鸡脾脏重全基因组关联分析

doi:10.3864/j.issn.0578-1752.2018.06.019

摘要/Abstract

摘要： 【目的】利用全基因组关联分析（genome-wide association study, GWAS）技术解析产蛋后期母鸡脾脏重的分子机制和遗传特征，为改善产蛋后期母鸡的健康状况提供理论依据。【方法】利用东乡绿壳蛋鸡和白来航蛋鸡构建资源群体，以72周龄F2代501只母鸡脾脏重为研究材料。首先利用高密度600 K 基因芯片对试验群体基因组进行SNPs检测。其次利用APT软件进行质控、BEAGLE软件进行基因型填充、PLINK软件进行主成分分析，GEMMA软件进行全基因组关联分析，最终获得脾脏重的显著和潜在显著关联位点。然后利用GCTA软件计算基于SNP数据的脾脏重遗传力以及染色体遗传力，并利用Haploview软件对显著或潜在关联位点进行连锁不平衡分析。最后通过显著位点区域的相关基因功能注释来筛选影响母鸡产蛋后期脾脏重的候选基因。【结果】由72周龄母鸡脾脏重的表型数据可知，在蛋鸡产蛋后期存在较大的变异系数，脾脏重的遗传力为0.236。通过基因型分析得到43万个高质量的SNP进行进一步分析。群体结构分析发现基因膨胀系数为1.042，表明试验群体没有群体分层的现象，避免了关联分析中假阳性结果的出现。利用单变量混合线性模型分析共发现了412和281个SNPs位点与脾脏重显著和潜在显著关联，位于1、4、16、28号染色体上。显著性关联位点在1号染色体161-174 Mb区间和28号染色体0.47-1.27 Mb区间，潜在性显著位点在4号染色体76 Mb区间和16号染色体175kb区间。由于显著区域可能存在的连锁不平衡，对显著性位点进行了条件分析和连锁不平衡检验，以1号染色体位点rs314001986和28号染色体上位点rs312729296进行条件分析，经分析后原先显著关联的位点均不显著，即以rs314001986和rs312729296作为候选SNP进行基因注释分析。对4号染色体和16号染色体潜在显著位点进行连锁不平衡分析，结果显示潜在性显著位点间存在强的连锁不平衡，即以性状表型方差贡献率最大的SNP rs315270535和rs314065899为候选位点进行进一步分析。参考鸡的galgal4基因组，对各显著及潜在性显著位点及区间初步筛选到KCTD4、LDB2、HEP21和PCASP2候选基因，鉴定的候选基因可能参与了脾脏生长以及免疫应答等过程。此外，将显著位点的基因型与群体的表型数据进行关联分析，发现rs314001986和rs312729296在基因型为GG时对脾脏均有增重效应。此外，基于群体的基因型数据得到1号染色体解释的遗传力为9.25%，28号染色体为4.55%。【结论】初步揭示了母鸡产蛋后期脾脏重的遗传特征，脾脏重的遗传力和染色体遗传力为首次报道。生物信息学分析鉴定到影响脾脏重的区域为新的发现，并初步筛选出4个候选基因。

关键词: 鸡, 脾脏, 全基因组关联分析, 资源群体

Abstract: 【Objective】 Genome-wide association study (GWAS) was used to demonstrate the molecular mechanism and genetic architecture of chicken spleen weight, which will provide a basis for improving hens health condition in late laying period. 【Method】 The resource population was from reciprocal by Dongxiang Blueshell Chicken and White Leghon, the spleen weight of 1 501 individuals from F2 generation was used as the experimental material. First, the F2 population genome DNA was genotyped by 600 K Affymetrix Axiom Chicken Genotyping Array. Then the quality control was conducted by APT software, some sporadic missing genotypes were imputed using BEAGLE procedure, principal component analysis was performed by PLINK software, genome-wide association study was carried out by GEMMA software, after these steps, the significant and suggestive loci association with spleen weight was identified. Besides, the heritability of spleen weight and chromosome was calculated by GCTA software. According to the false positive significant or suggestive loci, conditional analysis was carried out with the leading SNP as covariance and the linkage disequilibuium was analysis by Haploview. Eventually, the candidate genes were identified based on the gene annotation. 【Result】The phenotype of spleen weight showed extensive variations in late laying period. The heritability of spleen weight was 0.236. A total of 435 867 high quality SNPs were obtained after genotyped. The genomic inflation factor was 1.042 which showed that there is negligible inflation caused by population stratification. Totally, we found 412 and 281 SNPs for significant and suggestive association with spleen weight, respectively. The SNPs that located on GGA1 (gallus gallus chromosome 1), GGA4, GGA16 and GGA28, the significant region on GGA1 spanned from 161 to 174 Mb and ranged from 0.47 to 1.27 on GGA28, the suggestive significant SNPs located on 76 Mb on GGA4 and 175 kb on GGA16. Due to the linkage disequilibrium between the significant loci, the conditional analysis and linkage disequilibrium were performed. After conditional analysis of rs314001986 on GGA1 and rs312729296 on GGA28, the significant loci all dropped below threshold. The linkage disequilibrium analysis was performed by the significant loci on GGA4 and GGA16, the results showed that the suggestive loci showed strong linkage disequilibrium. The genes KCTD4, LDB2, HEP21, and PCASP2 that may involve in spleen growth development and immune response were considered as candidate gene after blasting against chicken genome reference assembly. Moreover, the heritability based on SNP of GGA1 was 9.25%, GGA28 was 4.55%. 【Conclusion】These results enriched the genetic architecture for spleen weight of adult hen in late laying period, the heritability of spleen weight was novel. By bioinformatics analysis the QTL detected for spleen weight was also novel, and 4 candidate genes identified.

Key words: chicken, spleen, genome-wide association study, resource population

沈曼曼，曲亮，窦套存，马猛，郭军，卢建，胡玉萍，李永峰，王克华. 鸡脾脏重全基因组关联分析[J]. 中国农业科学, 2018, 51(6): 1213-1222.

SHEN ManMan, QU Liang, DOU TaoCun, MA Meng, GUO Jun, LU Jian, HU YuPing, LI YongFeng, WANG KeHua. Genome-Wide Association of Spleen Weight in Layer Chicken[J]. Scientia Agricultura Sinica, 2018, 51(6): 1213-1222.

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