Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease Resistance

• 作者: Qian Zhou Ya-dong Chen Sheng Lu Yang Liu Wen-teng Xu Yang-zhen Li Lei Wang Na Wang Ying-ming Yang Song-lin Chen
• 来源期刊: 工程（英文）
• 年，卷（期）: 2021,（3）
• 所属期刊栏目: Breeding Engineering—Article
• 页码范围: 406-411
• 页数: 6页
• 语种: 英文

摘要

Single nucleotide polymorphism (SNP) arrays are a powerful genotyping tool used in genetic research and genomic breeding programs.Japanese flounder (Paralichthys olivaceus) is an economically-important aquaculture flatfish in many countries.However,the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder.We developed a 50K Japanese flounder SNP array,"Yuxin No.1," and report its utility in genomic selection (GS) for disease resistance to bacterial patho-gens.We screened more than 42.2 million SNPs from the whole-genome resequencing data of 1099 indi-viduals and selected 48697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology.Evaluation of the array performance with 168 fish showed that 74.7％ of the loci were successfully genotyped with high call rates (＞ 98％) and that the poly-morphic SNPs had good cluster separations.More than 85％ of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data.To validate "Yuxin No.1" for GS,the arrayed geno-typing data of 27 individuals from a candidate population and 931 individuals from a reference popula-tion were used to calculate the genomic estimated breeding values (GEBVs) for disease resistance to Edwardsiella tarda.There was a 21.2％ relative increase in the accuracy of GEBV using the weighted geno-mic best linear unbiased prediction (wGBLUP),compared to traditional pedigree-based best linear unbi-ased prediction (ABLUP),suggesting good performance of the "Yuxin No.1" SNP array for GS.In summary,we developed the "Yuxin No.1" 50K SNP array,which provides a useful platform for high-quality geno-typing that may be beneficial to the genomic selective breeding of Japanese flounder.