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| Map Set Name: |
F2: G. hirsutum race "Palmeri" x G. barbadense Acc. "K101" |
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| Abbreviated Name: |
cotton_GhpalmerixK101 |
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| Accession ID: |
1 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 January, 2004 |
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Description:
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We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome. |
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| Map Set Name: |
F2: Acala-44 x Pima S-7 2004 |
[ Show Only This Set ] |
| Abbreviated Name: |
AP-F2 |
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| Accession ID: |
34 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
02 January, 2004 |
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Description:
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Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton (Gossypium hirsutum L.) and Pima or Egyptian cotton (G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F2 population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits. |
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| Map Set Name: |
BC1: ((Guazuncho2 x VH8-4602) x Guazuncho2 |
[ Show Only This Set ] |
| Abbreviated Name: |
cotton_Guazuncho2xVH8-BC1 |
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| Accession ID: |
2 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 June, 2004 |
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Description:
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Microsatellite [simple-sequence repeat (SSR)] markers were developed and positioned on the genetic map of tetraploid cotton. Three hundred and ninety-two unique microsatellite sequences, all but two containing a (CA/GT) repeat, were isolated, and the deduced primers were used to screen for polymorphism between the Gossypium hirsutum and G. barbadense parents of the mapping population analyzed in our laboratory. The observed rate of polymorphism was 56%. The 204 polymorphic SSRs revealed 261 segregating bands, which ultimately gave rise to 233 mapped loci. The updated status of our genetic map is now of 1,160 loci and 5,519 cM, with an average distance between two loci of 4.8 cM. The presence of a total of 466 microsatellite loci, with an average distance of 12 cM between two SSR loci, now provides wide coverage of the genome of tetraploid cotton and thus represents a powerful means for the production of a consensus map and for the effective tracking of QTLs.
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| Map Set Name: |
BC2: ((Guazuncho2 x VH8-4602) x Guazuncho2) |
[ Show Only This Set ] |
| Abbreviated Name: |
cotton_Guazuncho2xVH8-BC2 |
[ Download Map Set Data ] |
| Accession ID: |
8 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 January, 2005 |
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Description:
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Cotton fiber properties are essential predictors of yarn performance. The suite of fiber quality traits that collectively affect the utility of the fiber for the textile industry include the length, the strength, the fineness and the color. These properties have been shown to be moderately to highly heritable. In an attempt to overcome the limitations of conventional breeding we undertook a marker-assisted selection program aimed at introgressing fiber quality QTLs from Gossypium barbadense L. into G. hirsutum L. We describe the QTL analysis of 11 fiber properties measured on three phenotypic data sets. The three populations studied were the 1st (BC1) and 2nd (BC2 and BC2S1) backcross generations derived from the cross between 'Guazuncho 2', G. hirsutum, and 'VH8', G. barbadense. Collectively we detected 80 QTLs, of which 50 surpassed the permutation-based LOD thresholds (3.2-5.7). The most economically important traits, length (two correlated properties), strength, fineness (four properties), and color (two properties) were influenced by 15, 12, 21, and 16 QTLs, respectively, that could be detected in one or more populations. As expected, for the majority of QTLs, the favorable alleles came from the G. barbadense parent. Altogether one third (26) of the QTLs confirmed the map position and phenotypic effect of QTLs reported in the literature also detected in interspecific G. hirsutum x G. barbadense populations. Cases of colocalization of QTLs for different traits were more frequent than isolated positioning. Taking these QTL-rich chromosomal regions into consideration, 19 regions on 15 different chromosomes, were identified as target regions for the marker-assisted introgression strategy. |
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| Map Set Name: |
F2: Yumian-1 x T586 2005 |
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| Abbreviated Name: |
YT-F2 |
[ Download Map Set Data ] |
| Accession ID: |
33 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
26 January, 2005 |
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Description:
