Whole-genome analyses reveal selective signals in four Xinjiang cattle breeds

IF 1 Q4 GENETICS & HEREDITY Gene Reports Pub Date : 2024-08-03 DOI:10.1016/j.genrep.2024.102000
Yilin Wen , Junxi Huang , Yunyun Zhang , JiaHui Li , Lei Xu , Qiuming Chen , Yang Guo , Juan Geng
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Abstract

Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly Bos taurus, the proportion of Bos indicus ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.

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全基因组分析揭示了四个新疆牛品种的选择信号
新疆有三个本土牛种(新疆蒙古牛、阿勒泰白头牛和哈萨克牛)和一个杂交牛种(新疆褐牛),每个牛种都具有鲜明而显著的特征。在这项研究中,我们对这四个牛种与世界上八个具有代表性的牛种进行了全面的基因组分析。尽管这些本土牛种以金牛为主,但随着纬度的升高,其金牛血统的比例也在降低。这种混合基因组组成有助于提高核苷酸多样性、降低连接不平衡和扩大有效种群规模。值得注意的是,新疆褐牛在短距离上表现出更高的连接不平衡度、更快的连接不平衡度衰减和最大的有效种群规模,表明其具有杂交特征。此外,我们还发现了阿勒泰白头牛脂质动态和被毛颜色、哈萨克牛对当地病原体的免疫抵抗力、新疆蒙古牛的水电解质平衡和免疫反应、新疆褐牛的快速生长和大体型以及三种本地牛的物质代谢的选择信号。我们的研究结果不仅加深了对牛种起源和多样性的了解,而且为探索牛种特性的遗传机制和进一步改良牛种奠定了基础。
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来源期刊
Gene Reports
Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.30
自引率
7.70%
发文量
246
审稿时长
49 days
期刊介绍: Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.
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