Original Paper

Molecular Genetics and Genomics

, Volume 275, Issue 5, pp 479-491

First online:

Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

  • James E. FrelichowskiJrAffiliated withUSDA-ARS, W.I.C.S. Res. Unit, Cotton Enhancement Program
  • , Michael B. PalmerAffiliated withDepartment of Genetics and Biochemistry, Clemson University
  • , Dorrie MainAffiliated withDepartment of Genetics and Biochemistry, Clemson University
  • , Jeffrey P. TomkinsAffiliated withDepartment of Genetics and Biochemistry, Clemson University
  • , Roy G. CantrellAffiliated withCotton Incorporated
  • , David M. StellyAffiliated withTexas A&M University
  • , John YuAffiliated withUSDA-ARS
  • , Russell J. KohelAffiliated withUSDA-ARS
  • , Mauricio UlloaAffiliated withUSDA-ARS, W.I.C.S. Res. Unit, Cotton Enhancement Program Email author 

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Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala ‘Maxxa’, 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat 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 2,126.3 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 A02/D03 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.


Simple sequence repeat (SSR) Bacterial artificial chromosome (BAC) BAC-end sequencing Genetic mapping Quantitative trait loci (QTL) Fine mapping Molecular tagging