Construction of a High-Density SNP Genetic Map for Pacific White Shrimp Litopenaeus vannamei

Genetic linkage map is essential to Quantitative Trait Loci (QTL) detection and comparative genomics study. Next generation sequencing (NGS) technology has facilitated high throughput and low cost Single Nucleotide Polymorphism (SNP) marker genotyping and high-density linkage map construction. One powerful method for genotyping using NGS technology is next generation restriction-site associated DNA (RAD) sequencing, Specific-locus amplified fragment sequencing (SLAF-seq) is base on RAD sequencing and has proved to be effective for linkage map construction recently. In this study, we report the construction of high-density linkage map of Pacific white shrimp Litopenaeus vannamei using SLAF-seq. Four sequencing libraries were constructed using genomic DNA from two parents and 205 corresponding offspring, a total of 456,620,260 reads were generated on Illunima Hiseq 2500 platform using paired-end sequencing. The average data coverage was 176 X and 35 X for parents and progenies genome separately. De novo SNP discovery resulted in 25,140 polymorphism markers. Considering the marker coverage over the individuals and reads depth, a total of 6,359 markers with high quality were selected for linkage map construction basing on double pseudo-test cross strategy in JoinMap 4.0 software. In the constructed linkage map, 4,396 markers were mapped to the female map and 4,201 were mapped to the male map. The female and male map contained 44 linkage groups, which was accordance with the number of chromosome pairs in L. vannamei. For the integrated 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. This high density linkage map will not only be useful tool in QTL detection, genetic improvement and marker-assisted breeding, but also will play important role in comparative genomic and genome assembly of L. vannamei and other penaeid shrimp.