Genomic Selection Using BayesCπ and GBLUP for Resistance Against Edwardsiella tarda in Japanese Flounder (Paralichthys olivaceus)
- 467 Downloads
The Japanese flounder is one of the most widely farmed economic flatfish species throughout eastern Asia including China, Korea, and Japan. Edwardsiella tarda is a major species of pathogenic bacteria that causes ascites disease and, consequently, a huge economy loss for Japanese flounder farming. After generation selection, traditional breeding methods can hardly improve the E. tarda resistance effectively. Genomic selection is an effective way to predict the breeding potential of parents and has rarely been used in aquatic breeding. In this study, we chose 931 individuals from 90 families, challenged by E. tarda from 2013 to 2015 as a reference population and 71 parents of these families as selection candidates. 1,934,475 markers were detected via genome sequencing and applied in this study. Two different methods, BayesCπ and GBLUP, were used for genomic prediction. In the reference population, two methods led to the same accuracy (0.946) and Pearson’s correlation results between phenotype and genomic estimated breeding value (GEBV) of BayesCπ and GBLUP were 0.912 and 0.761, respectively. In selection candidates, GEBVs from two methods were highly similar (0.980). A comparison of GEBV with the survival rate of families that were structured by selection candidates showed correlations of 0.662 and 0.665, respectively. This study established a genomic selection method for the Japanese flounder and for the first time applied this to E. tarda resistance breeding.
KeywordsGenomic selection BayesCπ GBLUP Edwardsiella tarda Japanese flounder
We sincerely thank Prof. Xijiang Yu and Prof. Hengde Li for their assistance with the improvement of our genomic selection algorithm.
SC initiated, managed, and conceived the research; YL, SL, and FL analyzed the data; QZ, CS, and NW discovered SNPs; YL, YY, YZ, HS, and WZ prepare the sample; YL and SL wrote the paper; and SC revised the paper . All the authors reviewed the manuscript.
This study was supported by grants from the following: (1) the Central Public-interest Scientific Institution Basal Research Fund, CAFS (No. 2016HY-ZD02); (2) the National Natural Science Foundation of China (31461163005, 31570078); (3) the Taishan Scholar Climbing Program of Shandong Province, China.
Compliance with Ethical Standards
The collection and handling of the animals in the study was approved by the Animal Care and Use Committee at the Chinese Academy of Fishery Sciences, and all experimental animal protocols were carried out in accordance with the guidelines for the care and use of laboratory animals at the Chinese Academy of Fishery Sciences.
The authors declare that there is no conflict of interest.
- Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2009) ASReml-R reference manual. The State of Queensland, Department of Primary Industries and Fisheries, BrisbaneGoogle Scholar
- Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, Song W, An N, Chalopin D, Volff JN, Hong Y, Li Q, Sha Z, Zhou H, Xie M, Yu Q, Liu Y, Xiang H, Wang N, Wu K, Yang C, Zhou Q, Liao X, Yang L, Hu Q, Zhang J, Meng L, Jin L, Tian Y, Lian J, Yang J, Miao G, Liu S, Liang Z, Yan F, Li Y, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao Y, Schartl M, Tang Q, Wang J (2014) Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 46:253–260CrossRefPubMedGoogle Scholar
- Liu F (2015) Genetic analysis and a preliminary genomic selection research of economic traits in Cynoglossus semilaevis. Ph. D. Dissertation. Shanghai: Shanghai Ocean University. (In Chinese)Google Scholar
- Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S (2015) Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 22(2):161–170CrossRefPubMedPubMedCentralGoogle Scholar
- Shao C, Bao B, Xie Z, Chen X, Li B, Jia X, Yao Q, Orti G, Li W, Li X, Hamre K, Xu J, Wang L, Chen F, Tian Y, Schreiber AM, Wang N, Wei F, Zhang J, Dong Z, Gao L, Gai J, Sakamoto T, Mo S, Chen W, Shi Q, Li H, Xiu Y, Li Y, Xu W, Shi Z, Zhang G, Power DM, Wang Q, Schartl M, Chen S (2017) The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry. Nat Genet 49(1):119–124CrossRefPubMedGoogle Scholar
- Song W, Li Y, Zhao Y, Liu Y, Niu Y, Pang R, Miao G, Liao X, Shao C, Gao F, Chen S (2012a) Construction of a high-density microsatellite genetic linkage map and mapping of sexual and growth-related traits in half-smooth tongue sole (Cynoglossus semilaevis). PLoS One 7:e52097CrossRefPubMedPubMedCentralGoogle Scholar
- Song W, Pang R, Niu Y, Gao F, Zhao Y, Zhang J, Sun J, Shao C, Liao X, Wang L, Tian Y, Chen S (2012b) Construction of high-density genetic linkage maps and mapping of growth-related quantitative trail loci in the Japanese flounder (Paralichthys olivaceus). PLoS One 7(11):e50404CrossRefPubMedPubMedCentralGoogle Scholar
- Vallejo RL, Leeds TD, Fragomeni BO, Gao G, Hernandez AG, Misztal I, Welch TJ, Wiens GD, Palti Y (2016) Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in rainbow trout: insights on genotyping methods and genomic prediction models. Front Genet 7:96CrossRefPubMedPubMedCentralGoogle Scholar
- Wang L, Fan C, Liu Y, Zhang Y, Liu S, Sun D, Deng H, Xu Y, Tian Y, Liao X, Xie M, Li W, Chen S (2014) A genome scan for quantitative trait loci associated with Vibrio anguillarum infection resistance in Japanese flounder (Paralichthys olivaceus) by bulked segregant analysis. Mar Biotechnol 16(5):513–521CrossRefPubMedGoogle Scholar
- Wolc A, Stricker C, Arango J, Settar P, Fulton JE, O’Sullivan NP, Preisinger R, Habier D, Fernando R, Garrick D, Lamont SJ, Dekkers JCM (2011) Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genet Sel Evol 43(1):5CrossRefPubMedPubMedCentralGoogle Scholar
- Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Lošo T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Wang J, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Zhang S, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang J, Wang Q, Steinberg CE, Wang H, Li N, Qian L, Zhang G, Li Y, Yang H, Liu X, Wang J, Yin Y, Wang J (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490(7418):49–54CrossRefPubMedGoogle Scholar
- Zheng WW, Chen SL, Li ZY, Wei ZF, Gao J, Li YZ, Liu Y, Tian YS, Liu ST, Sun DQ, Yang YM, Wang L (2016) Analyzing of heritability and breeding value of disease resistance for Edwardsiella tarda in Japanese flounder (Paralichthys olivaceus). J Agric Biotechnol 24(8):1181–1189 (In Chinese)Google Scholar