Development of a High Density SNP-Based Linkage Map of Pacific White Shrimp (Litopenaeus vannamei) Using Next Generation Sequencing

Genetic linkage map is essential to Quantitative Trait Loci (QTL) detection and comparative genomics study. With the help of next generation sequencing (NGS) technology, Single Nucleotide Polymorphism (SNP) genotyping and high-density linkage map construction have become more and more efficient and cost-effective. Specific-locus amplified fragment sequencing (SLAF-seq) is an efficient method for large-scale SNP genotyping based on NGS technology and has proved to be effective for linkage map construction. In the present study, a high-density linkage map of Pacific white shrimp Litopenaeus vannamei was constructed using SLAF-seq method. 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 technology. The average data coverage was 176 X and 35 X for parents and progenies, respectively. De novo SNP discovery generated 25,140 polymorphism markers. Considering the marker coverage among individuals and reads depth, a total of 6,359 markers with high quality were selected for linkage map construction based on double pseudo-test cross strategy using JoinMap 4.0 software. In the constructed linkage map, 4,396 markers were mapped to female map and 4,201 were mapped to male map. Both the female map and the male map contained 44 linkage groups, which was in accordance with the number of chromosome pairs in L. vannamei. The integrated map was also constructed. 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. The high density genetic linkage map will not only be useful in QTL detection, genetic improvement and marker-assisted breeding, but also play an important role in comparative genomics and genome assembly for L. vannamei and other penaeid shrimp.

Key words: Linkage map, SLAF-seq, SNP, Litopenaeus vannamei .

 Corresponding author: Jianhai Xiang; Nanhai Road, Qingdao, Shandong 266071, China;

 Tel.: +86 532 82898568; fax: +86 532 82898578; E-mail address: jhxiang@qdio.ac.cn