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A genetic linkage map with 70 loci (55 SSR, 12 AFLP and 3 morphological loci) was constructed using 117 F2 plants obtained from a cross between two upland cotton cultivars Yumian 1 and T586, which have relatively high levels of DNA marker polymorphism and differ remarkably in fiber-related traits. The linkage map comprised of 20 linkage groups, covering 525 cM with an average distance of 7.5 cM between two markers, or approximately 11.8% of the recombination length of the cotton genome. The present genetic linkage map was used to identify and map the quantitative trait loci (QTLs) affecting lint percentage and fiber quality traits in 117 F2:3 family lines. Sixteen QTLs for lint percentage and fiber quality traits were identified in six linkage groups by multiple interval mapping: four QTLs for lint percentage, two QTLs for fiber 2.5% span length, three QTLs for fiber length uniformity, three QTLs for fiber strength, two QTLs for fiber elongation and two QTLs for micronaire reading. The QTL controlling fiber-related traits were mainly additive, and meanwhile including dominant and overdominant. Several QTLs affecting different fiber-related traits were detected within the same chromosome region, suggesting that genes controlling fiber traits may be linked or the result of pleiotropy. |
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| Map Set Name: |
F2: G. hirsutum 'Handan208' x G. barbadense 'Pima90' 2005 |
[ Show Only This Set ] |
| Abbreviated Name: |
Handan208 x Pima90 (2005) |
[ Download Map Set Data ] |
| Accession ID: |
10 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 April, 2005 |
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Description:
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Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the worlds cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence-related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty-nine F2 progeny from the interspecific cross of Handan208 x Pima90 were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty-eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A χ2 test for significance of deviations from the expected ratio (1 : 2 : 1 or 3 : 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.1828.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker-assisted selection. |
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| Map Set Name: |
DH: Vgs x (TM-1 x Hai-7124) 2005 |
[ Show Only This Set ] |
| Abbreviated Name: |
VTH-DHv05 |
[ Download Map Set Data ] |
| Accession ID: |
23 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
03 June, 2005 |
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Description:
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Simple sequence repeat (SSR) genetic maps have been separately constructed based on doubled haploid (DH) and (or) haploid and BC1 populations from the same cross between Gossypium hirsutum L. 'TM-1' and Gossypium barbadense L. 'Hai7124'. The BC1 population was produced by pollinating individual plants of the 'TM-1' x 'Hai7124' F1 with 'TM-1', whereas the DH and (or) haploid population developed from the offspring of Vsg x ('TM-1' x 'Hai7124'). Vsg is a virescently marked semigamy line of Gossypium barbadense L. Pima. The BC1 map included 34 linkage groups with an average distance between markers of 9.80 cM (Kosambi, K) and covered 4331.2 cM (K) or approximately 78.7% of the tetraploid cotton genome constructed using 440 SSR and 2 morphological marker genes. Among them, 26 were assigned to 20 chromosomes, 7 to A or D subgenomes, and 1 was unassigned. The haploid map comprised 444 SSR markers mapped to 40 linkage groups with an average distance of 7.35 cM (K) between markers, covering 3262.9 cM (K) or approximately 60.0% of the tetraploid genome. Twenty-nine linkage groups were assigned to all 19 identified chromosomes, 10 to A or D subgenomes, and 1 was unassigned. Fairly good collinearity of marker order was observed along most of the chromosomes or linkage groups. Significant differences in recombination between maps was observed at the chromosomal and genomic level and possible reasons were discussed. Map comparison and combined data provided an essential basis for further mapping of interested genes and QTLs and for studies of diversity, population structure, and phylogeny in Gossypium species. |
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| Map Set Name: |
F2: TM-1 x WT-936 2005 |
[ Show Only This Set ] |
| Abbreviated Name: |
TW-F2 |
[ Download Map Set Data ] |
| Accession ID: |
32 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
04 August, 2005 |
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Description:
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The existence of five tetraploid species that derive from a common polyploidization event about 1 million years ago makes Gossypium (cotton) an attractive genus in which to study polyploid evolution and offers opportunities for crop improvement through introgression. To date, only crosses (HB) between the cultivated tetraploid cottons Gossypium hirsutum and G. barbadense have been genetically mapped. Genetic analysis of a cross (HT) between G. hirsutum and the Hawaiian endemic G. tomentosum is reported here. Overall, chromosomal lengths are closely correlated between the HB and HT maps, although there is generally more recombination in HT, consistent with a closer relationship between the two species. Interspecific differences in local recombination rates are observed, perhaps involving a number of possible factors. Our data corroborate cytogenetic evidence that chromosome arm translocations have not played a role in the divergence of polyploid cottons. However, one terminal inversion on chromosome (chr.) 3 does appear to differentiate G. tomentosum from G. barbadense; a few other apparent differences in marker order fall near gaps in the HT map and/or lack the suppression of recombination expected of inversions, and thus remain uncertain. Genetic analysis of a discrete trait that is characteristic of G. tomentosum, nectarilessness, mapped not to the classically reported location on chr. 12 but to the homoeologous location on chr. 26. We propose some hypotheses for further study to explore this incongruity. Preliminary quantitative trait locus (QTL) analysis of this small population, albeit with a high probability of false negatives, suggests a different genetic control of leaf morphology in HT than in HB, which also warrants further investigation. |
