title: Association mapping of seed and disease resistance traits in Theobroma cacao L.
abstract: Microsatellite and single nucleotide polymorphism markers that could be used in marker assisted breeding of cacao were identified for number of filled seeds, black pod resistance and witches' broom disease resistance. An association mapping approach was employed to identify markers for seed number and resistance to black pod and witches' broom disease (WBD) in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms (SNPs) were assessed on 483 unique trees in the International Cocoa Genebank Trinidad (ICGT). Linkage disequilibrium (LD) and association mapping studies were conducted to identify markers to tag the phenotypic traits. Decay of LD occurred over an average 9.3 cM for chromosomes 1-9 and 2.5 cM for chromosome 10. Marker/trait associations were generally identified based on general linear models (GLMs) that incorporated principal components from molecular information on relatedness factor. Seven markers (mTcCIR 8, 66, 126, 212; TcSNP368, 697, 1370) on chromosomes 1 and 9 were identified for number of filled seeds (NSEED). A single marker was found for black pod resistance (mTcCIR280) on chromosome 3, whereas six markers on chromosomes 4, 5, 6, 8, and 10 were detected for WBD (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374). It is expected that this association mapping study in cacao would contribute to the knowledge of the genetic determinism of cocoa traits and that the markers identified herein would prove useful in marker assisted breeding of cacao.
authors.affiliation: Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago. lambert.motilal@sta.uwi.edu.
authors.forename: Lambert A
authors.initials: LA
authors.lastname: Motilal
authors.affiliation: USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Zhang
authors.affiliation: USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
authors.forename: Sue
authors.initials: S
authors.lastname: Mischke
authors.affiliation: USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
authors.forename: Lyndel W
authors.initials: LW
authors.lastname: Meinhardt
authors.affiliation: Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago.|CIRAD-UMR AGAP (Centre de coopération internationale en recherche agronomique pour le développement), Montpellier Cedex 5, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Boccara
authors.affiliation: CIRAD-UMR AGAP (Centre de coopération internationale en recherche agronomique pour le développement), Montpellier Cedex 5, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Fouet
authors.affiliation: CIRAD-UMR AGAP (Centre de coopération internationale en recherche agronomique pour le développement), Montpellier Cedex 5, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Lanaud
authors.affiliation: Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago.
authors.forename: Pathmanathan
authors.initials: P
authors.lastname: Umaharan
mesh_terms: D002099:Cacao / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping; D005819:Genetic Markers / Q000235:genetics / Q000502:physiology; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats / Q000235:genetics / Q000502:physiology; D000069600:Plant Breeding; D057865:Plant Immunity / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics / Q000502:physiology; D019655:Quantitative Trait, Heritable; D012639:Seeds / Q000235:genetics* / Q000502:physiology
chemical_list: D005819:Genetic Markers
keywords: Black pod disease; Cocoa seeds; Linkage disequilibrium; Microsatellite markers; Single nucleotide polymorphism; Witches’ broom disease