2013) found that a consistent region on chicken GGA4 was associated with carcass weight and eviscerated weight.…”

“…In chickens, Sun et al (2013) identified 14 new genes related to meat quality traits in chicken using a GWAS. Liu et al (2013) found that a consistent region on chicken GGA4 was associated with carcass weight and eviscerated weight. Gu et al (2011) used an F 2 resource population derived from Silky Fowl and White Plymouth Rock chickens to detect SNPs associated with body weight at 7-14 weeks of age in a region of GGA4 (71.6-80.2 Mb).…”

Polymorphisms in GJA1 and their association with growth traits in chicken

“…Several quantitative trait loci (QTLs) have been investigated in different chromosomal regions of chicken for the BW (Kerje et al, 2003;Pinard-van der Laan et al, 2009), CW , and TMW (Nones et al, 2006) traits. A few genome wide association studies (GWAS) have also identified several loci on chromosomes 1 and 4 that are strongly associated with BW, CW, EW, BMW, and TMW traits (Gu et al, 2011;Xie et al, 2012;Liu et al, 2013) in chicken. However, a limited number of genetic markers invested on chromosome 3 either by QTL or GWAS for growth traits in chicken.…”