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United States Department of Agriculture

Agricultural Research Service

Title: Toward Development of An Integrated Physical/genetic Map of the Cotton Genome: Large-Scale Generation of Ssr Markers from a Bac Library of the Cotton Genetic Standard Line Tm-1

item Kohel, Russell
item Yu, John

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 17, 2002
Publication Date: January 17, 2002
Citation: Dong, J., Kohel, R.J., Zhang, H., Yu, J. 2002. Toward development of an integrated physical/genetic map of the cotton genome: Large-scale generation of SSR markers from a BAC library of the cotton genetic standard line TM-1 [abstract]. Plant, Animal, and Microbe Genomes X Conference. Paper No. P220.

Technical Abstract: All existing cotton SSRs were produced by sequencing small-insert genomic DNA clones enriched for SSRs. We present here the large-scale generation of SSR markers from a large-insert BAC library of the cotton genome. The generation of SSR markers from large-insert BAC libraries would provide numerous advantages over that from small-insert DNA libraries for genome research. The large-insert BACs of SSR markers will provide bridges to integrate BAC-based physical maps with genetic maps and enable generation of polymorphic DNA markers of any kinds for a target region for molecular breeding. The genetic mapping of the BAC-derived SSR markers will streamline high-resolution mapping and positional cloning of QTLs and genes of interest. With recently developed three large-insert BAC libraries (about 160,000 clones and 10x AD genome equivalents) from the Upland cotton genetic standard TM-1, we are generating a large number of SSR markers from the TM-1 HindIII BAC library. Three hundreds seventy-nine positive subclones were produced from 384 SSR-containing BACs, and sequenced. Each of these subclones was found to contain one or more of the 4 SSR oligo sequences (CA, GA, TA, and GAA) that were used as probes. Sequence analysis by BLAST search showed that only 49 of the 379 subclone sequences were duplicated with the existing cotton SSR database, indicating that the cotton genome is abundant in SSR loci. Primer pairs were designed from the unique flanking sequences of the new SSR loci and used to estimate the polymorphism information content (PIC) among a panel of diverse Upland cottons.

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