{"title":"在一个受外来遗传影响较大的小型奶牛种群中,用元创始人建立缺失血统模型并验证单步基因组预测结果","authors":"R.D. López-Correa , A. Legarra , I. Aguilar","doi":"10.3168/jds.2023-23732","DOIUrl":null,"url":null,"abstract":"<div><p>Genetic improvement in small countries rely heavily on foreign genetics. In an importing country such as Uruguay, consideration of unknown parent groups (UPG) for foreign sires is essential. However, the use of UPG in genomic model evaluations may lead to bias in genomic estimated breeding values (GEBV). The objective of this study was to study different models including UPG or metafounders (MF) in the Uruguayan Holstein evaluation and to analyze bias, dispersion, and accuracy of GEBV predictions in BLUP and single-step genomic BLUP (ssGBLUP). A gamma matrix (<strong>Γ</strong>) was estimated either by using base allele population frequencies obtained by bounded linear regression (MFbounded), or by using 2 values to design Γ (i.e., a single value for the diagonal and a different value for the off-diagonal [MFrobust]). Both <strong>Γ</strong> estimators performed well in terms of GEBV predictions, but MFbounded was the best option. There is, however, some bias whose origin was not completely understood. UPG or MF seem to model correctly genetic progress for unknown parents except for the very first groups (earlier time period). As for validation bulls, bias was observed across all models, whereas for validation cows it was only observed with UPG in BLUP. Overdispersion was found in all models, but it was mostly detected in validation bulls. Ratio of accuracies indicated that ssGBLUP gave better predictions than BLUP.</p></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022030224000547/pdfft?md5=afbc5208b50edcf6123238c43e9db3d5&pid=1-s2.0-S0022030224000547-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Modeling missing pedigree with metafounders and validating single-step genomic predictions in a small dairy cattle population with a great influence of foreign genetics\",\"authors\":\"R.D. López-Correa , A. Legarra , I. Aguilar\",\"doi\":\"10.3168/jds.2023-23732\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Genetic improvement in small countries rely heavily on foreign genetics. In an importing country such as Uruguay, consideration of unknown parent groups (UPG) for foreign sires is essential. However, the use of UPG in genomic model evaluations may lead to bias in genomic estimated breeding values (GEBV). The objective of this study was to study different models including UPG or metafounders (MF) in the Uruguayan Holstein evaluation and to analyze bias, dispersion, and accuracy of GEBV predictions in BLUP and single-step genomic BLUP (ssGBLUP). A gamma matrix (<strong>Γ</strong>) was estimated either by using base allele population frequencies obtained by bounded linear regression (MFbounded), or by using 2 values to design Γ (i.e., a single value for the diagonal and a different value for the off-diagonal [MFrobust]). Both <strong>Γ</strong> estimators performed well in terms of GEBV predictions, but MFbounded was the best option. There is, however, some bias whose origin was not completely understood. UPG or MF seem to model correctly genetic progress for unknown parents except for the very first groups (earlier time period). As for validation bulls, bias was observed across all models, whereas for validation cows it was only observed with UPG in BLUP. Overdispersion was found in all models, but it was mostly detected in validation bulls. Ratio of accuracies indicated that ssGBLUP gave better predictions than BLUP.</p></div>\",\"PeriodicalId\":354,\"journal\":{\"name\":\"Journal of Dairy Science\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2024-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0022030224000547/pdfft?md5=afbc5208b50edcf6123238c43e9db3d5&pid=1-s2.0-S0022030224000547-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Dairy Science\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0022030224000547\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Dairy Science","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0022030224000547","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
Modeling missing pedigree with metafounders and validating single-step genomic predictions in a small dairy cattle population with a great influence of foreign genetics
Genetic improvement in small countries rely heavily on foreign genetics. In an importing country such as Uruguay, consideration of unknown parent groups (UPG) for foreign sires is essential. However, the use of UPG in genomic model evaluations may lead to bias in genomic estimated breeding values (GEBV). The objective of this study was to study different models including UPG or metafounders (MF) in the Uruguayan Holstein evaluation and to analyze bias, dispersion, and accuracy of GEBV predictions in BLUP and single-step genomic BLUP (ssGBLUP). A gamma matrix (Γ) was estimated either by using base allele population frequencies obtained by bounded linear regression (MFbounded), or by using 2 values to design Γ (i.e., a single value for the diagonal and a different value for the off-diagonal [MFrobust]). Both Γ estimators performed well in terms of GEBV predictions, but MFbounded was the best option. There is, however, some bias whose origin was not completely understood. UPG or MF seem to model correctly genetic progress for unknown parents except for the very first groups (earlier time period). As for validation bulls, bias was observed across all models, whereas for validation cows it was only observed with UPG in BLUP. Overdispersion was found in all models, but it was mostly detected in validation bulls. Ratio of accuracies indicated that ssGBLUP gave better predictions than BLUP.
期刊介绍:
The official journal of the American Dairy Science Association®, Journal of Dairy Science® (JDS) is the leading peer-reviewed general dairy research journal in the world. JDS readers represent education, industry, and government agencies in more than 70 countries with interests in biochemistry, breeding, economics, engineering, environment, food science, genetics, microbiology, nutrition, pathology, physiology, processing, public health, quality assurance, and sanitation.