Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Abstract

Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

“…The highest levels of recombination are found in the middle of each chromosome. This pattern is exactly opposite the pattern observed in stickleback and catfish, where recombination is highest at the ends of the chromosomes [72,73].…”

Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers

“…Similarly, for map-based cloning, a high density of markers is needed to get as close as possible to the target candidate gene, implying the availability of an accurate dense map. Dense genetic maps were successfully used for anchoring physical contigs (Raats et al 2013) and sequence scaffolds (Mascher and Stein 2014) to LGs and controlling the quality of sequence assembly (Hedgecock et al 2015;Zeng et al 2017). High-coverage shotgun sequencing in combination with new analytical tools of sequence scaffolding, ultradense mapping, and three-dimensional chromosome-conformationcapture-sequencing data was successfully used for highquality sequencing of such a big and complex genome as wheat (https://www.wheatgenome.org/News2/RefSeq-v1.0-URGI).…”

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

“…Particularly with the SNP discovery through whole genome re-sequencing approaches, and improvement of genotyping techniques, commercially accessible assays have grown from thousands of markers, to hundreds of thousands markers for some species [e.g. salmon 130K [36], catfish 250K [37] and 690K [38], common carp 250K [39]]. While this is useful for some applications (e.g.…”