title: Evaluation of the 2b-RAD method for genomic selection in scallop breeding.
abstract: The recently developed 2b-restriction site-associated DNA (2b-RAD) sequencing method provides a cost-effective and flexible genotyping platform for aquaculture species lacking sufficient genomic resources. Here, we evaluated the performance of this method in the genomic selection (GS) of Yesso scallop (Patinopecten yessoensis) through simulation and real data analyses using six statistical models. Our simulation analysis revealed that the prediction accuracies obtained using the 2b-RAD markers were slightly lower than those obtained using all polymorphic loci in the genome. Furthermore, a small subset of markers obtained from a reduced tag representation (RTR) library presented comparable performance to that obtained using all markers, making RTR be an attractive approach for GS purpose. Six GS models exhibited variable performance in prediction accuracy depending on the scenarios (e.g., heritability, sample size, population structure), but Bayes-alphabet and BLUP-based models generally outperformed other models. Finally, we performed the evaluation using an empirical dataset composed of 349 Yesso scallops that were derived from five families. The prediction accuracy for this empirical dataset could reach 0.4 based on optimal GS models. In summary, the genotyping flexibility and cost-effectiveness make 2b-RAD be an ideal genotyping platform for genomic selection in aquaculture breeding programs.
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.|Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore.
authors.forename: Jinzhuang
authors.initials: J
authors.lastname: Dou
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Wenqian
authors.initials: W
authors.lastname: Jiao
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Yangping
authors.initials: Y
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Tianqi
authors.initials: T
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.
authors.forename: Yangfan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.|Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China.
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.|Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, China.
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D000818:Animals; D001947:Breeding; D066264:Datasets as Topic; D005828:Genetics, Population; D023281:Genomics / Q000379:methods; D008957:Models, Genetic; D015233:Models, Statistical; D049897:Pectinidae / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*