Abstract

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish (Silurus meridionalis). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

Highlights

  • Discovering the genes or chromosomal regions that control morphological, physiological and behavioural characteristics is critical for understanding adaptive evolution and the evolutionary responses of natural populations

  • Especially the use of ethanol for euthanasia, were conducted in accordance with the regulations provided by the guide for care and use of laboratory animals and were approved by the Committee of Laboratory Animal Experimentation of the Southwest University (Chongqing, China)

  • Taking advantage of massively parallel sequencers, we constructed and characterized a high-density single-nucleotide polymorphisms (SNPs) linkage map of southern catfish derived from restriction site-associated DNA sequencing (RAD-seq)

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Summary

Introduction

Discovering the genes or chromosomal regions that control morphological, physiological and behavioural characteristics is critical for understanding adaptive evolution and the evolutionary responses of natural populations. To identify such genes, a fine linkage map, which is an ordered listing of genetic markers located along the chromosomes in the genome, is needed. The linkage map is obtained by calculating the recombination frequency between genetic markers. It shows the relative position between genetic markers rather than the physical location of the genes on the chromosome. The phenomenon of genetic linkage underpins the genetic map. Linkage maps serve as a link between genomic information of model organisms and that of related non-model organisms through the comparison of their genomes to facilitate the discovery of candidate genes of non-model organisms [2,3,4]

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