title: Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea.
abstract: Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used anEcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such asAPOB,CRATandOSBPL10. Notably,PPT2Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified thatEcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Panpan
authors.initials: P
authors.lastname: Wang
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Linsong
authors.initials: L
authors.lastname: Dong
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Yaguang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Zhaofang
authors.initials: Z
authors.lastname: Han
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Qiurong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Fisheries College, Jimei University , Xiamen , Fujian , China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Wang
keywords: Genotyping-By-Sequencing (GBS); Large yellow croaker; Marker development; Single nucleotide polymorphism (SNP); Teleost