Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends.

Authors: Frelichowski, James - Jim; PALMER, MICHAEL - CLEMSON UNIV, CLEMSON, SC; MAIN, DORRIE - CLEMSON UNIV, CLEMSON, SC; TOMKINS, JEFFREY - CLEMSON UNIV, CLEMSON, SC; CANTRELL, ROY - COTTON INC., CARY, NC; STELLY, DAVID - TEXAS A&M, COLLEGE STN,TX; Yu, John; Kohel, Russell; Ulloa, Mauricio

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/26/2005
Publication Date: 2/25/2006
Citation: Frelichowski, J.E., Palmer, M.B., Main, D., Tomkins, J.P., Cantrell, R.G., Stelly, D.M., Yu, J., Kohel, R.J., Ulloa, M. 2006. Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Mol. Genet. Genom. 275:479-491.

Interpretive Summary: Genetic improvement of the fiber quality and yield of cultivated cotton is essential to maintain the marketability and profitability of cotton as a textile crop. Genetic mapping of the cotton genomes and molecular identification of genes will assist in variety improvement. Toward this goal, a genetic map was being developed with a new set of molecular markers from DNA Gossypium hirsutum Acala cv Maxxa. [Markers are unique segments of DNA that can help identify where specific genes are located]. Assignment of these markers to specific chromosomes is essential so the genes can be followed during the breeding process. The genetic map includes a total of 407 DNA marker fragments, covering approximately 45% of the cotton genome. All markers were assigned to twenty-three of 26 cotton chromosomes. Limited analysis suggested that markers on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. These data are useful to scientists involved in cotton breeding because most of these markers provide information about fiber and other functional genes. The placement of markers into the genetic map will contribute to the development of a more complete map and enable the physical alignment of the cotton chromosomes. This will improve the assessment of fine mapping for a particular region that possibly affects fiber, and/or resistance to pests.

Technical Abstract: Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2603 new BAC-end genomic sequences from Gossypium hirsutum Acala ‘Maxxa’, 1316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat (SSR) motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A03/D02 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton.