Identification of Growth-Associated Genes by Genome-Wide Association Study and Their Potential Application in the Breeding of Pacific White Shrimp (Litopenaeus vannamei).

Ding Lyu,Quanchao Wang,Yang Yu,Jianhai Xiang,Xiaojun Zhang,Zheng Luo,Qian Zhang,Fuhua Li

doi:10.3389/fgene.2021.611570

Abstract

The Pacific white shrimp (Litopenaeus vannamei) is the most widely cultured shrimp in the world. A great attention has been paid to improve its body weight (BW) at harvest through genetic selection for decades. Genome-wide association study (GWAS) is a tool to dissect the genetic basis of the traits. In this study, a GWAS approach was conducted to find genes related to BW through genotyping 94,113 single nucleotide polymorphisms (SNPs) in 200 individuals from a breeding population. Four BW-related SNPs located in LG19 and LG39 were identified. Through further candidate gene association analysis, the SNPs in two candidate genes, deoxycytidylate deaminase and non-receptor protein tyrosine kinase, were found to be related with the body weight of the shrimp. Marker-assisted best linear unbiased prediction (MA-BLUP) based on the SNPs in these two genes was used to estimate the breeding values, and the result showed that the highest prediction accuracy of MA-BLUP was increased by 9.4% than traditional BLUP. These results will provide useful information for the marker-assisted breeding in L. vannamei.

Highlights

The Pacific white shrimp, Litopenaeus vannamei, is the most widely cultured shrimp all over the world (FAO, 2019)
The 2b-restriction-site-associated DNA (RAD) sequencing data were mapped to the published genome sequence, and the single nucleotide polymorphisms (SNPs) were called based on the reference sequence, Genome-wide association study (GWAS) for body weight (BW) was performed
According to the reference genome information (Zhang et al, 2019), a total of 83,015 SNPs were distributed along the 44 linkage groups (LGs) with one SNP per 0.05 cM on average, while the other 11,098 SNPs were not assigned to any LGs

Summary

INTRODUCTION

The Pacific white shrimp, Litopenaeus vannamei, is the most widely cultured shrimp all over the world (FAO, 2019). Growth Related Genes in Pacific White Shrimp by best linear unbiased prediction (BLUP) (Castillo-Juárez et al, 2007; Sui et al, 2016; Nolasco-Alzaga et al, 2018), which is essentially based on an “infinitesimal model” (Mather, 1941) This model assumes that the quantitative trait is controlled by an infinite number of gene loci that are evenly distributed across the genome and each locus has an infinitely small effect (Fisher, 1918; Bulmer, 1971). As the genome was assembled, another growth-related candidate gene, MMD2, was found based on the correlation analysis results in Wang et al (2019) and further validated (Wang et al, 2020) These researches illustrated the power of identifying QTLs or genes using GWAS in L. vannamei, low marker density and simple population structure restrict their applied values. These results will provide useful information for marker-assisted selection in L. vannamei

MATERIALS AND METHODS

RESULTS

DISCUSSION

DATA AVAILABILITY STATEMENT