This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.

中文翻译：

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牛和猪基因组中拟议致病变异的证据和定位

本文回顾了当代猪和牛参考基因组中已发表的潜在致病变异的定位及其因果关系的证据。尽管从遗传图谱和全基因组关联研究中识别致病变异存在固有的困难，但动物遗传学研究人员已经提出了与牲畜育种相关的几种性状的假定致病变异。在这篇综述中，我们阅读了支持牛和猪 13 个基因（ABCG2、DGAT1、GHR、IGF2、MC4R、MSTN、NR6A1、PHGK1、PRKAG3、PLRL、RYR1、SYNGR2 和 VRTN）潜在致病变异的文献，并进行了本地化它们在当代参考基因组中。我们审查了其因果关系的证据，旨在将基因座、拟议的致病基因和拟议的致病变异的证据分开，并报告定位牛或猪基因组中的序列变异所需的生物信息学搜索和策略。总而言之，通常有充分的证据证明基因座水平上的关联，一些证据表明存在八个基因座的特定致病基因，以及一些实验证据表明存在六个基因座的特定致病变异。我们建议报告新的潜在致病变异的研究人员使用参考坐标系，显示本地序列上下文，并将变异提交到存储库。