Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

中文翻译：

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全基因组扫描以识别两种伊朗本土鸡生态型的选择特征

几千年来，鸡基因组的各个区域一直处于自然和人工选择之下。来自不同地理区域的鸡之间存在的大量多样性为研究选择的基因组区域提供了绝佳的机会，这反过来又将增加我们对鸡多样性和适应机制的了解。已经开发了几种统计数据来检测正在选择的基因组区域。在这项研究中，我们应用了基于群体之间等位基因或单倍型频率（分别为 FST 和 hapFLK）的差异、连续纯合序列（ROH）的长片段差异的方法，以及种群内等位基因频率的差异（复合似然比（CLR）），以确定两种伊朗本土鸡生态型（拉里斗鸡和哈扎克或爬行者（短腿）鸡）的种群间和种群内选择痕迹。使用来自两种鸡生态型的 32 个个体的全基因组重测序数据，检测到大约 1190 万个单核苷酸多态性 (SNP)，并在质量处理后用于基因组分析。检查两个群体中 ROH 的分布表明 ROH 短到长，范围从 0.3 到 5.4 Mb。我们发现 90 个基因被四种应用方法中的至少两种检测到。选择下检测到的推定区域的基因注释揭示了与生长相关的候选基因（DCN、MEOX2 和 CACNB1），繁殖（ESR1 和 CALCR）、抗病性（S1PR1、ALPK1 和 MHC-B）、行为模式（AGMO、GNAO1 和 PSEN1）和形态特征（IHH 和 NHEJ1）。我们的研究结果表明，这两种表型不同的本土鸡种群一直在选择繁殖、免疫、行为和形态特征。结果表明，选择可以在塑造两个鸡群基因组景观的分化特征方面发挥重要作用。