Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows
We assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor co...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-05-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/12/5/718 |
| _version_ | 1797601067093983232 |
|---|---|
| author | Atsushi Zoda Shinichiro Ogawa Rino Kagawa Hayato Tsukahara Rui Obinata Manami Urakawa Yoshio Oono |
| author_facet | Atsushi Zoda Shinichiro Ogawa Rino Kagawa Hayato Tsukahara Rui Obinata Manami Urakawa Yoshio Oono |
| author_sort | Atsushi Zoda |
| collection | DOAJ |
| description | We assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (<b>A</b> matrix) and the other considering both pedigree and SNP marker genotype information (<b>H</b> matrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using the <b>H</b> matrix, which were both slightly lower than when using the <b>A</b> matrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when using <b>H</b> and <b>A</b> matrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using the <b>H</b> matrix than when using the <b>A</b> matrix. This advantage seems more prominent for cows with low reliability when using the <b>A</b> matrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection. |
| first_indexed | 2024-03-11T03:56:15Z |
| format | Article |
| id | doaj.art-f8c2902a6624465481dc39d58d2f54ee |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-11T03:56:15Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-f8c2902a6624465481dc39d58d2f54ee2023-11-18T00:33:27ZengMDPI AGBiology2079-77372023-05-0112571810.3390/biology12050718Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor CowsAtsushi Zoda0Shinichiro Ogawa1Rino Kagawa2Hayato Tsukahara3Rui Obinata4Manami Urakawa5Yoshio Oono6Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanDivision of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, JapanResearch and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, JapanWe assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (<b>A</b> matrix) and the other considering both pedigree and SNP marker genotype information (<b>H</b> matrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using the <b>H</b> matrix, which were both slightly lower than when using the <b>A</b> matrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when using <b>H</b> and <b>A</b> matrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using the <b>H</b> matrix than when using the <b>A</b> matrix. This advantage seems more prominent for cows with low reliability when using the <b>A</b> matrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection.https://www.mdpi.com/2079-7737/12/5/718Japanese Black cattlesuperovulatory response traitpedigreesingle-nucleotide polymorphismsingle-step genomic prediction |
| spellingShingle | Atsushi Zoda Shinichiro Ogawa Rino Kagawa Hayato Tsukahara Rui Obinata Manami Urakawa Yoshio Oono Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows Biology Japanese Black cattle superovulatory response trait pedigree single-nucleotide polymorphism single-step genomic prediction |
| title | Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows |
| title_full | Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows |
| title_fullStr | Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows |
| title_full_unstemmed | Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows |
| title_short | Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows |
| title_sort | single step genomic prediction of superovulatory response traits in japanese black donor cows |
| topic | Japanese Black cattle superovulatory response trait pedigree single-nucleotide polymorphism single-step genomic prediction |
| url | https://www.mdpi.com/2079-7737/12/5/718 |
| work_keys_str_mv | AT atsushizoda singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT shinichiroogawa singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT rinokagawa singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT hayatotsukahara singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT ruiobinata singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT manamiurakawa singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows AT yoshiooono singlestepgenomicpredictionofsuperovulatoryresponsetraitsinjapaneseblackdonorcows |