This Is AuburnElectronic Theses and Dissertations

Development of 690K SNP arrays for whole genome mapping and genetic studies in catfish




Zeng, Qifan

Type of Degree

PhD Dissertation


Fisheries and Allied Aquacultures


Catfish is the leading aquaculture species in the United States, accounting for approximately 60% of U.S. aquaculture production. However, the catfish industry is facing great challenges including escalating feed and fuel costs, intense international competition, and devastating diseases. Application of genetic markers facilitate elucidating the genetic basis for quantitative traits, and enabling characterization of the major quantitative trait loci (QTLs) and underlying causative genes. Efficient marker systems need to be developed to allow automated and efficient genotyping at an affordable cost. In catfish, the first SNP array with previously identified 250,113 SNPs have been developed to facilitate the analysis of quantitative traits. It has been developed by using Axiom genotyping technology which provides a flexible solution to design arrays with customizable markers from non-model organisms. Recently, the advancement of array technologies improved the performance of the Axiom genotyping arrays with expended capacities, enabling the construction of high density SNP arrays. In the first chapter of this dissertation, I will provide detailed description of a catfish 690K SNP arrays with the Axiom genotyping platform. The catfish 690K SNP array includes 690,662 unique SNPs markers which were identified from whole genome sequencing, RNA-seq, and genotyping by sequencing (GBS) data over 1,200 catfish. With the guidance of channel catfish reference genome sequence, the selected SNPs were relatively evenly distributed across the entire genome, with 0.8 kb interquartile range of intervals, and covered 99% of the genome scaffolds and 93.9% of the BAC-based physical map contigs. With enhanced marker density and power of discrimination, the catfish 690K SNP array should be a valuable tool for catfish research community and greatly improve the genetic and genomic studies. In the second chapter of this dissertation, I will describe the application of the 690K SNP array for the construction of a very high density genetic linkage map. Construction of accurate and high density genetic linkage map is fundamental for genetic and genomic studies. In the present work, I constructed a new generation of channel catfish genetic linkage map with improved marker density and resolution with four large reference families genotyped using the catfish 690K SNP array. Over 250,000 SNPs were finally placed on the linkage map, which contains, to the best of our knowledge, the highest marker density among all the aquaculture species. The total estimated genetic size of the new linkage map is 3,004 cM with a resolution of 0.1 cM for sex-averaged genetic map. The sex-specific linkage maps constructed in each sex revealed that the recombination rate is 1.4-fold larger in females than in males. After integration with the recently constructed catfish reference genome assembly, over 1,500 of the whole-genome sequencing contigs were anchored to the linkage groups, covering a physical length of 766 Mb that account for about 97.8% of the total genome assembly. Over 900 previously unmapped scaffolds were placed onto the linkage map, which greatly improves the catfish reference genome assembly. With the unprecedented coverage, it should also serve as a valuable tool for genetic analysis, especially GWAS and fine-scale QTL mapping for genes associated with economically important traits.