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.
Highlights
A robust, high-density genetic linkage map is a useful tool for genome assembly, as well as for mapping quantitative trait loci (QTL) of economically important traits[14,15]
G, was estimated as 2.64 Gb according to the following empirical formula: G = K_num/K_depth, where K_num is the total number of K-mers, and K_depth is the maximal frequency[35]
Compared to the L. vannamei genome size of 2.45 Gb estimated by flow cytometry[36], the estimate of 2.6 Gb is closer to the true value
Summary
A robust, high-density genetic linkage map is a useful tool for genome assembly, as well as for mapping quantitative trait loci (QTL) of economically important traits[14,15]. One of the major methods used to construct high-density linkage maps, called restriction-site-associated DNA (RAD) sequencing, has been widely used in non-model species[25]. This method has been applied in QTL mapping, population genetic studies and comparative genome studies[26]. Only one QTL mapping study for L. vannamei has been published based on AFLP and SSR markers; three QTLs for body weight and body length were identified[23] As this linkage map was constructed primarily with AFLP markers and the marker interval was large (7.6 cM), further mapping and cloning of growth related genes would be difficult. Based on the high-density linkage map, QTL mapping was conducted to detect markers related to growth traits
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