从多品种基因组评估中间接预测具有SNP效应的牛品种。

IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Marisol Londoño-Gil, Jorge Hidalgo, Andres Legarra, Claudio U Magnabosco, Fernando Baldi, Daniela Lourenco
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引用次数: 0

摘要

间接预测(IP)用于缺乏表型(自身或后代)或来自商业畜群的年轻基因型动物。前者可以被抛在后面,因为它们对官方的基因组评估没有贡献。后者通常被排除在评估之外,因为它们没有注册,可能没有系谱信息。包括这些动物可能导致夸大和有偏差的基因组育种价值(GEBV)。在巴西,Brahman、Guzerat和Tabapua等重要品种的系谱、表型和基因型信息很少,而Nellore品种则有大量的信息。基于较大参考种群的这些品种幼畜的IP可以提高基因组选择的准确性。本研究的目的是通过单种和多种分析计算年轻基因型Nellore、Brahman、Guzerat和Tabapua动物的IP,使用或不使用元创始人(MF)来模拟不同品种的遗传差异。使用了巴西国家育种和研究协会(ancp - ribebe o Preto, SP, Brazil)的四个育种项目的记录。数据包括所有品种的系谱(4.2 M)、表型(329 K)和基因型(63.5 K)。Nellore、Brahman、Guzerat和Tabapua各品种基因型动物数量分别为58,574只、3102只、1389只和427只。所分析的性状分别为210 (W210)和450 (W450)日龄的体重和365 (SC365)日龄的阴囊周长。IP是用不同参考群体(有或没有MF的多品种、Nellore或品种内)对基因含量加权的SNP效应之和。使用线性回归(LR)方法比较各情景的偏差、离散度和准确性。加入中频可减少偏置和色散不足或过色散,并略微提高IP精度。品种组合提高了IP的准确性,主要受益于基因型较少的品种。这些研究结果表明,当巴西zebuine牛的年轻基因型动物不包括在官方的多品种评估中时,无论品种如何,都可以通过适当的建模获得强大的IP。这有助于获得幼龄动物的快速基因组预测,而不会使太多动物的评估系统不堪重负。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Indirect Genomic Predictions for Indicine Cattle Breeds With SNP Effects From a Multi-Breed Genomic Evaluation.

Indirect predictions (IP) are used for young genotyped animals that lack phenotypes (of their own or from progeny) or are from commercial herds. The former can be left behind because they do not contribute to the official genomic evaluations. The latter are often excluded from the evaluations because they are not registered and may not have pedigree information. Including such animals could result in inflated and biased genomic breeding values (GEBV). In Brazil, pedigree, phenotype and genotype information is scarce for important breeds like Brahman, Guzerat, and Tabapua, while the Nellore breed has a substantial amount of information. IP for young animals of these breeds based on a larger reference population could enhance genomic selection accuracy. Our objective in this study was to compute IP for young genotyped Nellore, Brahman, Guzerat, and Tabapua animals using single- and multi-breed analyses, with or without metafounders (MF) to model genetic differences across breeds. Records from the four breeding programs of the National Association of Breeders and Researchers (ANCP-Ribeirão Preto, SP, Brazil) were used. Data included pedigree (4.2 M), phenotypes (329 K), and genotypes (63.5 K) across all breeds. The number of genotyped animals within each breed was 58,574 for Nellore, 3102 for Brahman, 1389 for Guzerat, and 427 for Tabapua. The analysed traits were adjusted weight at 210 (W210) and 450 (W450) days of age and the scrotal circumference at 365 (SC365) days of age. IP were derived as the sum of the SNP effects weighted by the gene content using different reference populations: multi-breed with or without MF, Nellore, or within-breed. Scenarios were compared using the linear regression (LR) method for bias, dispersion, and accuracy. Adding MF decreased bias and under- or overdispersion and slightly increased the accuracy of IP. Combining breeds increased the accuracy of IP, mainly benefiting breeds with a small number of genotypes. These findings suggest that when young genotyped animals are not included in an official multi-breed evaluation in zebuine cattle from Brazil, robust IP can be obtained with proper modelling, regardless of the breed. This helps obtain fast genomic predictions for young animals without overwhelming the evaluation system with too many animals.

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来源期刊
Journal of Animal Breeding and Genetics
Journal of Animal Breeding and Genetics 农林科学-奶制品与动物科学
CiteScore
5.20
自引率
3.80%
发文量
58
审稿时长
12-24 weeks
期刊介绍: The Journal of Animal Breeding and Genetics publishes original articles by international scientists on genomic selection, and any other topic related to breeding programmes, selection, quantitative genetic, genomics, diversity and evolution of domestic animals. Researchers, teachers, and the animal breeding industry will find the reports of interest. Book reviews appear in many issues.
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