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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #309510
Title: Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Author
item LI, YUN - Auburn University
item LIU, SHIKAI - Auburn University
item QIN, ZHENKUI - Auburn University
item Waldbieser, Geoffrey - Geoff
item WANT, RUIJIA - Auburn University
item SUN, LUYANG - Auburn University
item BOA, LISUI - Auburn University
item DANZMANN, ROY - University Of Guelph
item DUNHAM, REX - Auburn University
item LIU, ZHANJIANG - Auburn University

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2014
Publication Date: 11/26/2014
Citation: Li, Y., Liu, S., Qin, Z., Waldbieser, G.C., Want, R., Sun, L., Boa, L., Danzmann, R.G., Dunham, R., Liu, Z. 2014. Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish. DNA Research. 22:39-52.

Interpretive Summary: Genome-based selection of catfish broodstock requires knowledge of genome structure and the generation of positioned markers, that is, DNA sequence variants, along the genome. Catfish genetic maps had been produced at low resolution, but the present research was performed to provide a higher density genetic map of the channel catfish genome. Genomic DNA was isolated from grandparents, parents, and offspring of three pedigreed catfish families, and genotypes were obtained at 64,889 single nucleotide polymorphism (SNP) loci. Co-inheritance of SNP locus alleles was used to order 54,342 of these loci on the genome. The resulting genetic map contained, on average, one marker per 0.22 centiMorgans. This high resolution genetic map provides a high density of genetic markers across the catfish genome that are useful for tracking inheritance of chromosomal segments, and correlating that inheritance with production trait phenotypes, in order to select catfish with improved performance.

Technical Abstract: Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K SNP array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4495.1 cM in females and 2593.7 cM in males, presenting a ratio of 1.7:1 between female and male in recombination fraction. After integration with previously established physical map, over 87% of physical map contigs were anchored to the linkage groups which covered a physical length of 867 Mb, accounting for about 90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole genome assembly, and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.