Abstract
BackgroundEdwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China’s aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance to E. tarda in Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance to E. tarda by using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP.ResultsWe estimated a heritability of 0.13 ± 0.02 for resistance to E. tarda in Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction.ConclusionsResistance to E. tarda in Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance to E. tarda in Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.
Highlights
Edwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China’s aquaculture sector
We found that genomic BLUP (GBLUP) and BayesCπ yielded similar estimates of GEBV, and that accuracy of prediction was not improved substantially when the number of single nucleotide polymorphisms (SNPs) was increased beyond 50 k
We estimated the heritability of resistance to Edwardsiella tarda in Japanese flounder to be 0.13 using a fivegeneration pedigree
Summary
Edwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China’s aquaculture sector. The Japanese flounder (Paralichthys olivaceus) is an economically important aquatic species that is cultured widely in the coastal areas of China, South Korea, and Japan. This fish is popular among consumers for its meat quality and good flavor. E. tarda causes acute symptoms with ascites in many cultured fish, e.g., Japanese flounder, turbot, and channel catfish [2,3,4,5]. Because of the lack of effective measures to control this pathogen, the increasing mortality rate and associated farming costs are severe problems in the Japanese flounder industry in China. Several positive cases of increased resistance to diseases through selective breeding methods have been reported in cultured fish, e.g., Atlantic salmon, rainbow trout, and Atlantic cod [6,7,8,9,10,11,12,13,14]
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