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| Map Set Name: |
RIL_2005: TM-1 (G. hirsutum (AD1)) x 3-79 (G. barbadense (AD2)) |
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| Abbreviated Name: |
MUSS_MUCS_TM1x3-79_RIL_2005 |
[ Download Map Set Data ] |
| Accession ID: |
3 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 September, 2005 |
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Description:
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A new set of microsatellites, or simple (SSR) and complex (CSR) markers with di-, tri-, tetra-, and pentanucleotide sequence repeats were developed from approximately 14,000 consensus sequences of the Gossypium arboreum L. fiber data base EST (http://cfgc.ucdavis.edu/ssr). Microsatellites were developed using 1,557 EST-containing SSRs (=10bp) and 5,794 EST-containing CSRs (=12bp) sequences. From a total of 1,232 EST-derived SSR (MUSS) and CSR (MUCS) primer-pairs, 1,019 (83%) of the DNA markers successfully amplified PCR products from a survey panel of six Gossypium species, of which 202 (19.8%) were polymorphic between the species G. hirsutum and G. barbadense using electrophoretic separation on an agarose gel system. Genetic map position and chromosomal location on the tetraploid cotton were assigned for some polymorphic markers. These fiber loci were mapped to 19 chromosomes and 11 linkage groups. New microsatellite loci were designated MUSS and MUCS: M for microsatellite, U last name of principal investigator, SS for simple sequences, and CS for complex sequence repeats. The information provided here includes: description, primers sequence, map and chromosomal location, and polymorphic data for the 1,232 MUSS and MUCS markers from the panel of six Gossypium species. |
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Contact:
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Mauricio Ulloa |
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| Map Set Name: |
BC1: (G.hirsutum "TM-1" x G.barbadense "Hai7124") x "TM-1" 2006 |
[ Show Only This Set ] |
| Abbreviated Name: |
[(TM-1 x Hai7124) x TM-1] 2006 |
[ Download Map Set Data ] |
| Accession ID: |
7 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 February, 2006 |
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Description:
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In order to construct a saturated genetic map
and facilitate marker-assisted selection (MAS) breeding, it is necessary to enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants (Kantety et al., Plant Mol Biol 48:501510, 2002).Many ESTs are publicly available now
and represent a good tool in developing EST-SSRs. From 13,505 ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by dinucleotides
(30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC(4.5%). One hundred and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross [(TM-17Hai7124)TM-1]. EST-SSR markers were distributed over 20 chromosomes and 6 linkage groups in the map. These EST-SSR markers can be used in genetic mapping, identification of quantitative trait loci (QTLs), and comparative genomics studies of cotton. |
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| Map Set Name: |
RIL_2006: TM-1(G. hirsutum (AD1)) x 3-79 (G. barbadense (AD2)) |
[ Show Only This Set ] |
| Abbreviated Name: |
MUSB_TM1 x 3-79_RIL_2006 |
[ Download Map Set Data ] |
| Accession ID: |
9 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
25 February, 2006 |
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Description:
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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. |
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Contact:
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Mauricio Ulloa |
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| Cross-references: |
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| Map Set Name: |
F2: G. hirsutum "Handan208" x G. barbadense "Pima90" 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
Handan208 x Pima90 (2007) |
[ Download Map Set Data ] |
| Accession ID: |
6 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 January, 2007 |
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Description:
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A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful for a marker-assisted breeding program. Four kinds of markers - simple sequence repeats (SSRs), sequence-related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP) - were used to assay an F2 population from a cross between Handan208 (Gossypium hirsutum) and Pima (Gossypium barbadense). Sixty-nine F2 plants were used for map construction using 834 SSRs, 437 SRAPs, 107 RAPDs, and 16 REMAPs. Linkage analysis revealed that 1,029 loci could be mapped to 26 linkage groups that extended for 5,472.3 cM, with an average distance between 2 loci of 5.32 cM. The corresponding 69 F2:3 families were grown, arranged in two replicates, and scored for eight phenotypes. Quantitative trait
loci (QTL) analysis was performed by means of composite interval mapping using WinQtlCart ver
2.0. A total of 52 distinct QTLs were detected: 4 QTLs for lint index, 8 for seed index, 11 for lint yield, 4 for seed cotton yield, 9 for number of seed per boll, 3 for fiber strength, 5 for fiber length, and 8 for micronaire value. The present map and QTL analysis may provide a useful tool for breeders to transfer desirable traits from G. barbadense to the mainly cultivated species, G. hirsutum.
