title: 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.
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Qifan
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, Mississippi 38776, United States of America.
authors.forename: Geoff
authors.initials: G
authors.lastname: Waldbieser
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, Mississippi 38776, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Bosworth
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Yang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Lisui
authors.initials: L
authors.lastname: Bao
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Zihao
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, United States of America.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D001483:Base Sequence; D002397:Catfishes / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D005260:Female; D005819:Genetic Markers; D016678:Genome; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012015:Reference Standards; D015203:Reproducibility of Results; D018401:Sample Size; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers