title: BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.
abstract: A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.
authors: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas 77843.
authors: Amanda M
authors: http://orcid.org/0000-0001-9670-9433
authors: AM
authors: Hulse-Kemp
authors: Seed Biotechnology Center, University of California, Davis, California 95616.
authors: Hamid
authors: http://orcid.org/0000-0002-2094-2367
authors: H
authors: Ashrafi
authors: Seed Biotechnology Center, University of California, Davis, California 95616.
authors: Kevin
authors: http://orcid.org/0000-0002-3468-4119
authors: K
authors: Stoffel
authors: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843.
authors: Xiuting
authors: http://orcid.org/0000-0002-8574-4708
authors: X
authors: Zheng
authors: Clemson University Genomics Institute, Clemson University, Clemson, South Carolina 29634.
authors: Christopher A
authors: http://orcid.org/0000-0002-2780-4274
authors: CA
authors: Saski
authors: USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi 38766.
authors: Brian E
authors: http://orcid.org/0000-0003-1968-8952
authors: BE
authors: Scheffler
authors: USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.
authors: David D
authors: http://orcid.org/0000-0003-0036-5459
authors: DD
authors: Fang
authors: Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712.
authors: Z Jeffrey
authors: ZJ
authors: Chen
authors: Seed Biotechnology Center, University of California, Davis, California 95616.
authors: Allen
authors: http://orcid.org/0000-0002-2093-0577
authors: A
authors: Van Deynze
authors: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas 77843 stelly@tamu.edu.
authors: David M
authors: DM
authors: Stelly
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D016000:Cluster Analysis; D003198:Computer Simulation; D020451:Contig Mapping; D057225:Data Mining; D004171:Diploidy; D008040:Genetic Linkage; D056426:Genetic Loci; D005819:Genetic Markers; D016680:Genome, Bacterial; D003368:Gossypium / Q000235:genetics*; D006579:Heterozygote; D006720:Homozygote; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011123:Polyploidy; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D005819:Genetic Markers
keywords: BAC-derived SNPs; SNP genotyping; cotton genomics; intraspecific; resequencing