Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)

Shiyong Zhang; Xinhui Zhang; Xiaohui Chen; Tengfei Xu; Minghua Wang; Qin Qin; Liqiang Zhong; Hucheng Jiang; Xiaohua Zhu; Hongyan Liu; Junjie Shao; Zhifei Zhu; Qiong Shi; Wenji Bian; Xinxin You

doi:10.3389/fgene.2019.00251

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)

Front Genet. 2019 Mar 26:10:251. doi: 10.3389/fgene.2019.00251. eCollection 2019.

Authors

Shiyong Zhang^{1

2

3}, Xinhui Zhang⁴, Xiaohui Chen^{2

3}, Tengfei Xu⁴, Minghua Wang^{2

3}, Qin Qin^{2

3}, Liqiang Zhong^{2

3}, Hucheng Jiang^{2

3}, Xiaohua Zhu², Hongyan Liu², Junjie Shao², Zhifei Zhu⁵, Qiong Shi^{1

4}, Wenji Bian^{2

3}, Xinxin You^{1

4}

Affiliations

¹ BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.
² National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.
³ The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China.
⁴ Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China.
⁵ BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China.

Abstract

A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F₁ family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.

Keywords: channel catfish; growth-related genes; linkage map; quantitative trait locus (QTL); sex-related marker.