Edea Z, Dadi H, Kim S-W, Park J-H, Shin G-H, Dessie T, Kim K-S
Department of Animal Science, Chungbuk National University, Cheongju, Korea; International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
J Anim Breed Genet. 2014 Oct;131(5):358-66. doi: 10.1111/jbg.12083. Epub 2014 Mar 6.
Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D' and r(2) between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r(2) and D' values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers.
尽管观察到了广泛的表型多样性以及对不同生态条件的适应性，但对于发展中国家本土牛品种基因组中的适应性遗传学研究却很少。在此，我们研究了连锁不平衡（LD），并确定了在适应埃塞俄比亚不同生态条件的牛群中高度分化的异常位点子集。具体而言，我们使用牛50K SNP芯片对从高海拔和低海拔环境中采样的47只无亲缘关系的动物进行了基因分型。使用相邻SNP之间的D'和r(2)评估连锁不平衡。我们按照分层岛屿模型方法，计算了不同显著性水平下的FST和杂合度，作为高海拔和低海拔种群之间每个位点遗传分化的指标。我们鉴定出816个位点（p < 0.01）显示出选择信号，并且与可能在局部适应中起作用的基因相关。其中一些与参与代谢（ATP2A3、CA2、MYO18B、SIK3、INPP4A和IREB2）、缺氧反应（BDNF、TFRC和PML）以及热应激（PRKDC、CDK1和TFDC）的候选基因相关。对于次要等位基因频率（MAF）≥ 0.05，平均r(2)和D'值分别为0.14 ± 0.21和0.57 ± 0.34，并且发现它们随着MAF值的增加而增加。在所研究的埃塞俄比亚牛群中鉴定出的异常位点表明存在因适应不同环境条件而产生/形成的遗传变异，并为使用合理样本量和高密度标记进行进一步验证和功能分析提供了基础。
