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| Genome-wide Association Study on Feet Weight in Chicken (Gallus gallus) |
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Abstract The feet weight trait of chicken (Gallus gallus) is one of the most important economic traits in the chicken industry. In order to reveal the genetic basis of feet weight trait and scan molecular markers which can be used to improve the feet weight trait, the feet weight trait was measured after Jinghai yellow chicken in core group being slaughtered. Genome-wide association study was carried to detect SNPs that was associated with feet weight trait by using specific-locus amplified fragment sequencing technology. Chicken reference genome was analyzed using the prediction software based on the gene characteristics to choose the appropriate restriction enzyme. Then a series of procedures were put into effect to create database to do the sequencing by IlluminaHiSeq2000. A total of 103 680 specific-locus amplified fragment sequencing technology (SLAFs) were found with an average read depth of 5.46 in the research population. Of these, 88 135 were found to be polymorphic (85%). The distribution of the SLAFs was even throughout the whole genome. After SNPs were detected among the defined SLAF fragments, 90 929 SNPs were identified after quality control measures. Then the SNPs that associated with chicken's feet weight trait were used to do enome level SNP classification and analysis method (GWAS) analysis, 16 SNPs that were related to feet weight were detected. 2 SNPs of rs475641139 and rs475548810 reached 5% Bonferroni genome-wide significance (P＜5.5E-07) and the rest of 14 SNPs reached "suggestive" genome-wide significance (P＜1.1E-05). At last, 9 potential functional genes were got after screening every important SNPs' ambient 1 Mb window areas (SNP location right and left 0.5 Mb). The cellular component, molecular function and biological process were analyzed by using Gene Ontology (GO) database. Furthermore, all 13 SNPs were distributed in the region of 72.8~77.9 Mb on chromosome 4. Nine genes of dihydropteridine deductase gene (QDPR), LIM domain-binding protein 2 gene (LDB2), family with sequence similarity 184 member B gene (FAM184B), recombination signal binding protein for immunoglobulin kappa J region gene (RBPJ), fibroblast growth factor-binding protein 2 gene (FGFBP2), F-box and leucine-rich repeat protein 5 gene (FBXL5), cholecystokinin receptor type A gene (CCK1R), WD repeat containing protein 1 gene (WDR1) and tubby like protein 4 gene (TULP4) and 72.8~77.9 Mb region on chromosome 4 were important candidate genes and region affecting feet weight trait in Jinghai yellow chcken. This study can provide the theory basis for the feet weight trait's marker assisted selection.
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Received: 07 April 2016
Published: 06 August 2016
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