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; Yang Yu; Quanchao Wang; Zheng Luo; Qian Zhang; Xiaojun Zhang; Jianhai Xiang; Fuhua Li

doi:10.3389/fgene.2021.611570

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

Front Genet. 2021 Apr 7:12:611570. doi: 10.3389/fgene.2021.611570. eCollection 2021.

Authors

Ding Lyu^{1

2

3}, Yang Yu^{1

2

3}, Quanchao Wang^{1

3

4}, Zheng Luo^{1

3

5}, Qian Zhang^{1

3

5}, Xiaojun Zhang^{1

2

3}, Jianhai Xiang^{1

3}, Fuhua Li^{1

2

3

6}

Affiliations

¹ Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
² Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
³ Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
⁴ Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.
⁵ University of Chinese Academy of Sciences, Beijing, China.
⁶ The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China.

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.

Keywords: GWAS; Litopenaeus vannamei; genetic breeding; growth trait; marker assisted BLUP.