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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS Title: A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome

Authors
item Yu, John
item Kohel, Russell
item Fang, David
item Cho, Jaemin
item Van Deynze, Allen -
item Ulloa, Mauricio
item Hoffman, Steven -
item Pepper, Alan -
item Stelly, David -
item Jenkins, Johnie
item Saha, Sukumar
item Kumpatla, Siva -
item Shah, Manali -
item Hugie, William -
item Percy, Richard

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 4, 2011
Publication Date: January 1, 2012
Citation: Yu, J., Kohel, R.J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.M., Jenkins, J.N., Saha, S., Kumpatla, S.P., Shah, M.R., Hugie, W.V., Percy, R.G. 2012. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. Genes, Genomes, Genetics. 2:43-58.

Interpretive Summary: The contemporary cotton genome has 26 chromosomes that belong to A and D subgenomes. Mapping of portable DNA markers such as simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers to the 26 cotton chromosomes provides an important foundation for investigation of the genome complexity and other basic scientific studies. Using 186 recombinant inbred progeny of an interspecific cross between the two cotton genetic standards (acc. TM-1 and 3-79), 2,072 loci (1,825 SSRs and 247 SNPs) were mapped to the 26 chromosomes, with the total genome coverage of 3,380 centiMorgan (cM), at an average interval of 1.63 cM per locus. These DNA markers were developed from diverse sources including genomic and complementary DNA templates. Two sets of SSR markers were derived from the bacterial artificial chromosome (BAC) clones of Upland cottons, which facilitates the integration of genetic and physical maps of the cotton genome. The genetic mapping of 247 SNP markers along with various SSR markers is the first major effort that helps detect structural and sequence variation among the cotton chromosomes. The research confirms two major chromosomal exchanges and several DNA duplications among and within the cotton chromosomes. Such cotton genome maps with portable DNA markers provide useful resources for germplasm characterization, gene discovery for molecular breeding, and the eventual assembly of finished genome sequence for cottons.

Technical Abstract: Cotton genome complexity was investigated with a saturated molecular genetic map that combined several sets of microsatellites or simple sequence repeats (SSR) and the first major public set of single nucleotide polymorphism (SNP) markers in cotton genomes (Gossypium spp.), and that was constructed on the basis of 186 recombinant inbred lines (RILs) derived from an interspecific cross between the genetic standards of G. hirsutum (acc. TM-1) and G. barbadense (acc. 3-79). This map comprised of 2,072 loci (1,825 SSRs and 247 SNPs), covering 3,380 cM on the 26 cotton chromosomes. Among the SSR markers, MUSB and TMB were developed from bacterial artificial chromosome (BAC) clones of Upland cottons Acala Maxxa and TM-1, respectively, facilitating integration of genetic and physical maps of cotton. Mapping of 247 SNP markers with SSR markers shed light to structural and sequence variation among the cotton chromosomes (chr.). The cotton genome produced equivalent recombination frequencies in its two subgenomes (A and D), with 1,138 loci (54.9%) mapped on 13 A-subgenome chromosomes at 1,726.8 cM (51.1%) and 934 loci (45.1%) on 13 D-subgenome chromosomes at 1,653.1 cM (48.9%). It was revealed that the genetically and physically smallest homeologous pair of chromosomes was A04 (chr. 04) and D04 (chr. 22), and the largest homeologous pair was A05 (chr. 05) and D05 (chr. 19). Mapping analysis also confirmed the presence of two reciprocal translocations (between chromosomes A02 and A03; and between A04 and A05). A possible breakpoint between the A02 and A03 was inferred by TMB1025, a TM-1 BAC derived SSR marker. The map provides new insights into the cotton genome complexity, and it represents an important genomic foundation for germplasm characterization, gene discovery, and the eventual assembly of finished genome sequence for cotton.

Last Modified: 10/20/2014
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