儋州鸡体尺性状全基因组关联分析

【目的】 挖掘影响地方鸡体尺性状的有效SNP位点及功能基因, 给儋州鸡育种工作提供有效的数据基础和理论支撑。【方法】 共采集200只儋州鸡血样并提取基因组DNA, 利用10×全基因组重测序技术获得全基因组SNP标记并对试验个体基因型进行分型。使用EMMAX软件基于混合线性模型对70日龄的儋州鸡体尺性状(胫长、胫围、体斜长、胸宽、髋骨宽、胸深、龙骨长)进行全基因组关联分析。【结果】 共发现与胫长性状和胫围性状基因组水平显著相关的SNPs位点有12和8个, 与胫长性状相关SNPs分别定位于1、2、4和8号染色体上; 与胫围性状相关的SNPs定位于2、4、8和13号染色体上。预测与胫长相关的候选基因为KCNA1、TPK1、EZH2、FSTL5和AMY2A基因, 与胫围相关的候选基因为TPK1、FSTL5、AMY2A、TGFBI、LECT2和IL-9。通过KEGG通路分析和GO注释发现, 8个基因参与钾离子跨膜转运、硫胺素新陈代谢、细胞增殖、钙离子结合、骨骼肌卫星细胞维持与骨骼肌再生、细胞受体相互作用、生长因子活性等生物学进程。【结论】 本研究发现了20个与儋州鸡体尺性状关联的SNPs位点, 并筛选到8个目标性状候选基因, 为儋州鸡育种提供候选的分子标记, 为地方鸡标记辅助选择提供新的思路。

Genome-wide Association Study of Body Size Traits in Danzhou Chickens

【Objective】 This experiment was aimed to explore the effective SNP and functional genes related to body size traits in chickens, and provide effective theoretical support for Danzhou chickens.【Method】 Blood samples of 200 Danzhou chickens were collected and used to extract genomic DNA.Genome-wide SNP markers were obtained by using a depth of 10× whole genome resequencing, and analyzed the genotypes of individuals.Genome-wide association study (GWAS) was performed using a mixed-effects model and linear regression approach for body size traits (shank length, shank circumference, body slope length, breast width, pelvis width, breast depth, and fossil bone length) of 70-day-old Danzhou chickens by EMMAX.【Result】 The results showed that 12 and 8 SNPs were significantly related to the shank length and the shank circumference.SNPs associated with shank length traits were located on chromosomes 1, 2, 4 and 8.SNPs associated with shank circumference traits were located on chromosomes 2, 4, 8 and 13.The experiment predicted that the candidate genes associated with shank length were KCNA1, TPK1, EZH2, FSTL5 and AMY2A, and the candidate genes associated with shank circumference were TPK1, FSTL5, AMY2A, TGFBI, LECT2 and IL-9.Through KEGG pathway analysis and GO annotation, it was found that 8 genes were involved in biological processes such as potassium ion transmembrane transport, thiamine metabolism, cell proliferation, calcium binding, skeletal muscle satellite cell maintenance and skeletal muscle regeneration, cell receptor interaction, growth factor activity and so on.【Conclusion】 In this experiment, 20 SNPs associated with body size traits were found, and 8 candidate genes for the target traits were screened, which provided candidate molecular markers for Danzhou chickens breeding and new ideas for marker assisted selection of local.