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| Map Set Name: |
T. cacao - Pugh (2004) |
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| Abbreviated Name: |
Pugh (2004) |
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| Accession ID: |
pugh |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
04 February, 2004 |
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Description:
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A linkage map of cacao based on codominant
markers has been constructed by integrating 201 new
simple sequence repeats (SSR) developed in this study
with a number of isoenzymes, restriction fragment length
polymorphisms (RFLP), microsatellite markers and resistance
and defence gene analogs (Rgenes-RFLP) previously
mapped in cacao. A genomic library enriched for
(GA)n and (CA)n was constructed, and 201 new microsatellite
loci were mapped on 135 individuals from the
same mapping population used to establish the first
reference maps. This progeny resulted from a cross
between two heterozygous cacao clones: an Upper-Amazon
Forastero (UPA 402) and a Trinitario (UF 676). The
new map contains 465 markers (268 SSRs, 176 RFLPs,
five isoenzymes and 16 Rgenes-RFLP) arranged in ten
linkage groups corresponding to the haploid chromosome
number of cacao. Its length is 782.8 cM, with an average
interval distance between markers of 1.7 cM. The new
microsatellite markers were distributed throughout all
linkage groups of the map, but their distribution was not
random. The length of the map established with only
SSRs was 769.6 cM, representing 94.8% of the total map.
The current level of genome coverage is approximately
one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across
different mapping populations and will allow the identification
and comparison of the most important regions
involved in the variation of the traits of interest and the
development of marker-assisted selection strategies. |
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Reference:
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Pugh et al (2004) A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite marker. Theor Appl Genet (2004) 108:1151-1161 |
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| Map Set Name: |
T. cacao - F2 Brazil (2005) |
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| Abbreviated Name: |
F2 Brazil (2005) |
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| Accession ID: |
F2_brazil |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 May, 2005 |
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Description:
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A genetic linkage map was created from 146 cacao trees (Theobroma cacao) using an F2 population produced by selfing an F1 progeny of the cross Sca6 and ICS1. Simple sequence repeat (SSR) markers (170) were used principally for this map, with 12 candidate genes [eight resistance gene homologues (RGH) and four stress related WRKY genes], for a total of 182 markers. Joinmap software was used to create the map, and 10 linkage groups were clearly obtained, corresponding to the 10 known chromosomes of cacao. Our map encompassed 671.9 cM, approximately 100 cM less than most previously reported cacao maps, and 213.5 cM less than the one reported high-density map. Approximately 27% of the markers showed significant segregation distortion, mapping together in six genomic areas, four of which also showed distortion in other cacao maps. Two quantitative trait loci (QTL) for resistance to witches' broom disease were found, one producing a major effect and one a minor effect, both showing important dominance effects. One QTL for trunk diameter was found at a point 10.2 cM away from the stronger resistance gene. One RGH flanked the minor QTL for witches' broom resistance, implying possible association. QTLs mapped in F2 populations produce estimates of additive and dominance effects, not obtainable in F1 crosses. As dominance was clearly shown in the QTL found in this study, this population merits further study for evaluation of dominance effects for other traits. This F2 cacao population constitutes a useful link for genomic studies between cacao and cotton, its only widely grown agronomic relative.
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Reference:
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Brown et al (2005) Resistance
gene mapping for witches' broom disease in Theobroma cacao L. in a F2 population using SSR markers and candidate genes. J Am Soc Hortic Sci 130(3):366-373 |
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| Map Set Name: |
T. cacao - F1 CATIE (2007) |
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| Abbreviated Name: |
F1 CATIE (2007) |
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| Accession ID: |
F1_catie |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
01 January, 2006 |
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Description:
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A heterozygous F1 mapping population of cacao
(Theobroma cacao L.) was created and evaluated
for resistance to frosty pod [caused by
Moniliophthora roreri (Cif. and Par.) Evans et al.],
and black pod [caused by Phytophthora palmivora
(Butl.) Butl.] and for fi ve horticultural traits
at CATIE in Turrialba, Costa Rica. The population
consisted of 256 F1 progeny from the cross
'Pound 7' x 'UF 273'. Progeny were used to form
a linkage map using 180 markers. The linkage
map contained 10 linkage groups (LGs), numbered
as the LG in the cacao reference map, and
was used to locate putative quantitative trait loci
(QTL) for resistance to the aforementioned diseases
and five horticultural traits. Resistance to
frosty pod was measured by internal and external
pod resistance. Five QTLs for frosty pod
resistance were found on three LGs, 2, 7, and 8,
with UF 273 appearing to be the source of resistance.
