基因组概况:通过基于 SNP 阵列的全面基因分型,揭示家畜育种的基因组概况。

IF 1.8 3区 生物学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Animal genetics Pub Date : 2024-07-17 DOI:10.1111/age.13466
Ina Hulsegge, Aniek C. Bouwman, Martijn F. L. Derks
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引用次数: 0

摘要

在家畜育种中,单核苷酸多态性阵列已成为现代家畜育种的基石。SNP 阵列有助于鉴定与重要经济性状相关的遗传标记,并为预测育种价值提供了有力工具。然而,传统的育种计划往往忽略了 SNP 阵列数据中包含的其他基因组特征,而这些特征可以为了解育种品系的遗传多样性、拷贝数变异、近交水平和潜在挑战提供有价值的信息。在此,我们介绍一种利用基于 SNP 阵列的基因组数据的工具 genomeprofile,该工具可提供育种动物的全面概况,包括拷贝数变异和同源染色体的鉴定,以及非整倍体的筛选。通过将这些功能整合到育种环境中,基因组档案能够更全面地反映基因组变异情况,最终提高精准育种策略。为了说明基因组剖面图的实用性和有效性,我们将该工具应用于四个猪育种品系的数据集。genomeprofile 工具是一款用户友好型工具,它能将 finalreport 或 plink ped 格式的基因型数据高效处理为有用的输出结果。输出结果包括每个个体和不同种群的拷贝数变异、同源性、选择特征、非整倍体和近交。这样,育种公司和研究人员就能根据日常收集的数据,识别基因组中的独特个体或感兴趣的区域。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping

genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping

In livestock breeding, single nucleotide polymorphism arrays have become a cornerstone of modern livestock breeding. SNP arrays facilitate the identification of genetic markers linked to economically important traits and provide a powerful tool for predicting breeding values. However, conventional breeding programs often overlook additional genomic features contained in the SNP array data that can provide valuable insights into the genetic diversity, copy number variation, inbreeding levels and potential challenges in breeding lines. Here we present genomeprofile, a tool using SNP array-based genomic data, offering a comprehensive profile of breeding animals including the identification of copy number variants and runs of homozygosity, and screening for aneuploidy. By integrating these features into the breeding landscape, genomeprofile enables a more comprehensive picture of genomic variation, ultimately enhancing precision breeding strategies. To illustrate the practicality and efficacy of genomeprofile, we applied the tool to a dataset of four pig breeding lines. The genomeprofile tool is a user-friendly tool that processes genotype data in finalreport or plink ped format efficiently into useful output. The output contains copy number variations, runs of homozygosity, selection signatures, aneuploidy and inbreeding per individual and across populations. This allows breeding companies and researchers to identify unique individuals or regions in the genome of interest based on routinely collected data.

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来源期刊
Animal genetics
Animal genetics 生物-奶制品与动物科学
CiteScore
4.60
自引率
4.20%
发文量
115
审稿时长
5 months
期刊介绍: Animal Genetics reports frontline research on immunogenetics, molecular genetics and functional genomics of economically important and domesticated animals. Publications include the study of variability at gene and protein levels, mapping of genes, traits and QTLs, associations between genes and traits, genetic diversity, and characterization of gene or protein expression and control related to phenotypic or genetic variation. The journal publishes full-length articles, short communications and brief notes, as well as commissioned and submitted mini-reviews on issues of interest to Animal Genetics readers.
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