Abstract：
Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, FST, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.
摘要：
动物驯化,随着时间的推移气候变化,人工选择在塑造各种动物物种的基因组结构方面发挥了重要作用，包括牛。这些过程导致了几种具有独特遗传特征的土著牛品种的出现。这项研究的重点是揭示伊朗八个土著牛品种的遗传多样性并确定候选基因组区域。数据包括来自伊朗本土牛的89只动物的777962个单核苷酸多态性（SNP），这些动物分布在全国各地。我们采用了各种方法，包括综合单倍型评分，FST,和跨种群复合似然比，进行基因组扫描，以检测牛种群内部和之间的选择信号。群体间平均观察到的杂合性为0.36，范围为0.32-0.40。此外,观察到种群中近亲繁殖（FIS）的阴性和低比率。全基因组分析揭示了几个基因组区域，这些区域包含与生产性状相关的候选基因(例如，MFSD1,TYW5,ADRB2,BLK,和CRTC3），适应当地环境限制(CACNA2D1、CXCL3和GRO1)，和外套颜色（DYM）。最后,对牛基因组中已报道的数量性状基因座（QTL）区域的研究表明，已识别的区域与与重要性状（如牛奶成分）相关的QTL相关。体重,每日增益，饲料转换，和剩余饲料摄入量。总的来说,这项研究有助于更好地了解伊朗土著牛品种重要性状的遗传多样性和潜在候选基因，这可以为未来的育种和保护工作提供信息。
