Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>)
The meat yield (MY) is a key economic trait in Pacific whiteleg shrimp (<i>Penaeus vannamei</i>) breeding, necessitating accurate genomic prediction for efficient genetic improvement. In this study, we investigated single-trait (STGMs) and multi-trait genomic models (MTGMs) for predictin...
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2025-04-01
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| author | Shiwei Zhang Jie Kong Jian Tan Xianhong Meng Ping Dai Jiawang Cao Kun Luo Mianyu Liu Qun Xing Yi Tian Juan Sui Sheng Luan |
| author_facet | Shiwei Zhang Jie Kong Jian Tan Xianhong Meng Ping Dai Jiawang Cao Kun Luo Mianyu Liu Qun Xing Yi Tian Juan Sui Sheng Luan |
| author_sort | Shiwei Zhang |
| collection | DOAJ |
| description | The meat yield (MY) is a key economic trait in Pacific whiteleg shrimp (<i>Penaeus vannamei</i>) breeding, necessitating accurate genomic prediction for efficient genetic improvement. In this study, we investigated single-trait (STGMs) and multi-trait genomic models (MTGMs) for predicting MY and related traits, using two cross-validation strategies reflecting different data-availability scenarios. A total of 899 individuals from 63 full-sibling families were phenotyped for MY, net meat weight (MW), body weight (BW), body length (BL), and abdominal segment length (AL). We estimated the genomic heritability and genetic correlations of MY and related traits in <i>P. vannamei</i>, followed by comparing the prediction accuracy of STGMs and MTGMs for MY and MW. Two validation approaches were then applied: CV1 retained auxiliary traits in the validation sets, and CV2 excluded both target and auxiliary traits. Heritability estimates indicated that MY had low heritability (STGM: 0.160; MTGMs: 0.145–0.156), whereas MW, BW, BL, and AL showed low-to-moderate heritability (0.099–0.204). Genetic correlations revealed strong associations between MY and MW/BW/BL (<i>r<sub>g</sub></i> = 0.605–0.783), yet a low positive correlation with AL (<i>r<sub>g</sub></i> = 0.286). Across all comparisons, MTGMs consistently surpassed STGMs. For MY, MTGMs improved the accuracy by 4.8–58.8% relative to STGM (0.187), with the MY-MW model achieving the highest accuracy (0.297) under CV1. Similarly, MTGMs enhanced MW prediction by 36.6–138.2% over STGM (0.254), with the MW-BW model reaching the highest accuracy (0.605) under CV1. Notably, retaining auxiliary traits (CV1) boosted accuracy gains substantially (up to 138.2%), whereas excluding them (CV2) yielded only marginal improvements (≤8.6%). Moreover, incorporating AL as an auxiliary trait increased heritability estimates for MW, BW, and BL by 5.4–7.6%, indicating its synergistic value in MTGMs. Overall, these results demonstrate that MTGMs markedly enhance genomic prediction for carcass traits compared to STGMs, particularly when auxiliary trait data are accessible (CV1). The findings underscore the importance of maintaining auxiliary trait records in breeding populations, offering a robust framework for improving <i>P. vannamei</i> through multi-trait genomic prediction models. |
| format | Article |
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| spelling | doaj-art-9bd4d2d503964a94a1e40ce8b29f05412025-08-20T02:28:40ZengMDPI AGAnimals2076-26152025-04-01158116510.3390/ani15081165Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>)Shiwei Zhang0Jie Kong1Jian Tan2Xianhong Meng3Ping Dai4Jiawang Cao5Kun Luo6Mianyu Liu7Qun Xing8Yi Tian9Juan Sui10Sheng Luan11College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaBLUP Aquabreed Co., Ltd., Weifang 261311, ChinaCollege of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao 266071, ChinaThe meat yield (MY) is a key economic trait in Pacific whiteleg shrimp (<i>Penaeus vannamei</i>) breeding, necessitating accurate genomic prediction for efficient genetic improvement. In this study, we investigated single-trait (STGMs) and multi-trait genomic models (MTGMs) for predicting MY and related traits, using two cross-validation strategies reflecting different data-availability scenarios. A total of 899 individuals from 63 full-sibling families were phenotyped for MY, net meat weight (MW), body weight (BW), body length (BL), and abdominal segment length (AL). We estimated the genomic heritability and genetic correlations of MY and related traits in <i>P. vannamei</i>, followed by comparing the prediction accuracy of STGMs and MTGMs for MY and MW. Two validation approaches were then applied: CV1 retained auxiliary traits in the validation sets, and CV2 excluded both target and auxiliary traits. Heritability estimates indicated that MY had low heritability (STGM: 0.160; MTGMs: 0.145–0.156), whereas MW, BW, BL, and AL showed low-to-moderate heritability (0.099–0.204). Genetic correlations revealed strong associations between MY and MW/BW/BL (<i>r<sub>g</sub></i> = 0.605–0.783), yet a low positive correlation with AL (<i>r<sub>g</sub></i> = 0.286). Across all comparisons, MTGMs consistently surpassed STGMs. For MY, MTGMs improved the accuracy by 4.8–58.8% relative to STGM (0.187), with the MY-MW model achieving the highest accuracy (0.297) under CV1. Similarly, MTGMs enhanced MW prediction by 36.6–138.2% over STGM (0.254), with the MW-BW model reaching the highest accuracy (0.605) under CV1. Notably, retaining auxiliary traits (CV1) boosted accuracy gains substantially (up to 138.2%), whereas excluding them (CV2) yielded only marginal improvements (≤8.6%). Moreover, incorporating AL as an auxiliary trait increased heritability estimates for MW, BW, and BL by 5.4–7.6%, indicating its synergistic value in MTGMs. Overall, these results demonstrate that MTGMs markedly enhance genomic prediction for carcass traits compared to STGMs, particularly when auxiliary trait data are accessible (CV1). The findings underscore the importance of maintaining auxiliary trait records in breeding populations, offering a robust framework for improving <i>P. vannamei</i> through multi-trait genomic prediction models.https://www.mdpi.com/2076-2615/15/8/1165<i>Penaeus vannamei</i>meat yieldnet meat weightheritabilitymulti-trait genomic prediction |
| spellingShingle | Shiwei Zhang Jie Kong Jian Tan Xianhong Meng Ping Dai Jiawang Cao Kun Luo Mianyu Liu Qun Xing Yi Tian Juan Sui Sheng Luan Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) Animals <i>Penaeus vannamei</i> meat yield net meat weight heritability multi-trait genomic prediction |
| title | Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) |
| title_full | Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) |
| title_fullStr | Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) |
| title_full_unstemmed | Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) |
| title_short | Multi-Trait Genomic Prediction of Meat Yield in Pacific Whiteleg Shrimp (<i>Penaeus vannamei</i>) |
| title_sort | multi trait genomic prediction of meat yield in pacific whiteleg shrimp i penaeus vannamei i |
| topic | <i>Penaeus vannamei</i> meat yield net meat weight heritability multi-trait genomic prediction |
| url | https://www.mdpi.com/2076-2615/15/8/1165 |
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