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.
Highlights
Genetic-map construction is a critically important tool for further genomic studies, as well as for genetic breeding of economically important aquatic species
A genetic linkage map can provide important genomic information and allow for exploration of quantitative trait locus (QTL), which can be used to maximize the selection of target traits in breeding animals
Availability of a large number of genetic markers is essential for constructing a good genetic linkage map and for QTL mapping of available genetic traits
Summary
Genetic-map construction is a critically important tool for further genomic studies, as well as for genetic breeding of economically important aquatic species It has been employed for genome assembly (Jiao et al, 2014), comparative genome analysis (Xiao et al, 2015; Zhu et al, 2015; Peng et al, 2016), and quantitative trait locus (QTL) identification for important economic traits (Liu F. et al, 2013; Zhang et al, 2018). Most of the early genetic linkage map constructions used amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR), but these maps had few molecular markers with low density (Zhang et al, 2011), which limited identification of QTL and related researches. The RAD-seq technology is a popular tool for establishment of high-density genetic linkage maps in many aquaculture species, such as Zhikong scallop (Chlamys farreri) (Jiao et al, 2014), mandarin fish (Siniperca chuatsi) (Lijavetzky et al, 2007), tilapia (Oreochromis niloticus L.) (Palaiokostas et al, 2013b), Asian seabass (Lates calcarifer) (Wang L. et al, 2015), and Chinese mitten crab (Eriocheir sinensis) (Cui et al, 2015)
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