Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state. We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified, with a homozygous deficiency ranging from 84 to 100%. These haplotypes are located on Ovis aries chromosome (OAR)1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5), and OAR20 (MTRDHH1), and have carrier frequencies ranging from 7.8 to 16.6%. When comparing at-risk matings between DHH carriers to safe matings between non-carriers, two DHH (MTRDHH1 and 2) were linked with decreased insemination success and/or increased stillbirth incidence. We investigated the MTRDHH1 haplotype, which substantially increased stillbirth rate, and identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the methylmalonyl-CoA mutase (MMUT) gene by using a whole-genome sequencing approach. We generated homozygous lambs for the MMUT mutation by at-risk mating between heterozygous carriers, and most of them died within the first 24 h after birth without any obvious clinical symptoms. Reverse transcriptase-qPCR and western blotting on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in the mutant homozygous lambs. We identified five homozygous deficient haplotypes that are likely to harbor five independent deleterious recessive variants in sheep. One of these was detected in the MMUT gene, which is associated with lamb lethality in the homozygous state. A specific management of these haplotypes/variants in the MTR dairy sheep selection program would help enhance the overall fertility and lamb survival.

中文翻译：

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在 Manech Tête Rousse 奶羊中寻找纯合单倍型缺陷，发现 MMUT 基因中存在影响新生羔羊活力的无义变异


众所周知，隐性有害变异在牲畜群体中会分离，就像在人类中一样，有些在纯合状态下可能是致命的。我们使用定相 50 k 单核苷酸多态性 (SNP) 基因型和谱系数据扫描 6845 只 Manech Tête Rousse 奶羊的基因组，以寻找纯合单倍型 (DHH) 的缺陷。鉴定出五种 Manech Tête Rousse 缺陷纯合单倍型（MTRDHH1 至 5），纯合缺陷范围为 84% 至 100%。这些单倍型位于绵羊染色体 (OAR)1（MTRDHH2 和 3）、OAR10 (MTRDHH4)、OAR13 (MTRDHH5) 和 OAR20 (MTRDHH1) 上，载波频率范围为 7.8% 至 16.6%。当比较 DHH 携带者之间的危险交配与非携带者之间的安全交配时，两种 DHH（MTRDHH1 和 2）与授精成功率下降和/或死产率增加有关。我们研究了 MTRDHH1 单倍型，该单倍型大大增加了死产率，并通过使用全基因组测序方法鉴定了在甲基丙二酸单酰辅酶 A 变位酶 (MMUT) 基因中诱导过早终止密码子 (p.Gln409*) 的单核苷酸变异 (SNV) 。我们通过杂合子携带者之间的高危交配产生了MMUT突变纯合子羔羊，其中大多数在出生后24小时内死亡，没有任何明显的临床症状。对死后肝脏和肾脏生物样本的逆转录酶 qPCR 和蛋白质印迹显示，突变纯合羔羊肝脏中 MMUT mRNA 的表达降低，并且缺乏全长 MMUT 蛋白。我们鉴定了五种纯合缺陷单倍型，它们可能在绵羊中携带五种独立的有害隐性变异。 其中之一是在 MMUT 基因中检测到的，该基因与纯合状态下羔羊的致死率相关。 MTR 奶羊选择计划中对这些单倍型/变异体的具体管理将有助于提高整体生育力和羔羊存活率。