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Euphytica

, Volume 161, Issue 3, pp 361–370 | Cite as

BAC-derived SSR markers chromosome locations in cotton

  • Yufang Guo
  • Sukumar Saha
  • John Z. Yu
  • Johnie N. Jenkins
  • Russell J. Kohel
  • Brian E. Scheffler
  • David M. Stelly
Article

Abstract

Bacterial artificial chromosome (BAC) libraries with large DNA fragment inserts have rapidly become the preferred choice for physical mapping. BAC-derived microsatellite or simple sequence repeats (SSRs) markers facilitate the integration of physical maps with genetic maps. The objective of this research was to identify chromosome locations of the BAC-derived SSR markers in tetraploid cotton. A total of 192 SSR primer pairs were derived from BAC clones of an Upland cotton genetic standard line TM-1 (Gossypium hirsutum L.). Metaphor agarose gel electrophoresis results revealed 76 and 59 polymorphic markers between TM-1 and 3–79 (G. barbadense) or G. tomentosum, respectively. Using deletion analysis method, we assigned 39 markers out of the 192 primer pairs to 17 different chromosomes or chromosome arms. Among them, 19 and 17 markers were localized to A-subgenomes (chromosome 1–13) and D-subgenomes (chromosome 14–26), respectively. The subgenome status for the remaining three markers remained unclear due to their two potential chromosome locations achieved by tertiary monosomic stocks deletion analysis. Chromosomal assignment of these BAC-derived SSR markers will help in integrating physical and cotton genetic linkage maps and thus facilitate positional candidate gene cloning, comparative genome analysis, and the coordination of chromosome-based genome sequencing project in cotton.

Keywords

BAC-derived SSR Chromosome location Cotton (GossypiumAneuploid lines 

Abbreviations

BAC

Bacterial artificial chromosome

EST

Expressed sequence tag

FISH

Fluorescence in situ hybridization

QTL

Quantitative trait locus

SCAR

Sequence characterized amplified region

SSR

Simple sequence repeat

SNP

Single nucleotide polymorphisms

TMB

TM-1 BAC/BIBAC

NTN

Tertiary monosomic cytogenetic stock

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Copyright information

© GovernmentEmployee: U. S. Department of Agriculture, Agricultural Research Service 2007

Authors and Affiliations

  • Yufang Guo
    • 1
  • Sukumar Saha
    • 2
  • John Z. Yu
    • 3
  • Johnie N. Jenkins
    • 2
  • Russell J. Kohel
    • 3
  • Brian E. Scheffler
    • 4
  • David M. Stelly
    • 5
  1. 1.Department of Plant and Soil SciencesMississippi State UniversityMississippi StateUSA
  2. 2.USDA-ARS, Crop Science Research LaboratoryMississippi StateUSA
  3. 3.USDA-ARS, Crop Germplasm Research UnitCollege StationUSA
  4. 4.USDA-ARS-CGRUStonevilleUSA
  5. 5.Department of Soil and Crop SciencesTexas A&M UniversityCollege StationUSA

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