BACKGROUND Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. RESULTS We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6  × 10- 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. CONCLUSIONS We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

中文翻译：

---

使用全基因组测序数据评估原始Braunvieh牛的基因组多样性和选择标记。

背景技术本地牛是遗传变异的重要来源，因为它们可能携带等位基因，使它们能够适应当地环境和食物条件。Original Braunvieh（OB）是瑞士的本地牛品种，用于高山地区的牛肉和牛奶生产。使用49个主要祖先的全基因组测序（WGS）数据，我们以核苷酸分辨率表征了瑞士OB牛的基因组多样性，基因组近交和选择签名。结果我们注释了49 OB关键祖先中分别发现的15722,811个SNP和1,580,878个Indel，包括10,738个和2763个错义有害和高影响变体。六个孟德尔与性状相关的变体，以前在OB以外的其他品种中被发现，分离在测序的关键祖先中，包括因隐性黄嘌呤尿症和白化病引起的变异。OB中的平均核苷酸多样性（1.6×10-3）比许多欧洲主流牛品种要高。因此，在49例OB关键祖先动物中，来自纯合（ROH）运行的平均基因组近交相对较低（FROH = 0.14）。但是，由于纯合子的长距离（> 1 Mb）运行次数增加，近代OB牛（FROH = 0.16）的基因组近交更高。使用两种可能性的方法，复合似然比检验和综合单倍型评分，我们分别鉴定了包含136和157个蛋白质编码基因的95和162个基因组区域，这些区域显示了过去和正在进行的选择的证据（P <0.005）。这些选择信号丰富了与牛肉性状有关的定量性状基因座，包括肉质，饲料效率和体重以及与凝血，神经和感觉刺激有关的途径。结论我们提供了瑞士OB牛基因组序列变异的全面概述。利用WGS数据，我们观察到，与许多欧洲主流牛品种相比，OB中的基因组多样性更高，而近交比则更少。在可能与肉质和适应当地环境有关的基因组区域中检测到选择的足迹。考虑到种群数量少，并且在过去的几代中基因组近亲繁殖增加，似乎有必要采用最佳的交配策略来维持瑞士OB牛种群的遗传多样性。