SLAF-based high-density genetic map construction and QTL mapping for major economic traits in sea urchin Strongylocentrotus intermedius

Yaqing Chang,Jian Song,Weijie Zhang,Dan Li,Yuhui Xu,Lei Li,Jun Ding

doi:10.1038/s41598-017-18768-y

Yaqing Chang, Jian Song + Show 5 more

Open Access

https://doi.org/10.1038/s41598-017-18768-y

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Abstract

Sea urchin (Strongylocentrotus intermedius) has long been a model species for developmental and evolutionary research, but only a few studies have focused on gene mapping. Here, we reported a high-density genetic map containing 4,387 polymorphism specific-length amplified fragment (SLAF) markers spanning 21 linkage groups (LG) for sea urchin. Based on this genetic map and phenotyping data for eight economic traits, 33 potentially significant QTLs were detected on ten different LGs with explanations ranging from 9.90% to 46.30%, partly including 10 QTLs for test diameter, six QTLs for body weight and eight QTLs for Aristotle’s lantern weight. Moreover, we found a QTL enrichment LG, LG15, gathering QTLs for test diameter, body weight, gonad weight, light orange-yellow color difference (≥E1) and light yellow color difference (≥E2). Among all QTLs, we genotyped four QTLs for test diameter, Aristotle’s lantern weight and body weight using High Resolution Melting (HRM) technology. Finally, we used the verified SNP marker (detected using SLAF sequencing) to explore their marker-assisted selection (MAS) breeding application potential and found that SNP-29 associated tightly with body weight and that heterozygous genotype was a dominant genotype, indicating that SNP-29 was a promising marker for MAS.

Highlights

Sea urchin (Strongylocentrotus intermedius) is native to the eastern Pacific Ocean, mainly in the northern Sea of Japan and the Russian far coast
Many Single nucleotide polymorphism (SNP)-based markers developed by reduced-representation sequencing or whole genome resequencing were used for high-density genetic map construction and QTL mapping[4,18,19,20]
specific-length amplified fragment (SLAF)-seq technology was successfully applied in other aquatic species[5,6,8,21], indicating that SLAF-seq is an effective method for high-density genetic map construction

Summary

Introduction

Sea urchin (Strongylocentrotus intermedius) is native to the eastern Pacific Ocean, mainly in the northern Sea of Japan and the Russian far coast. High-density genetic linkage maps have been constructed for many aquaculture species, including sea cucumber[4], pacific white shrimp[5], Hyriopsis cumingii[6], Haliotis diversicolor[7], Odontobutis potamophila[8], and cophthalmus maximus[9]. A high-density linkage map was constructed in 2015, and based on this genetic map, several economic-related QTLs were mapped. We employed a recently developed SLAF-seq approach to achieve rapid discovery of SNP markers for sea urchin. Using these newly developed markers, a high–density genetic map was constructed, and the www.nature.com/scientificreports/. HRM analysis was applied to verify the genotyping results for some QTLs by SLAF-seq and screen potential functional SNP markers for MAS breeding

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