Nascimento A V, Cardoso D F, Santos D J A, Romero A R S, Scalez D C B, Borquis R R A, Neto F R A, Gondro C, Tonhati H
Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil.
Department of Animal Science, University of Maryland, College Park 20742.
J Dairy Sci. 2021 Feb;104(2):1917-1927. doi: 10.3168/jds.2020-18397. Epub 2020 Nov 30.
Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
纯合性的特征分析对于监测遗传多样性以及在育种计划中管理近亲繁殖水平具有重要意义。识别纯合性热点区域能够揭示受经济重要性状选择影响的基因组区域，并有助于确定选择的候选基因。在本研究中，我们估计了巴西穆拉水牛群体在进行产奶性状（特别是产奶量）选择时的近亲繁殖水平。我们还研究了纯合性片段（ROH）岛的分布，并确定了受选择的推定基因和数量性状位点（QTL）。我们对422头穆拉水牛的51,611个单核苷酸多态性（SNP）进行了基因分型；其中350头水牛的ROH长度超过10 Mb，表明在过去5代中发生了近亲繁殖。每头动物的ROH平均长度为4.28 ± 1.85 Mb。根据基因组关系矩阵、系谱和ROH计算了近亲繁殖系数，估计值在0.242至0.035之间。系谱的近亲繁殖估计值与基因组估计值的相关性较低，基因组关系矩阵的估计值远高于系谱或ROH的估计值。在位于1、2、3、5、16和18号染色体上的6个基因组区域中鉴定出了选择信号，共包含190个基因和174个QTL。鉴定出的许多基因（如APRT和ACSF3）和QTL与产奶性状相关，如产奶量、乳脂产量和百分比以及乳蛋白产量和百分比。其他基因与繁殖和免疫反应性状以及水牛物种的形态特征有关。该群体的近亲繁殖水平仍然较低，但由于选择作用而在增加，应加以管理以避免未来因近亲繁殖衰退而造成损失。与产奶性状相关的基因与繁殖和免疫系统性状相关基因的接近性表明，有必要将后一类基因纳入育种计划，以避免因选择生产性状而对它们产生负面影响。
