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

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.

Zeng Q ，Fu Q ，Li Y ，Waldbieser G ，Bosworth B ，Liu S ，Yang Y ，Bao L ，Yuan Z ，Li N ，Liu Z ... -  《Scientific Reports》

Linkage mapping bovine EST-based SNP.

Snelling WM ，Casas E ，Stone RT ，Keele JW ，Harhay GP ，Bennett GL ，Smith TP ... -  《BMC GENOMICS》

A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome.

Ganal MW ，Durstewitz G ，Polley A ，Bérard A ，Buckler ES ，Charcosset A ，Clarke JD ，Graner EM ，Hansen M ，Joets J ，Le Paslier MC ，McMullen MD ，Montalent P ，Rose M ，Schön CC ，Sun Q ，Walter H ，Martin OC ，Falque M ... -  《PLoS One》

Development of the catfish 250K SNP array for genome-wide association studies.

Quantitative traits, such as disease resistance, are most often controlled by a set of genes involving a complex array of regulation. The dissection of genetic basis of quantitative traits requires large numbers of genetic markers with good genome coverage. The application of next-generation sequencing technologies has allowed discovery of over eight million SNPs in catfish, but the challenge remains as to how to efficiently and economically use such SNP resources for genetic analysis. In this work, we developed a catfish 250K SNP array using Affymetrix Axiom genotyping technology. The SNPs were obtained from multiple sources including gene-associated SNPs, anonymous genomic SNPs, and inter-specific SNPs. A set of 640K high-quality SNPs obtained following specific requirements of array design were submitted. A panel of 250,113 SNPs was finalized for inclusion on the array. The performance evaluated by genotyping individuals from wild populations and backcross families suggested the good utility of the catfish 250K SNP array. This is the first high-density SNP array for catfish. The array should be a valuable resource for genome-wide association studies (GWAS), fine QTL mapping, high-density linkage map construction, haplotype analysis, and whole genome-based selection.

Liu S ，Sun L ，Li Y ，Sun F ，Jiang Y ，Zhang Y ，Zhang J ，Feng J ，Kaltenboeck L ，Kucuktas H ，Liu Z ... -  《-》

Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.

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 single-nucleotide polymorphism (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 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼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.

Li Y ，Liu S ，Qin Z ，Waldbieser G ，Wang R ，Sun L ，Bao L ，Danzmann RG ，Dunham R ，Liu Z ... -  《-》