Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

Xiaoli Huang,Lei Xia,Xiaocui Ma,Xiao-Qin Xia,Yingyin Cheng,Mijuan Shi,Yaxin Chen,Nan Wu,Yanxin Jiang,Wanting Zhang,You Duan,Yaping Wang

doi:10.1186/s12864-020-6730-x

Xiaoli Huang, Lei Xia + Show 10 more

Open Access

https://doi.org/10.1186/s12864-020-6730-x

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Abstract

BackgroundGrass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture.ResultsIn this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.ConclusionA high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

Highlights

Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture
single nucleotide polymorphisms (SNPs) marker filtration The genomic high-throughput sequencing data from 2 parents and 100 progenies was screened by SOAP2 [33] and RADtyping software [34]
In order to construct genetic linkage maps quickly and accurately, the location markers that were identical were merged, which allowed for the absence of missing genotypes in offsprings, due to the limitations of joinmap 4.1 regarding the number of makers

Summary

Introduction

Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. The grass carp (Ctenopharyngodon idellus) belongs to the Cyprinidae family and is the only species of the genus Ctenopharyngodon. As one of the most important freshwater-cultured fish, the global production of grass carp was approximately 5.8 million tons, accounting for. Most studies about grass carp focused on fish immunity [2,3,4], nutrition [5,6,7], and stress resistance [8]. A few growth-related studies in grass carp were focused on the impacts of the additives, dietary, or the growth hormones [9]. Growth traits are typical quantitative traits, which are influenced by multiple genes, and perhaps no any single

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