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CPSF","award":["2024M751448"],"award-info":[{"award-number":["2024M751448"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["2021YFD13011011"],"award-info":[{"award-number":["2021YFD13011011"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["2021YFD1301105"],"award-info":[{"award-number":["2021YFD1301105"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["CX(20)1003"],"award-info":[{"award-number":["CX(20)1003"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["JBGS(2021)024"],"award-info":[{"award-number":["JBGS(2021)024"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["PZCZ201732"],"award-info":[{"award-number":["PZCZ201732"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["2023ZD04045"],"award-info":[{"award-number":["2023ZD04045"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["2024M751448"],"award-info":[{"award-number":["2024M751448"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The number of ribs (NRs) and the carcass length (CL) are important economic traits. The traits are usually measured after slaughter. To improve the prediction performance of genomic selection (GS) for NRs and CL, one strategy is to integrate the significant loci identified from whole-genome sequencing (WGS) data by genome-wide association study (GWAS) into the genomic prediction (GP) model. This study investigated the GP of different genomic best linear unbiased prediction (GBLUP) and Bayesian models using chip genotype data, imputed WGS (iWGS) data and modeling significant single-nucleotide polymorphisms (SNPs) in different ways for the GP of NRs and CL in the Suhuai pig population. The prediction accuracy, bias and running time of 15 different GP models were evaluated by 10-fold cross-validation. The prediction accuracy of GBLUP using chip data for NRs and CL was 0.314 \u00b1 0.022 and 0.194 \u00b1 0.040, respectively. For NRs, based on the iWGS data, treating the most significant SNP as fixed effects in the GBLUP model had the highest predictive performance, with a prediction accuracy of 0.528 \u00b1 0.023. For CL, based on the chip data, the model that added all the significant SNPs identified by imputed data by GWAS into the multi-trait GBLUP as the second random additive effect was the highest predictive performance, with a prediction accuracy of 0.305 \u00b1 0.027. This study provides insights into optimizing GP models for small populations with phenotypes that are difficult to measure.<\/jats:p>","DOI":"10.3390\/ani15030412","type":"journal-article","created":{"date-parts":[[2025,2,3]],"date-time":"2025-02-03T08:47:57Z","timestamp":1738572477000},"page":"412","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Integrating Significant SNPs Identified by GWAS for Genomic Prediction of the Number of Ribs and Carcass Length in Suhuai Pigs"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2552-5391","authenticated-orcid":false,"given":"Kaiyue","family":"Liu","sequence":"first","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4686-9118","authenticated-orcid":false,"given":"Yanzhen","family":"Yin","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Binbin","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenxi","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wuduo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peipei","family":"Niu","sequence":"additional","affiliation":[{"name":"Huaian Academy, Nanjing Agricultural University, Huai\u2019an 223005, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4722-2271","authenticated-orcid":false,"given":"Ruihua","family":"Huang","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"},{"name":"Huaian Academy, Nanjing Agricultural University, Huai\u2019an 223005, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pinghua","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"},{"name":"Huaian Academy, Nanjing Agricultural University, Huai\u2019an 223005, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5993-5584","authenticated-orcid":false,"given":"Qingbo","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China"},{"name":"Huaian Academy, Nanjing Agricultural University, Huai\u2019an 223005, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1111\/j.1439-0388.2004.00482.x","article-title":"The number of ribs and vertebrae in a Pietrain cross: Variation, heritability and effects on performance traits","volume":"121","author":"Borchers","year":"2004","journal-title":"J. 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