Abstract：
Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.
摘要：
水牛是全球乳制品行业的重要贡献者。了解水牛种群产奶性状的遗传基础对于育种计划和提高生产率至关重要。在这项研究中,我们对来自29个不同亚洲品种的387个水牛基因组进行了全基因组重测序，包括132条河水牛,129只沼泽水牛，和126只杂交水牛。我们鉴定了36,548个拷贝数变体（CNVs），跨越133.29Mb的水牛基因组，产生2,100个拷贝数变异区（CNVR），在研究的水牛类型中发现了1,993个共享CNVR。分析CNVRs强调了河流和沼泽水牛亚种之间的不同遗传差异，通过进化树和主成分分析进行了验证。混合物分析将水牛分为河流和沼泽类别，杂种水牛显示混合血统。为了确定与产奶性状相关的候选基因，我们采用了三种方法。首先,我们使用了基于Vst的人口分化，揭示了CNVRs中的11个基因，这些基因在不同水牛品种之间表现出明显的差异，包括与产奶性状相关的基因。第二,表达定量位点（eQTL）分析揭示了与产奶性状相关的CNVR驱动基因（DECGs）的差异表达。值得注意的是,已知的产奶相关基因在这些DECG中，验证其相关性。最后,一项全基因组关联研究(GWAS)确定了3个CNVRs与产奶量峰值显著相关.我们的研究为水牛种群提供了全面的基因组见解，并鉴定了与产奶性状相关的候选基因。这些发现促进了遗传育种计划，旨在提高这种经济上重要的牲畜物种的产奶量和质量。
