Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)

Jingou Tong,Shunping He,Xiaomu Yu,Haiyang Liu,Xinhua Wang,Meixia Pang,Beide Fu

doi:10.1038/s41598-019-53469-8

Abstract

High-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F1 family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.

Highlights

Molecular markers are the basis for high-resolution genetic linkage map construction and quantitative trait loci (QTL) fine-mapping, which provide powerful tools for genetic analyses of economic traits in fish[1,2]
Benefits of simplest protocol, even distribution on genome, uniform fragments and tunable genome coverage[8], and this method has been successfully used for genetic maps construction in aquatic animals, such as pearl oyster (Pinctada fucata martensii)[5], Zhikong scallop (Chlamys farreri)[12], sea cucumber (Apostichopus japonicus)[13], bighead carp (Hypophthalmichthys nobilis)[14], crucian carp (Carassius auratus)[15], etc
This study aims to construct a high-density genetic linkage map using 2b-restriction site-associated DNA (RAD) technology and detect QTL intervals associating with growth traits of different stages in silver carp

Summary

Introduction

Molecular markers are the basis for high-resolution genetic linkage map construction and quantitative trait loci (QTL) fine-mapping, which provide powerful tools for genetic analyses of economic traits in fish[1,2]. Among the multiple genotyping-by-sequencing (GBS) methods, restriction site-associated DNA (RAD)[6] and its derivative methods, such as double-digest restriction site-associated DNA (dd-RAD)7, 2b-restriction site-associated DNA (2b-RAD)[8], genotyping by genome reducing and sequencing (GGRS)[9], specific-locus amplified fragments sequencing (SLAF)[10] and genome wide sampling sequencing (GWSS)[11], have been widely used for the construction of high-density genetic maps Among these RAD-related methods, 2b-RAD technology possesses the Traits BL1 BH1 HL1 BW1 BL2 BH2 HL2 BW2 BL3 BH3 HL3 BW3. This study aims to construct a high-density genetic linkage map using 2b-RAD technology and detect QTL intervals associating with growth traits of different stages in silver carp. This study would facilitate the genetic analysis of growth traits and provide valuable genomic resources for potential molecular breeding programs in silver carp

Objectives

Methods

Results