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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #334896
Research Project: Genetics, Breeding and Reproductive Physiology to Enhance Production of Catfish

Location: Warmwater Aquaculture Research Unit

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

Author
item ZENG, QIFAN - Auburn University
item FU, QIANG - Auburn University
item LI, YUN - Auburn University
item Waldbieser, Geoffrey - Geoff
item Bosworth, Brian
item LIU, SHIKAI - Auburn University
item YANG, YUJIA - Auburn University
item BAO, LISUI - Auburn University
item YUAN, ZIHAO - Auburn University
item LI, NING - Auburn University
item LIU, ZHANJIANG - Auburn University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/5/2016
Publication Date: 1/12/2017
Citation: Zeng, Q., Fu, Q., Li, Y., Waldbieser, G.C., Bosworth, B.G., Liu, S., Yang, Y., Bao, L., Yuan, Z., Li, N., Liu, Z. 2017. Development of a 690K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Scientific Reports. 7:40347.

Interpretive Summary: Problem: Efficient selection of superior catfish broodstock depends on the identification of positive genetic variation within the breeding population, and identification of variation throughout the genome requires new molecular tools for the catfish. Approach: Genomic DNA was sequenced from channel and blue catfish of varied backgrounds. Scientists at Auburn University produced a genotyping array that contained 690,000 single nucleotide variants within and between groups of channel and blue catfish. In cooperation with USDA, ARS scientists at the Warmwater Aquaculture Research Unit, Stoneville, MS, they genotyped four pedigreed catfish families to produce a genetic map that contained 30,615 unique markers along the 29 catfish chromosomes. The new map aligned to the recently published channel catfish genome assembly with a few exceptions. This analysis provided a validation and refinement of the genome assembly and it provided a new tool for assessing genetic variation in catfish broodstock for selective breeding.

Technical 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 690k array) that were relatively evenly distributed across the entire genome, with 0.8 kb interquartile range of intervals, and covered 98.6% of the genome scaffolds and 93.9% of the BAC-based physical map contigs. Here we also report linkage mapping using the 690K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. The total genetic size of the catfish genome is 3,004 cM. These markers were mapped to 29 linkage groups (LGs) with 30,615 unique marker positions, with a resolution of 0.1 cM for sex-averaged genetic map. The recombination frequency is 1.4-fold larger in females than in males. This linkage map anchored 1,546 scaffolds of the reference genome sequence to LGs, covering a physical length of 766 Mb, accounting for ~ 97.8% of the total genome assembly. A total of 950 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 analysis, especially for GWAS and QTL mapping for genes associated with economically important traits.