Department of Animal Science, Faculty of Agriculture, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 5756151818, Iran.
Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran.
BMC Genomics. 2018 Jun 11;19(1):449. doi: 10.1186/s12864-018-4759-x.
Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals.
A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (F) was used to detect signatures of selection. In total, 13 regions with outlier F values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2.
Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.
鉴定经历过选择的基因组区域可以揭示家畜群体的遗传历史，并有助于鉴定控制具有商业重要性表型的变异。阿塞拜疆和库泽斯坦水牛是伊朗最常见的本土品种，它们经历了不同的选择，适应了完全不同的地区。研究这些群体的遗传结构可以确定与适应不同环境和生产目标相关的基因组区域。
使用 Axiom®水牛基因分型 90K 阵列对来自阿塞拜疆（N=262）和库泽斯坦（N=123）品种的 385 头水牛样本进行了基因分型。使用无偏固定指数法（F）检测选择的特征。总共鉴定出 13 个具有异常 F 值（0.1%）的区域。使用 UMD3.1 牛基因组组装对这些区域进行注释，以在选定区域内找到潜在的候选基因和 QTL。鉴定出的潜在候选基因包括 FBXO9、NDFIP1、ACTR3、ARHGAP26、SERPINF2、BOLA-DRB3、BOLA-DQB、CLN8 和 MYOM2。
在潜在选择区域中鉴定出的候选基因与包括产奶、细胞骨架组织、生长、代谢功能、凋亡在内的生理途径有关，与免疫和神经系统发育相关的驯化相关变化包括在内。鉴定出的 QTL 与水牛的经济重要性状有关，包括乳成分、乳房结构、体细胞计数、肉质以及胴体和体重。
