Genome-wide Association Study on Market Weight Based on Specific-locus Amplified Fragment Sequencing (SLAF-seq) in Jinghai Yellow Chicken (Gallus gallus)
Abstract：In order to reveal the genetic basis of market weight trait and scan molecular markers and candidate genes which can be used to improve the market trait, market weight of 400 female Jinghai yellow chicken (Gallus gallus) in core group was measured at 16 weeks of age. Genome-wide association study (GWAS) was carried out using specific-locus amplified fragment sequencing technology to detect nucleotide polymorphisms (SNPs) associated with market weight. Finally, 15 single SNPs that associated with market weight were detected using General liner model (GLM). Four SNPs reached 5% Bonferroni genome-wide significance (P＜1.87E-06) and 11 SNPs reached “suggestive” genome-wide significance (P＜3.73E-05). 6 SNPs that associated with market weight were detected using mixed linear model (MLM). 2 SNPs reached 5% Bonferroni genome-wide significance (P＜1.87E-06) and 4 SNPs reached “suggestive” genome-wide significance (P＜3.73E-05). 6 SNPs of rs1169337928, rs475641139, rs31633105, rs475856030, rs476878211 and rs477915563 were detected both using GLM and MLM. Genes in the candidate regions with 1-Mb windows (SNP position±0.5 Mb) surrounding each significant SNP were screened. Finally, 14 candidate genes were obtained, among which 6 genes of FAM124A, QDPR, BCL11A, LDB2, BOD1L1 and WDR1 might be important candidate genes influencing market weight. Furthermore, It was also found that 9 out of 14 SNPs were distributed in the region of 75.641~79.592 Mb on chromosome 4, and this region was important candidate region which influenced the market weight of Jinghai yellow chicken. This study provides theory material for marker assisted selection of Jinghai yellow chicken.
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