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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR ANALYSIS OF DEVELOPMENT TO IMPROVE COTTON FIBER

Location: Cotton Fiber Bioscience Research Unit

Title: A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

Authors
item Blenda, Anna -
item Fang, David
item Rami, Jean-Francois -
item Garsmeur, Olivier -
item Luo, Feng -
item Lacape, Jean-Marc -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 23, 2012
Publication Date: September 24, 2012
Citation: Blenda, A., Fang, D.D., Rami, J., Garsmeur, O., Luo, F., Lacape, J. 2012. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS One. 7(9):e45739.

Interpretive Summary: A high density genetic linkage map plays important roles in understanding genome structure of tetraploid cotton, genetic dissection of economically important traits, identifying markers associated with a trait, and cloning a gene of interest through map-based cloning. In this research, we first conducted redundancy check of all molecular markers deposited in the cotton marker database based on clone sequences. Then we constructed an ultra-dense consensus (UDC) genetic map of tetraploid cotton using six high-density component maps. With redundant markers being removed, the UDC map consists of 8,254 unique loci, originating from 6,669 non-redundant markers, and spans 4,070 cM, with an average of 2 loci per cM. The UDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes, with an average of 64 duplications per AT/DT chromosome pair. Among the 6,669 mapped markers, 4,744 had sequence information with a majority representing gene-based markers. Sequences of mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome, indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map (13 DT chromosomes), with only a few minor possible structural rearrangements. Overall, this UDC map will serve as a valuable resource for agronomic trait mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.

Technical Abstract: An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,494) could be considered as redundant with some other markers. The marker redundancy information had been crucial part of the map integration process, in which six the most informative interspecific Gossypium hirsutum x G. barbadense genetic maps were used for assembling an ultra-dense consensus (UDC) map for tetraploid cotton. With redundant markers being removed, the UDC map could be constructed thanks to the sufficient number of collinear markers in common between the component maps. The UDC map consists of 8,254 unique loci, originating from 6,669 non-redundant markers, and spans 4,070 cM, with an average of 2 loci per cM. The UDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Among the 6,669 mapped markers, 4,744 had sequence information with a majority representing gene-based markers (EST-SSRs, STS-RFLPs, and EST-derived SNPs). Sequences of mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome, indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map (13 DT chromosomes), with only a few minor possible structural rearrangements. Overall, the UDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.

Last Modified: 9/22/2014