Development of a 38 K single nucleotide polymorphism array and application in genomic selection for resistance against Vibrio harveyi in Chinese tongue sole, Cynoglossus semilaevis

Sheng Lu; Qian Zhou; Yadong Chen; Yang Liu; Yangzhen Li; Lei Wang; Yingming Yang; Songlin Chen

doi:10.1016/j.ygeno.2021.03.034

Development of a 38 K single nucleotide polymorphism array and application in genomic selection for resistance against Vibrio harveyi in Chinese tongue sole, Cynoglossus semilaevis

Genomics. 2021 Jul;113(4):1838-1844. doi: 10.1016/j.ygeno.2021.03.034. Epub 2021 Apr 2.

Authors

Sheng Lu¹, Qian Zhou², Yadong Chen², Yang Liu², Yangzhen Li², Lei Wang², Yingming Yang², Songlin Chen³

Affiliations

¹ Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Wuxi Fisheries College, Nanjing Agricultural University, 214081 Wuxi, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China.
² Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China.
³ Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China. Electronic address: chensl@ysfri.ac.cn.

PMID: 33819565
DOI: 10.1016/j.ygeno.2021.03.034

Abstract

Based on 1572 re-sequenced Chinese tongue sole (Cynoglossus semilaevis), we investigated the accuracy of four genomic methods at predicting genomic estimated breeding values (GEBVs) of Vibrio harveyi resistance in C. semilaevis when SNPs varying from 500 to 500 k. All methods outperformed the pedigree-based best linear unbiased prediction when SNPs reached 50 k or more. Then, we developed an SNP array "Solechip No.1" for C. semilaevis breeding using the Affymetrix Axiom technology. This array contains 38,295 SNPs with an average of 10.5 kb inter-spacing between two adjacent SNPs. We selected 44 candidates as the parents of 23 families and genotyped them by the array. The challenge survival rates of offspring families had a correlation of 0.706 with the mid-parental GEBVs. This SNP array is a convenient and reliable tool in genotyping, which could be used for improving V. harveyi resistance in C. semilaevis coupled with the genomic selection methods.

Keywords: Cynoglossus semilaevis; Disease resistance; Genomic selection; SNP array; Vibrio harveyi.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
China
Fish Diseases* / genetics
Fish Diseases* / microbiology
Flatfishes* / genetics
Flatfishes* / microbiology
Genomics
Polymorphism, Single Nucleotide
Vibrio
Vibrio Infections* / genetics
Vibrio Infections* / veterinary

Supplementary concepts

Vibrio harveyi