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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS

Location: Crop Germplasm Research

Title: Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources

Authors
item Hulse, Amanda -
item Hoegenauer, Kevin -
item Wang, Fei -
item Stelly, David -
item Ashrafi, Hamid -
item Van Deynze, Allen -
item Zhang, Hongbin -
item Saski, Christopher -
item Patterson, Andrew -
item Schmutz, Jeremy -
item Chen, Z. Jeffrey -
item Udall, Joshua -
item Yu, John
item Jones, Don -

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Abstract Only
Publication Acceptance Date: September 1, 2012
Publication Date: N/A

Technical Abstract: Recent efforts in Gossypium SNP development have produced thousands of putative SNPs for G. barbadense, G. mustelinum, and G. tomentosum relative to G. hirsutum. Here we report on current efforts to localize putative SNPs using physical mapping resources. Recent advances in physical mapping resources in cotton have generated a genomic sequence of diploid extant D5-genome relative Gossypium raimondii, BAC and BIBAC physical maps with end sequences, interspecific F1 cytogenetic aneuploids, and populations of whole genome radiation hybrids. SNP sequences were aligned to the D5-genome to separate the D-subgenome sequences from the A-subgenome sequences and produce a tentative order for D-subgenome loci. Using the D5-genome based physical alignment as a guide, SNPs were grouped by relative position on chromosomes. Subsets of SNPs were tested with Kbioscience KASPar assay from chromosomes which were represented by cytogenetic aneuploid stocks. Putative SNPs that were amenable to KASPar assays were used to genotype the whole genome radiation hybrid population. BAC and BIBAC end sequences were blasted with putative SNP sequences to determine which SNPs were represented on the BAC and BIBAC physical maps. A random subset of BAC-associated SNPs was also tested using KASPar assays. A finalized AD-genome SNP localization resource will be beneficial for high density physical and linkage mapping for assisting AD-genome sequence generation as well as fine mapping traits of interest, such as disease and fiber traits, and marker assisted selection (MAS).

Last Modified: 7/28/2014
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