A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check.
A consensus genetic map of tetraploid cotton was constructed using six high-density 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...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3454346?pdf=render |
| _version_ | 1818193945460473856 |
|---|---|
| author | Anna Blenda David D Fang Jean-François Rami Olivier Garsmeur Feng Luo Jean-Marc Lacape |
| author_facet | Anna Blenda David D Fang Jean-François Rami Olivier Garsmeur Feng Luo Jean-Marc Lacape |
| author_sort | Anna Blenda |
| collection | DOAJ |
| description | A consensus genetic map of tetraploid cotton was constructed using six high-density 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 (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC 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 A(T) and D(T) chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per A(T)/D(T) chromosome pair. Sequences of 4,744 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, with only a few minor possible structural rearrangements. Overall, the HDC 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. |
| first_indexed | 2024-12-12T00:54:28Z |
| format | Article |
| id | doaj.art-9b66b0b01d2a456780433a54e3eb2119 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T00:54:28Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9b66b0b01d2a456780433a54e3eb21192022-12-22T00:43:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0179e4573910.1371/journal.pone.0045739A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check.Anna BlendaDavid D FangJean-François RamiOlivier GarsmeurFeng LuoJean-Marc LacapeA consensus genetic map of tetraploid cotton was constructed using six high-density 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 (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC 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 A(T) and D(T) chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per A(T)/D(T) chromosome pair. Sequences of 4,744 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, with only a few minor possible structural rearrangements. Overall, the HDC 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.http://europepmc.org/articles/PMC3454346?pdf=render |
| spellingShingle | Anna Blenda David D Fang Jean-François Rami Olivier Garsmeur Feng Luo Jean-Marc Lacape A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS ONE |
| title | A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. |
| title_full | A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. |
| title_fullStr | A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. |
| title_full_unstemmed | A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. |
| title_short | A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. |
| title_sort | high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check |
| url | http://europepmc.org/articles/PMC3454346?pdf=render |
| work_keys_str_mv | AT annablenda ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT daviddfang ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT jeanfrancoisrami ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT oliviergarsmeur ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT fengluo ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT jeanmarclacape ahighdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT annablenda highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT daviddfang highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT jeanfrancoisrami highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT oliviergarsmeur highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT fengluo highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck AT jeanmarclacape highdensityconsensusgeneticmapoftetraploidcottonthatintegratesmultiplecomponentmapsthroughmolecularmarkerredundancycheck |