DEVELOPMENT OF PCR-BASED MARKERS FROM FIBER ESTS AND BAC-END SEQUENCES FOR THE CONSTRUCTION OF A CONSENSUS COTTON GENETIC MAP.

Authors: Ulloa, Mauricio; Frelichowski, James - Jim; PALMER, MICHAEL - CLEMSON UNIV, CLEMSON, SC; PARK, YOUNG-HOON - SAKATA SEED AMERICA INC.; ALABADY, MAGDY - UNIV. OF CA., DAVIS, CA.; WILKINS, THEA - UNIV. OF CA., DAVIS, CA.; Yu, John; Kohel, Russell; CANTRELL, ROY - COTTON INC., CARY, NC.; MAIN, DORRIE - CLEMSON UNIV, CLEMSON, SC; TOMKINS, JEFFREY - CLEMSON UNIV, CLEMSON, SC; STELLY, DAVID - TEXAS A&M, COLLEGE STN; VANDEYNZE, ALLEN - UNIV. OF CA., DAVIS, CA

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/14/2006
Publication Date: 1/14/2006
Citation: Ulloa, M., Frelichowski, J.E., Palmer, M., Park, Y.h., Alabady, M.S., Wilkins, T.A., Yu, J., Kohel, R., Cantrell, R., Main, D., Tomkins, J.P., Stelly, D., VanDeynze, A. 2006. Development of PCR-based markers from fiber ESTs and BAC-end sequences for the construction of a consensus cotton genetic map. Plant and Animal Genome XIV Conference Proceedings. p. 42.

Interpretive Summary:

Technical Abstract: A new set of molecular markers known as microsatellites or SSRs were developed from cotton fiber genes (EST) and genomic DNA inserted in bacteria artificial chromosomes (BAC-end sequences). Cotton genomics is in its infancy in that a high density PCR-based molecular map to facilitate marker-assisted breeding in the public domain is still lacking, despite ongoing efforts by the cotton community. In collaboration with U.C. Davis, Clemson Univ, and partial financial support from Cotton Incorporated, we tested a total of 1,232 EST-derived microsatellite (MUSS) and (MUCS) markers, which 1,019 (83%) of the DNA markers successfully amplified PCR products from a survey panel of six Gossypium species, of which 202 (19.8%) were polymorphic between Upland (Gossypium hirsutum) and Pima (G. barbadense) cottons. In addition, from a total of 2603 BAC-end sequences, 1316 PCR primer pairs (MUSB markers) were designed to flank SSR sequences and 1164 (88%) pairs successfully amplified DNA from three species, and 365 markers (21%) were polymorphic between cv. TM-1 (Upland) and acc. 3-79 (Pima), using electrophoretic separation on an agarose gel system. A consensus genetic map is under development which will include some of the new MUSB (125), MUCS (43), and MUSS (66) markers, in addition, public markers such as BNL, JESPR, and CIR. These markers also have been assigned to twenty-three of 26 cotton chromosomes from hypoanueploid deficiency analysis and previously mapped SSR markers. The placement of BAC-end MUSB markers into the genetic map will contribute to the development of a consensus map and enable the physical alignment of the cotton genome.