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| Cross-references: |
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| Map Set Name: |
F2: G. hirsutum race "Palmeri" x G. barbadense Acc. "K101" 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
PK-F2 |
[ Download Map Set Data ] |
| Accession ID: |
31 |
[ View Map Set In Matrix ] |
| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
01 January, 2007 |
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| Maps: |
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| Map Set Name: |
BC1: [(G. hirsutum TM-1 x G. barbadense Hai7124) x TM-1] 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
[(TM-1 x Hai7124) x TM-1] 2007 |
[ Download Map Set Data ] |
| Accession ID: |
4 |
[ View Map Set In Matrix ] |
| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
03 April, 2007 |
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Description:
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In order to construct a saturated genetic map and facilitate marker-assisted selection (MAS) breeding, it is necessary to enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants. Many ESTs are publicly available now and represent a good tool in developing EST-SSRs. From 13,505 ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by dinucleotides (30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC (4.5%). One hundred and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross [(TM-1xHai7124)The mapping of functional genes plays an important role in studies of
genome structure, function, and evolution, as well as allowing gene cloning and
marker-assisted selection to improve agriculturally-important traits. Simple sequence
repeats (SSRs) developed from expressed sequence tags (ESTs), EST-SSR (eSSR),
can be employed as putative functional marker loci to easily tag corresponding
functional genes. In this paper, 2,218 eSSRs, 1,554 from G. raimondii-derived and
754 from G. hirsutum-derived ESTs, were developed and used to screen
polymorphisms in order to enhance our backbone genetic map in allotetraploid cotton.
Out of 1,554 G. raimondii-derived eSSRs, 744 eSSRs were able to successfully
amplify polymorphisms between our two mapping parents, TM-1 and Hai7124,
presenting a polymorphic rate of 47.9%. However, an only 23.9% (159/754)
polymorphic rate was produced from G. hirsutum-derived eSSRs. No relationship was
observed between the level of polymorphism, motif type, and tissue origin, but the
polymorphism appeared to be correlated with repeat type. After integrating these new
eSSRs, our enhanced genetic map consists of 1,790 loci in 26 linkage groups and
covers 3425.8 cM with an average inter-marker distance of 1.91 cM. This
microsatellite-based, gene-rich linkage map contains 71.96% functional marker loci,
of which 87.11% are eSSR loci. There were 132 duplicated loci bridging 13
homeologous At/Dt chromosome pairs. Two reciprocal translocations after
polyploidization between A2 and A3, and between A4 and A5 chromosomes were
further confirmed. A functional analysis of 975 ESTs producing 1,122 eSSR loci
tagged in the map revealed that 60% had clear BLASTX hits (<1e-10) to the Uniprot
database and that 475 were mainly associated with genes belonging to the three major
gene ontology categories of biological-process, cellular-component, and
molecular-function; many of the ESTs were associated with two or more category
3
functions. The results presented here will provide new insights for future
investigations of functional and evolutionary genomics, especially those associated
with cotton fiber improvement. |
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| Map Set Name: |
RIL: Zhongmiansuo-12 x 8891 2007 |
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| Abbreviated Name: |
Z8-RIL |
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| Accession ID: |
36 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
18 April, 2007 |
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Description:
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A population of 180 recombinant inbred lines (RILs) was developed by single seed descended from the cross of high yield Upland cotton (Gossypium hirsutum L.) varieties Zhongmiansuo12 (ZMS12) and 8891, the two parents of Xiangzamian2 (XZM2). A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment (separate analysis) and a set of data from means of the three environments (joint analysis). A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton. |
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| Map Set Name: |
F2: G. hirsutum "CRI36" x G. barbadense "Hai7124" |
[ Show Only This Set ] |
