PDF(Pubmed)
Abstract：
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.
摘要：
存在-不存在变化（PAV）是重要的结构变化，其中包含一个或多个基因的基因组片段存在于一些个体中,但不存在于其他个体中。虽然PAV已经在植物中进行了广泛的研究,对牛的研究仍然有限。这项研究使用全基因组测序数据鉴定了173头荷斯坦公牛的PAV，并评估了它们与46个经济重要性状的关联。在28,772个牛基因中（来自最长的转录本），共鉴定出26,979个(93.77%)核心基因(存在于所有个体中)，而可变基因包括928个softcore(存在于95-99%的个体中)，494壳（5-94%），和371个云基因(存在于<5%)。云基因富含与激素和抗菌活性相关的功能，而shell基因在免疫功能上的富集。基于PAV的全基因组关联研究确定了基因PAV与包括牛奶在内的16个性状之间的关联。脂肪，和蛋白质产量，以及与健康和生殖有关的特征。在多个染色体上发现了关联，说明牛7号和15号染色体上的重要关联，涉及嗅觉受体和免疫相关基因，分别。通过在人口层面检查PAV，这项研究的结果为荷斯坦牛复杂性状的遗传结构提供了重要的见解。
