Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

Bailing Chen,Hao Su,Yulong Li,Yunfeng Li,Wei Sun,Meilin Tian

doi:10.1038/s41598-021-04431-0

Bailing Chen, Hao Su + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-04431-0

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Abstract

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the genetic linkage map and growth-related molecular markers are still lacking, hindering marker assisted selection (MAS) for genetic improvement of R. esculentum. Therefore, we firstly used 2b-restriction site-associated DNA (2b-RAD) method to sequence 152 R. esculentum specimens and obtained 9100 single nucleotide polymorphism (SNP) markers. A 1456.34 cM linkage map was constructed using 2508 SNP markers with an average interval of 0.58 cM. Then, six quantitative trait loci (QTLs) for umbrella diameter and body weight were detected by QTL analysis based on the new linkage map. The six QTLs are located on four linkage groups (LGs), LG4, LG13, LG14 and LG15, explaining 9.4% to 13.4% of the phenotypic variation. Finally, 27 candidate genes in QTLs regions of LG 14 and 15 were found associated with growth and one gene named RE13670 (sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1-like) may play an important role in controlling the growth of R. esculentum. This study provides valuable information for investigating the growth mechanism and MAS breeding in R. esculentum.

Highlights

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China
To improve the growth of R. esculentum through marker assisted selection (MAS) breeding, we identified single nucleotide polymorphism (SNP) markers by 2b-restriction site-associated DNA (2b-RAD) method and constructed the first genetic linkage map of R. esculentum
We identified 27 candidate genes in linkage groups (LGs) 14 and 15 corresponding to the growth of R. esculentum and RE13670 showed the most possibility in controlling the growth due to the EGF_CA domain, following the growth-related genes reported in C. auratus[8]

Summary

Introduction

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. Based on the constructed linkage maps, many QTLs related to economic traits, such as body weight, body length, nutritional metabolisms and sex have been identified[7,10,11,12]. The researchers only identified some markers in R. esculentum, such as microsatellite for detection of genetic diversity and conservation of germplasm r esources[14] and SNPs and simple sequence repeats (SSRs) for assisting MAS breeding[15]. To improve the growth of R. esculentum through MAS breeding, we identified SNP markers by 2b-RAD method and constructed the first genetic linkage map of R. esculentum. We detected some QTLs and genes related to growth traits of R. esculentum based on the linkage map. A total of 1539 million raw reads were generated by 2b-RAD sequencing, including

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