The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep
Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step gen...
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MDPI AG
2020-03-01
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Online Access: | https://www.mdpi.com/2076-2615/10/4/569 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chen Wei Hanpeng Luo Bingru Zhao Kechuan Tian Xixia Huang Yachun Wang Xuefeng Fu Yuezhen Tian Jiang Di Xinming Xu Weiwei Wu Hanikezi Tulafu Maerziya Yasen Yajun Zhang Wensheng Zhao |
spellingShingle |
Chen Wei Hanpeng Luo Bingru Zhao Kechuan Tian Xixia Huang Yachun Wang Xuefeng Fu Yuezhen Tian Jiang Di Xinming Xu Weiwei Wu Hanikezi Tulafu Maerziya Yasen Yajun Zhang Wensheng Zhao The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep Animals Chinese Merino sheep wool traits Bayesian inference single-step GBLUP |
author_facet |
Chen Wei Hanpeng Luo Bingru Zhao Kechuan Tian Xixia Huang Yachun Wang Xuefeng Fu Yuezhen Tian Jiang Di Xinming Xu Weiwei Wu Hanikezi Tulafu Maerziya Yasen Yajun Zhang Wensheng Zhao |
author_sort |
Chen Wei |
title |
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep |
title_short |
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep |
title_full |
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep |
title_fullStr |
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep |
title_full_unstemmed |
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep |
title_sort |
effect of integrating genomic information into genetic evaluations of chinese merino sheep |
publisher |
MDPI AG |
series |
Animals |
issn |
2076-2615 |
publishDate |
2020-03-01 |
description |
Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h<sup>2</sup> values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP. |
topic |
Chinese Merino sheep wool traits Bayesian inference single-step GBLUP |
url |
https://www.mdpi.com/2076-2615/10/4/569 |
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doaj-fd9f8fc06af148b6b9c81941b4e4ec3e2020-11-25T02:39:51ZengMDPI AGAnimals2076-26152020-03-011056956910.3390/ani10040569The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino SheepChen Wei0Hanpeng Luo1Bingru Zhao2Kechuan Tian3Xixia Huang4Yachun Wang5Xuefeng Fu6Yuezhen Tian7Jiang Di8Xinming Xu9Weiwei Wu10Hanikezi Tulafu11Maerziya Yasen12Yajun Zhang13Wensheng Zhao14College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaLaboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaLaboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaCollege of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaLaboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaKey Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, ChinaXinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, ChinaXinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, ChinaGenomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h<sup>2</sup> values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP.https://www.mdpi.com/2076-2615/10/4/569Chinese Merino sheepwool traitsBayesian inferencesingle-step GBLUP |