背景:中国土牛具有丰富的遗传多样性和悠久的人工选择历史,在适应性上给予当地品种优势,牧草的耐受性和抗性。选择性扫描的检测和选定品种和祖先群体的比较基因组分析为理解品种之间的差异以及候选基因的鉴定和利用提供了基础。我们调查了遗传多样性,人口结构,以及使用全基因组测序数据对秦川牛新品种进行选择的签名(QNC,n=21),祖传秦川牛(QCC,n=20),和枣生牛(ZSC,n=19)。
结果:种群结构分析表明,QNC和ZSC的祖先成分相似。此外,QNC和ZSC组的欧洲牛磺酸血统比例高于QCC,这可以解释QNC的更大的身体尺寸,在长期驯化和选择下接近欧洲牛的水平。邻居连接树显示QCC个体密切相关,而QNC形成了一个不同的群体。要在QNC基因组中搜索选择的签名,我们评估了核苷酸多样性(θπ),固定指数(FST)和Tajima'sD.重叠选择性扫描富集了一条KEGG通路,apelin信号通路,并包括五个候选基因(MEF2A,SMAD2、CAMK4、RPS6和PIK3CG)。我们对QNC中的基因组变异进行了全面回顾,QCC,和ZSC使用全基因组测序数据。品管圈具有丰富的新型遗传多样性,虽然QNC和ZSC牛的多样性由于强烈的人工选择而减少,与原始牛不同。
结论:我们鉴定了与生产性状相关的候选基因。这些结果支持了选育的成功,可以指导秦川牛的进一步育种和资源保护。
BACKGROUND: Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19).
RESULTS: A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima\'s D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle.
CONCLUSIONS: We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.