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

Engineering - Tập 7 - Trang 406-411 - 2021
Qian Zhou1,2, Ya-dong Chen1, Sheng Lu1, Yang Liu1, Wen-teng Xu1,2, Yang-zhen Li1, Lei Wang1, Na Wang1,2, Ying-ming Yang1, Song-lin Chen1,2
1Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
2Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China

Tài liệu tham khảo

Meuwissen, 2001, Prediction of total genetic value using genome-wide dense marker maps, Genetics, 157, 1819, 10.1093/genetics/157.4.1819 Pryce, 2010, Deterministic models of breeding scheme designs that incorporate genomic selection, J Dairy Sci, 93, 5455, 10.3168/jds.2010-3256 Matukumalli, 2009, Development and characterization of a high density SNP genotyping assay for cattle, PLoS ONE, 4, 10.1371/journal.pone.0005350 Chen, 2019, Fish genomic research: decade review and prospect, J Fish China, 43, 1 Houston, 2014, Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar), BMC Genomics, 15, 90, 10.1186/1471-2164-15-90 Poćwierz-Kotus, 2015, Restitution and genetic differentiation of salmon populations in the southern Baltic genotyped with the Atlantic salmon 7K SNP array, Genet Sel Evol, 47, 39, 10.1186/s12711-015-0121-9 Xu, 2014, Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio), BMC Genomics, 15, 307, 10.1186/1471-2164-15-307 Palti, 2015, The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout, Mol Ecol Resour, 15, 662, 10.1111/1755-0998.12337 Zeng, 2017, Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence, Sci Rep, 7, 40347, 10.1038/srep40347 Fuji, 2007, Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder (Paralichthys olivaceus), Aquaculture, 272, 291, 10.1016/j.aquaculture.2007.07.210 Shao, 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, 161, 10.1093/dnares/dsv001 Robledo, 2019, Discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in Atlantic salmon, Front Genet, 10, 56, 10.3389/fgene.2019.00056 Zhou, 2019, Genome-wide association mapping and gene expression analyses reveal genetic mechanisms of disease resistance variations in Cynoglossus semilaevis, Front Genet, 10, 1167, 10.3389/fgene.2019.01167 Shao, 2017, The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry, Nat Genet, 49, 119, 10.1038/ng.3732 Liu, 2018, Genomic selection using BayesCπ and GBLUP for resistance against Edwardsiella tarda in Japanese flounder (Paralichthys olivaceus), Mar Biotechnol, 20, 559, 10.1007/s10126-018-9839-z Zhou, 2013, QC-Chain: fast and holistic quality control method for next-generation sequencing data, PLoS ONE, 8, 10.1371/journal.pone.0060234 Li, 2009, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, 20, 1297, 10.1101/gr.107524.110 Purcell, 2007, PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet, 81, 559, 10.1086/519795 Danecek, 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156, 10.1093/bioinformatics/btr330 Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila–melanogaster strain w1118; iso-2; iso-3, Fly, 6, 80, 10.4161/fly.19695 Gao H, Pirani A, Webster T, Shen MM, inventors; Affymetrix, Inc., assignee. Systems and methods for SNP characterization and identifying off target variants. United States patent US 20140274749. 2014 Sep 18. Yang, 2011, GCTA: a tool for genome-wide complex trait analysis, Am J Hum Genet., 88, 76, 10.1016/j.ajhg.2010.11.011 Zhang, 2016, Weighting strategies for single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS, Front Genet, 7, 151, 10.3389/fgene.2016.00151 Wang, 2012, Genome-wide association mapping including phenotypes from relatives without genotypes, Genet Res, 94, 73, 10.1017/S0016672312000274 Gilmour, 2009 Wray, 2010, The genetic interpretation of area under the ROC curve in genomic profiling, PLoS Genet, 6, 10.1371/journal.pgen.1000864 Robin, 2011, pROC: an open-source package for R and S+ to analyze and compare ROC curves, BMC Bioinf, 12, 77, 10.1186/1471-2105-12-77 Lindgren, 2011, Genotyping techniques to address diversity in tumors, Adv Cancer Res, 112, 151, 10.1016/B978-0-12-387688-1.00006-5 Bangera, 2017, Genomic predictions can accelerate selection for resistance against Piscirickettsia salmonis in Atlantic salmon (Salmo salar), BMC Genomics, 18, 121, 10.1186/s12864-017-3487-y Odegård, 2014, Genomic prediction in an admixed population of Atlantic salmon (Salmo salar), Front Genet, 5, 402 Palaiokostas, 2018, Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing, Genet Sel Evol, 50, 30, 10.1186/s12711-018-0401-2 Zhang, 2020, Genomic prediction of columnaris disease resistance in catfish, Mar Biotechnol, 22, 145, 10.1007/s10126-019-09941-7