Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)
Zhang Shiyong,Xinhui Zhang,Xiaohui Chen,Tengfei Xu,Minghua Wang,Qin Qin,Liqiang Zhong,Jiang Hucheng,Xiaohua Zhu,Hongyan Liu,Junjie Shao,Zhu Zhifei,Qiong Shi,Qiong Shi,Wenji Bian,Xinxin You,Xinxin You +16 more
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TLDR
The high-density genetic linkage map is constructed and the sex-linked marker in channel catfish is developed, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.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.read more
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Research advances in the genomics and applications for molecular breeding of aquaculture animals
Xinxin You,Xinxin Shan,Qiong Shi +2 more
TL;DR: This review assesses the availability of complete genomes of aquaculture animals and then briefly discusses the sequencing technologies and SNP array for SNPs genotyping, and summarizes the current status of genetic linkage map construction, QTL mapping, GWAS, and GS in aquatic animals.
Journal ArticleDOI
Sex determination mechanisms and sex control approaches in aquaculture animals
TL;DR: This work synthesizes current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also reviews several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing.
Journal ArticleDOI
Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
Dengdong Wang,Xiyang Chen,Xinhui Zhang,Jia Li,Yunhai Yi,Chao Bian,Qiong Shi,Qiong Shi,Haoran Lin,Haoran Lin,Shuisheng Li,Shuisheng Li,Yong Zhang,Yong Zhang,Xinxin You +14 more
TL;DR: Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth and bacterial and viral diseases have become the main threats to the grouper industry.
Journal ArticleDOI
First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus).
Yang Liu,Haolong Wang,Haishen Wen,Yue Shi,Meizhao Zhang,Xin Qi,Kaiqiang Zhang,Qingli Gong,Jifang Li,Feng He,Hu Yanbo,Yun Li +11 more
TL;DR: This study reports the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology and detects the fgfr4 gene, which plays a pivotal role in myogenesis and bone growth.
Journal ArticleDOI
Construction of a high-density genetic linkage map and fine mapping of QTLs for growth and sex-related traits in red-tail catfish (Hemibagrus wyckioides)
TL;DR: This first high-density genetic linkage map of red-tail catfish based on 2b-RAD sequencing technology was constructed using one F1 family composed of 165 offspring and their parents and provides effective information for future marker-assisted selection and sex-control breeding in this species.
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