Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig
【Objective】Exploring the difference in prediction accuracy between genome selection (GS) and traditional BLUP methods in the presence of a large number of non-genotype reference populations. Assessing the application effect of GBLUP and ssGBLUP in the joint evaluation to provide recommendations for...
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| Format: | Article |
| Language: | English |
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Guangdong Academy of Agricultural Sciences
2023-11-01
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| Series: | Guangdong nongye kexue |
| Subjects: | |
| Online Access: | http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202311011 |
| _version_ | 1797353327153905664 |
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| author | Yujin LU Zhen HUANG Huazhao XU Shaolei SHI Jie ZHOU Zhe ZHANG Shuihua XIE |
| author_facet | Yujin LU Zhen HUANG Huazhao XU Shaolei SHI Jie ZHOU Zhe ZHANG Shuihua XIE |
| author_sort | Yujin LU |
| collection | DOAJ |
| description | 【Objective】Exploring the difference in prediction accuracy between genome selection (GS) and traditional BLUP methods in the presence of a large number of non-genotype reference populations. Assessing the application effect of GBLUP and ssGBLUP in the joint evaluation to provide recommendations for joint evaluation.【Method】Two straits of days to reach 100 kg (DAYS_100) and the average backfat thickness at 100 kg (BFT_100) were analyzed in six Yorkshire populations, and the heritability and genetic correlation of the two traits were estimated. Exploring the prediction accuracy of BLUP, GBLUP and ssGBLUP models in different populations and combined populations.【Result】(1) In F population, the heritability of BFT_100 was only 0.071, while in other populations it was between 0.205 and 0.383. The heritability of DAYS_100 in six populations ranged from 0.258 to 0.598. (2) The genetic correlation between the two traits in D population was 0.211, however, in other populations, the genetic correlations were negative, ranging from -0.462 to -0.200. (3) For DAYS_100 trait, the GBLUP model showed the best prediction accuracy in B, C, E, and F populations. For BFT_100 trait, the ssGBLUP model had the best prediction accuracy in populations A, B, and C, while the GBLUP model performed better in populations D and E. (4) The connectedness rating (CR) between F and A population was 3.096 %. In F population, single-step genomic selection using combined reference populations can improve the prediction accuracy of BFT_100 trait.【Conclusion】When the number of genotyped individuals in the population exceeds 500 and the proportion is above 7%, the prediction accuracy of GBLUP or ssGBLUP model will be higher than that of BLUP model. ssGBLUP model can be used to improve the prediction accuracy of low heritability traits in joint population that the CR reaches 3% between population. |
| first_indexed | 2024-03-08T13:29:32Z |
| format | Article |
| id | doaj.art-8365dfcad36a4d52b1df1e48f67d28fc |
| institution | Directory Open Access Journal |
| issn | 1004-874X |
| language | English |
| last_indexed | 2024-03-08T13:29:32Z |
| publishDate | 2023-11-01 |
| publisher | Guangdong Academy of Agricultural Sciences |
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| series | Guangdong nongye kexue |
| spelling | doaj.art-8365dfcad36a4d52b1df1e48f67d28fc2024-01-17T10:16:21ZengGuangdong Academy of Agricultural SciencesGuangdong nongye kexue1004-874X2023-11-01501111312210.16768/j.issn.1004-874X.2023.11.011202311011Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire PigYujin LU0Zhen HUANG1Huazhao XU2Shaolei SHI3Jie ZHOU4Zhe ZHANG5Shuihua XIE6Agriculture Technology Extension Centre of Guangdong Province, Guangzhou 510520, ChinaGuangdong iPig Technology Co., Ltd., Guangzhou 510470, ChinaAgriculture Technology Extension Centre of Guangdong Province, Guangzhou 510520, ChinaCollege of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong iPig Technology Co., Ltd., Guangzhou 510470, ChinaCollege of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaAgriculture Technology Extension Centre of Guangdong Province, Guangzhou 510520, China【Objective】Exploring the difference in prediction accuracy between genome selection (GS) and traditional BLUP methods in the presence of a large number of non-genotype reference populations. Assessing the application effect of GBLUP and ssGBLUP in the joint evaluation to provide recommendations for joint evaluation.【Method】Two straits of days to reach 100 kg (DAYS_100) and the average backfat thickness at 100 kg (BFT_100) were analyzed in six Yorkshire populations, and the heritability and genetic correlation of the two traits were estimated. Exploring the prediction accuracy of BLUP, GBLUP and ssGBLUP models in different populations and combined populations.【Result】(1) In F population, the heritability of BFT_100 was only 0.071, while in other populations it was between 0.205 and 0.383. The heritability of DAYS_100 in six populations ranged from 0.258 to 0.598. (2) The genetic correlation between the two traits in D population was 0.211, however, in other populations, the genetic correlations were negative, ranging from -0.462 to -0.200. (3) For DAYS_100 trait, the GBLUP model showed the best prediction accuracy in B, C, E, and F populations. For BFT_100 trait, the ssGBLUP model had the best prediction accuracy in populations A, B, and C, while the GBLUP model performed better in populations D and E. (4) The connectedness rating (CR) between F and A population was 3.096 %. In F population, single-step genomic selection using combined reference populations can improve the prediction accuracy of BFT_100 trait.【Conclusion】When the number of genotyped individuals in the population exceeds 500 and the proportion is above 7%, the prediction accuracy of GBLUP or ssGBLUP model will be higher than that of BLUP model. ssGBLUP model can be used to improve the prediction accuracy of low heritability traits in joint population that the CR reaches 3% between population.http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202311011genomic selectionsingle-step gblup (ssglup)yorkshirecombined populationsconnectedness ratingheritabilitygrowth trait |
| spellingShingle | Yujin LU Zhen HUANG Huazhao XU Shaolei SHI Jie ZHOU Zhe ZHANG Shuihua XIE Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig Guangdong nongye kexue genomic selection single-step gblup (ssglup) yorkshire combined populations connectedness rating heritability growth trait |
| title | Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig |
| title_full | Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig |
| title_fullStr | Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig |
| title_full_unstemmed | Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig |
| title_short | Application Effect Analysis of Single-step Genomic Selection in Multi-population of Yorkshire Pig |
| title_sort | application effect analysis of single step genomic selection in multi population of yorkshire pig |
| topic | genomic selection single-step gblup (ssglup) yorkshire combined populations connectedness rating heritability growth trait |
| url | http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202311011 |
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