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. 2015 Oct 27:5:15612.
doi: 10.1038/srep15612.

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

Yang Yu  1 , Xiaojun Zhang  1 , Jianbo Yuan  1 , Fuhua Li  1 , Xiaohan Chen  2 , Yongzhen Zhao  2 , Long Huang  3 , Hongkun Zheng  3 , Jianhai Xiang  1
Affiliations

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

Yang Yu et al. Sci Rep. .

Abstract

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

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Figures

Figure 1
Figure 1. Statistics of genotyped SLAF markers in six segregation patterns.
Figure 2
Figure 2. Demonstration of synteny analysis between female, male and sex average map.
Figure 3
Figure 3. Demonstration of the integration of linkage group LG1, genomic scaffolds and BAC clones.
See this image and copyright information in PMC

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