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Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

文献类型： 外文期刊

作者： Li, Jitao 1 ; Lv, Jianjian 1 ; Liu, Ping 1 ; Chen, Ping 1 ; Wang, Jiajia 1 ; Li, Jian 1 ;

作者机构： 1.CAFS, Minist Agr & Rural Affairs, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Dev Marine Fisheries, Qingdao 266071, Shandong, Peoples R China

2.Natl Lab Ocean Sci & Technol, Funct Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266071, Shandong, Peoples R China

关键词： Exopalaemon carinicauda; Genome; SNP; High-resolution linkage map; QTL mapping

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷

页码：

收录情况： SCI

摘要： BackgroundHigh-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.ResultsIn the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73cM and 0.55cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation.ConclusionsThe genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growthtraits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

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