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Genomic best linear unbiased prediction (GBLUP) is a robust method that has been routinely used in GS breeding programs. However, GBLUP assumes that markers contribute equally to the total genetic variance, which may not be the case. In this study, we developed a novel GS method called GA-GBLUP that leverages the genetic algorithm (GA) to select markers related to the target trait. We defined four fitness functions for optimization, including AIC, BIC, R2, and HAT, to improve the predictability and bin adjacent markers based on the principle of linkage disequilibrium to reduce model dimension. The results demonstrate that the GA-GBLUP model, equipped with R2 and HAT fitness function, produces much higher predictability than GBLUP for most traits in rice and maize datasets, particularly for traits with low heritability. Moreover, we have developed a user-friendly R package, GAGBLUP, for GS, and the package is freely available on CRAN (https:\/\/CRAN.R-project.org\/package=GAGBLUP).<\/jats:p>","DOI":"10.1093\/bib\/bbae385","type":"journal-article","created":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T10:50:37Z","timestamp":1722855037000},"source":"Crossref","is-referenced-by-count":16,"title":["GA-GBLUP: leveraging the genetic algorithm to improve the predictability of genomic selection"],"prefix":"10.1093","volume":"25","author":[{"given":"Yang","family":"Xu","sequence":"first","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanru","family":"Cui","sequence":"additional","affiliation":[{"name":"Hebei Agricultural University College of Agronomy, , Baoding, Hebei 071001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Zhou","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangning","family":"Yu","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyan","family":"Yang","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furong","family":"Li","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiusheng","family":"Guan","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuecai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Global Maize Program, International Maize and Wheat Improvement Centre , Texcoco 56237, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zefeng","family":"Yang","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shizhong","family":"Xu","sequence":"additional","affiliation":[{"name":"University of California Department of Botany and Plant Sciences, , Riverside, CA 92521, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1971-1086","authenticated-orcid":false,"given":"Chenwu","family":"Xu","sequence":"additional","affiliation":[{"name":"Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education\/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding\/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, , Yangzhou, Jiangsu 225009, 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