| Abbreviated Name: |
CIR36 x Hai7124 |
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| Accession ID: |
5 |
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| Species: |
Gossypium (cotton) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 May, 2007 |
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Description:
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A high-density linkage map was constructed for an F2 population derived from an interspecific cross of cultivated
allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the
interspecific cross of CRI 36 W Hai 7124 were genotyped at 1 252 polymorphic loci including a novel marker system,
target region amplification polymorphism (TRAP). The map consists of 1 097 markers, including 697 simple sequence
repeats (SSRs), 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length
polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1
cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes
were identified in tetraploid cotton. This map will provide an essential resource for high resolution mapping of
quantitative trait loci and molecular breeding in cotton. |
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| Map Set Name: |
RIL: 7235 x TM-1 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
7T-RIL |
[ Download Map Set Data ] |
| Accession ID: |
35 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
03 June, 2007 |
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Description:
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The improvement of cotton fiber quality has become more important because of changes in spinning technology. Stable quantitative trait loci (QTLs) for fiber quality will enable molecular marker-assisted selection to improve fiber quality of future cotton cultivars. A simple sequence repeat (SSR) genetic linkage map consisting of 156 loci covering 1,024.4 cM was constructed using a series of recombinant inbred lines (RIL) developed from an F2 population of an Upland cotton (Gossypium hirsutum L.) cross 7235 x TM-1. Phenotypic data were collected at Nanjing and Guanyun County in 2002 and 2003 for 5 fiber quality and 6 yield traits. We found 25 major QTLs (LOD >= 3.0) and 28 putative QTLs (2.0 < LOD < 3.0) for fiber quality and yield components in two or four environments independently. Among the 25 QTLs with LOD >= 3, we found 4 QTLs with large effects on fiber quality and 7 QTLs with large effects on yield components. The most important chromosome D8 in the present study was densely populated with markers and QTLs, in which 36 SSR loci within a chromosomal region of 72.7 cM and 9 QTLs for 8 traits were detected. |
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| Map Set Name: |
F2: Deltapine-61 x Texas-701 2007 |
[ Show Only This Set ] |
| Abbreviated Name: |
DT-F2 |
[ Download Map Set Data ] |
| Accession ID: |
29 |
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| Species: |
Gossypium (cotton) |
[ View Species Info ] |
| Map Type: |
Genetic |
[ View Map Type Info ] |
| Map Units: |
cM |
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| Published On: |
14 November, 2007 |
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Description:
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Primitive cottons (Gossypium spp.) represent resources for genetic improvement. Most primitive accessions are photoperiod sensitive; they do not flower under the long days of the U.S. cotton belt. Molecular markers were used to locate quantitative trait loci (QTLs) for node of first fruiting branch (NFB), a trait closely related to flowering time in cotton. An F2 population consisted of 251 plants from the cross of a day neutral cultivar Deltapine 61, and a photoperiod sensitive accession Texas 701, were used in this study. Segregation in the population revealed the complex characteristics of NFB. Interval mapping and multiple QTL mapping were used to determine QTLs contributing to NFB. Three significant QTLs were mapped to chromosome 16, 21, and 25; two suggestive QTLs were mapped to chromosome 15 and 16. Four markers associated with these QTLs accounted for 33% of the variation in NFB by single and multiple-marker regression analyses. Two pairs of epistasis interaction between markers were detected. Our results suggested that at least three chromosomes contain factors associated with flowering time for this population with epistasis interactions between chromosomes. This research represent the first flowering time QTL mapping in cotton. Makers associated with flowering time may have the potential to facilitate day neutral conversion of accessions. |
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