These alleles are being used for scoring
progeny in ongoing cooperative marker-assisted
selection projects, and constitute the first QTLs
identifi ed for frosty pod resistance. Three QTLs
for black pod resistance were found on LG 4,
8, and 10, with the most favorable alleles coming
from Pound 7. One QTL was found on LG 4
for average trunk growth rate, and two QTLs for
height of first jorquette were identifi ed on LGs 4 and 6. One QTL each for average trunk diameter growth and pod color was found on LG 4. |
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Reference:
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Brown et al. (2007) Mapping QTLs for Resistance to Frosty Pod and Black Pod Diseases and Horticultural Traits in Theobroma cacao L.
Crop Sci. 47:1851-1858 |
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| Maps: |
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| Map Set Name: |
T. cacao - F2 w/RGH, WRKY, TIR (2006) |
[ Show Only This Set ] |
| Abbreviated Name: |
F2 RGH (2006) |
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| Accession ID: |
F1_rgh_wrky |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
23 June, 2006 |
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Description:
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Identifying genetic markers linked to disease resistance in plants is an important goal in marker-assisted selection. Using a candidate-gene approach, we have previously developed genetic markers in cacao (Theobroma cacao L.) for two families of genes involved in disease resistance: non-TIR-NBS-LRR (Toll/Interleukin-1 Receptor-nucleotide binding site-leucine rich repeat) resistance gene homologues and WRKY transcription factor genes; however, we failed to isolate TIR-NBS-LRR genes. Using a novel algorithm to design degenerate primers, we have now isolated TIR-NBS-LRR loci as determined by DNA sequence comparison. These loci have been developed as genetic markers using capillary array electrophoresis (CAE) and single-strand conformational polymorphism (SSCP) analysis. We have mapped three distinct TIR-NBS-LRR loci in an F2 population of cacao and demonstrated that one is located on linkage group 3 and the other two on linkage group 5. |
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Reference:
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Kuhn et al (2006) Identification of cacao TIR-NBS-LRR resistance gene homologues and their use as genetic markers. J. Am. Soc. Hortic. Sci. 131:806-813.
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| Maps: |
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| Map Set Name: |
T. cacao - Composite Map (2008) |
[ Show Only This Set ] |
| Abbreviated Name: |
Composite (2008) |
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| Accession ID: |
composite |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
25 February, 2008 |
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Description:
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In this paper, we report the construction of the
first composite map of cacao from linkage data of one F2 and two F1 mapping populations with a high number of codominant markers in common. The combination of linkage information from all three maps results in the currently most precise estimates of marker locations and distances between markers, especially in densely marked areas. JoinMap V4 software was used for all marker quality assessment and mapping. Individual (sub-composite) maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes.
Homogeneity of marker placement was very high among sub-composite maps, the composite map, and the designated "reference" map. Care was exercised in the re-creation of sub-composite maps and the composite map to include only markers with acceptable mapping quality parameters. The composite map places more markers with higher precision than any individual map. This research clearly demonstrates for the first time a very high level of marker homogeneity among commercial cacao clones compared to other species.
The observed homogeneity between different maps, including the composite one, is probably due to a narrow genetic base of commercial cacao clones. Markers linked to identified quantitative trait loci (QTLs) are more likely to retain linkage in other commercial clones, rendering the QTLs in cacao potentially more stable than in other species. |
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Reference:
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J.S. Brown et al (2008) A Composite Linkage Map from Three Crosses Between Commercial Clones of Cacao, Theobroma cacao L. Tropical Plant Biology. 1(2):1935-9756 |
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| Maps: |
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| Map Set Name: |
T.cacao F2 w/RGH & SNP |
[ Show Only This Set ] |
| Abbreviated Name: |
F2 RGH SNP |
[ Download Map Set Data ] |
| Accession ID: |
34 |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
12 August, 2010 |
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| Map Set Name: |
Consensus Disease Resistance QTLs |
[ Show Only This Set ] |
| Abbreviated Name: |
Disease Resistance QTLs |
[ Download Map Set Data ] |
| Accession ID: |
DRQTL |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
07 October, 2010 |
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| Maps: |
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| Map Set Name: |
Hort Trait QTLs |
[ Show Only This Set ] |
| Abbreviated Name: |
Hort Trait QTLs |
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| Accession ID: |
HTQTL |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
07 October, 2010 |
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| Maps: |
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| Map Set Name: |
Schnell QTLs |
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| Abbreviated Name: |
Schnell QTLs |
[ Download Map Set Data ] |
| Accession ID: |
SQTL |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Genetic |
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| Map Units: |
cM |
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| Published On: |
07 October, 2010 |
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| Maps: |
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| Map Set Name: |
T.cacao physical map |
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| Abbreviated Name: |
Cacao physical map |
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| Accession ID: |
public |
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| Species: |
Theobroma cacao (Cacao) |
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| Map Type: |
Sequence |
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| Map Units: |
bp |
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| Published On: |
12 September, 2010 |
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