Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran.

IF 2.3 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Genome Pub Date : 2024-02-01 Epub Date: 2023-11-14 DOI:10.1139/gen-2022-0106
Nader Forough Ameri, Hasan Moradian, Ali Esmailizadeh Koshkoiyeh, Mahdiyeh Montazeri, Elaheh Rostamzadeh Madabi, Masood Asadi Fozi
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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.

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伊朗本土牛品种的遗传多样性和积极选择特征。
动物驯化、气候变化和人工选择在形成包括牛在内的各种动物物种的基因组结构方面发挥了重要作用。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。本研究的重点是揭示遗传多样性和确定候选基因组区域在伊朗的八个地方牛品种。数据包括分布在全国各地的89头伊朗本土牛的~ 777962个单核苷酸多态性(snp)。我们采用多种方法,包括整合单倍型评分、FST和跨群体复合似然比,进行基因组扫描,以检测牛群体内部和群体之间的选择信号。各群体平均杂合度为0.36,范围为0.32 ~ 0.40。此外,在种群中观察到负近交率和低近交率。全基因组分析显示,几个基因组区域包含与生产性状相关的候选基因(如MFSD1、TYW5、ADRB2、BLK和CRTC3)、对局部环境约束的适应性(CACNA2D1、CXCL3和GRO1)和毛色(DYM)。最后,对牛基因组中已报道的数量性状位点(QTL)区域的研究表明,所鉴定的区域与乳成分、体重、日增重、饲料转化率和剩余采食量等重要性状的QTL相关。总的来说,这项研究有助于更好地了解伊朗本土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。
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来源期刊
Genome
Genome 生物-生物工程与应用微生物
CiteScore
5.30
自引率
3.20%
发文量
42
审稿时长
6-12 weeks
期刊介绍: Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.
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