Abstract The objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.

中文翻译：

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使用固定长度单倍型和网络分析的全基因组关联研究揭示了黑脸羔羊线虫抗性和体重的新候选基因

摘要 本研究的目的是通过贝叶斯方法（BayesA、BayesB 或 BayesN）鉴定使用 GenSel 拟合固定长度单倍型或 SNP 的基因组区域。生成了五种长度（125、250、500 kb、1 或 2 Mb）的单倍型等位基因的协变量，并在三个阈值（1、5 或 10%）下去除了稀有单倍型。随后，我们进行了基因网络分析，以研究被鉴定为相同性状的基因所共享的生物过程。对 751 只苏格兰黑脸 (SBF) 羔羊的 OvineSNP50 面板上常见的 41,034 个 SNP 的基因型进行了定相。这是第一项使用 SBF 种群中整个基因组的单倍型来量化遗传变异比例的研究。在研究的跨性状中，基于单倍型的 GWAS 解释的遗传变异高于基于 SNP 的 GWAS。在这个群体中，用 1% 的频率阈值拟合 500kb 单倍型导致最高比例的遗传变异解释为线虫抗性，而用 10% 的频率阈值拟合 2Mb 单倍型改善了解释体重的遗传方差，与 BayesB 拟合 SNP 相当。候选基因，包括 CXCR4、STAT4、CCL1、CCL2、CCL3、CCL5、CCL8、CCL16、CCL18、CARMIL2 和 HSPA14 被鉴定为线虫抗性，ADH5、PPP3CA 和 FABP4 被鉴定为体重性状。网络分析提供了与所有已识别候选基因相关联的注释结果。这项研究支持了 GWAS 先前关于线虫抗性和体重的结果，并揭示了绵羊基因组中与这些重要经济性状相关的其他区域。