BACKGROUND Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. RESULTS Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low frequencies. For association analysis, imputation was performed using FImpute for 1129 French Alpine and Saanen males using within-breed and French panels on 23,338,436 filtered variants. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. CONCLUSION Even with very small reference populations, an acceptable imputation quality can be achieved in French dairy goats. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of identified regions while removing potential imputation errors.

中文翻译：

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基因组范围内对精液量和产奶量的全基因组关联分析，采用了不同的归因于法国奶山羊全基因组序列的策略。

背景技术山羊在10500年前就被驯化，以向人类提供有用的资源。从那时起，已经开发出适应其当地环境的专门品种，并显示出特定的遗传特征。VarGoats项目是一个1000个基因组重测序程序，旨在涵盖Capra属的遗传多样性。在这项研究中，我们的主要目标是评估序列数据的使用，以检测与法国高山和萨嫩品种感兴趣的性状相关的基因组区域。结果在这些品种中，使用FImpute和不同的参考小组对GoatSNP50 BeadChip基因型直接推算到序列水平进行了研究：内部品种，所有Capra hircus测序个体，欧洲山羊和法国本土山羊。法国山羊小组获得的最佳结果是，等位基因和基因型一致性比率在高山地区分别达到0.86和0.75，在萨嫩品种中分别达到0.86和0.73。由于频率较低的变体比例较高，两个品种的平均相关性往往较低。为了进行关联分析，使用FImpute对23,338,436个已过滤变体的内部和法国群体使用1129名法国阿尔卑斯和萨嫩男性进行插补。然后比较两种插补方案的关联结果。在两种情况下，在萨嫩山羊中，第19号染色体上的大区域都与精液量和产奶量显着相关。萨嫩山羊的19号染色体上的91个基因的产奶量显着变异。对于精液量，注释的基因包括YBOX2，其与其他物种的无精子症或少精子症有关。使用多品种面板时，在高山山羊的2号染色体和萨嫩山羊的5号染色体上检测到新的产奶信号。结论即使参考人口非常少，法国奶山羊的插补质量也可以达到可接受的水平。估算序列上的GWAS证实了QTL的存在，并确定了奶山羊感兴趣的新区域。将鉴定出的候选物添加到基因分型阵列中，并对更多个体进行测序可能会证实鉴定出的区域的参与，同时消除潜在的插补错误。结论即使参考人口很少，法国乳山羊的插补质量仍可以达到可接受的水平。估算序列上的GWAS证实了QTL的存在，并确定了奶山羊感兴趣的新区域。将鉴定出的候选物添加到基因分型阵列中，并对更多个体进行测序可能会证实鉴定出的区域的参与，同时消除潜在的插补错误。结论即使参考人口非常少，法国奶山羊的插补质量也可以达到可接受的水平。估算序列上的GWAS证实了QTL的存在，并确定了奶山羊感兴趣的新区域。将鉴定出的候选物添加到基因分型阵列中，并对更多个体进行测序可能会证实鉴定出的区域的参与，同时消除潜在的插补错误。