Evaluation of the 2b-RAD method for genomic selection in scallop breeding

• DOI: 10.1038/srep19244
• Publication Date: 2016-01-12T10:33:04Z
• Authors: Jinzhuang Dou; Xue Li; Qiang Fu; Wenqian Jiao; Yangping Li; Tianqi Li; Yangfan Wang; Xiaoli Hu; Shi Wang; Zhenmin Bao
• Keywords: Genomic Selection

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 in selection (GS) Yesso scallop ( Patinopecten yessoensis ) through simulation real data analyses using six statistical models. Our analysis revealed that prediction accuracies obtained 2b-RAD markers were slightly lower than those all polymorphic loci genome. Furthermore, small subset from reduced tag representation (RTR) library presented comparable to markers, making RTR be an attractive approach GS purpose. Six models exhibited variable accuracy depending on scenarios (e.g., heritability, sample size, population structure), but Bayes-alphabet BLUP-based generally outperformed other Finally, performed evaluation empirical dataset composed 349 scallops derived five families. could reach 0.4 based optimal In summary, flexibility cost-effectiveness make ideal breeding programs.