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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #322206

Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

Title: Association mapping of fruit, seed and disease resistance traits in Theobroma cacao L

Author
item Motilal, Lambert - University Of The West Indies
item Zhang, Dapeng
item Mischke, Barbara
item Meinhardt, Lyndel
item Boccara, Michel - University Of The West Indies
item Lanaud, Claire - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item Umaharan, Pathmanathan - University Of The West Indies

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2016
Publication Date: 8/17/2016
Citation: Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Boccara, M., Lanaud, C., Umaharan, P. 2016. Association mapping of fruit, seed and disease resistance traits in Theobroma cacao L. Planta. 244(6):1265-1276.

Interpretive Summary: Theobroma cacao is an important tropical crop because it is the source of cocoa butter and powder for the confectionery industry. The International Cocoa Genebank, Trinidad maintains the largest collection of cacao clones and families, which serves as a foundation for future breeding of new cacao varieties. Unlocking the genetic diversity using new molecular markers will improve the efficiency of evaluation and speed up the breeding process. Using single nucleotide polymorphic (SNP) and microsatellite markers, we assessed 483 unique clones in the International Cocoa Genebank, Trinidad and established marker-trait association for major agronomic traits, including color, size, girth and mass of fruits; seed number and butterfat content; and resistance to black pod and witches’ broom diseases. The resultant information is highly useful to facilitate the use of cacao genetic diversity for crop improvement. This information will be used by cacao breeders, scientists and Genebank curators to improve conservation and utilization of cacao genetic resources.

Technical Abstract: An association mapping approach was employed to find markers for color, size, girth and mass of fruits; seed number and butterfat content; and resistance to black pod and witches’ broom diseases 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. Decay of linkage disequilibrium occurred over an average 9.3 cM for chromosomes 1 – 9 and 2.5 cM for chromosome 10. A minimal set of 15 SSRs and 15 SNPs were associated with fruit, seed and disease traits, usually under general linear models that incorporated principal components from molecular information as the relatedness factor. Loci that tagged multiple traits included the SSRs mTcCIR126 (fruit girth, fruit mass, number of seeds), mTcCIR183 (mature unripe fruit color, log total witches’ broom/tree girth) and mTcCIR184 (fruit girth, fruit mass); and the SNPs TcSNP281 (fruit girth, fruit mass) and TcSNP1213 (fruit mass, fruit size). One marker for black pod resistance (mTcCIR280) but six markers for witches’ broom resistance (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374) were found. Markers for witches’ broom resistance were better supported in the literature than that for black pod resistance indicative of issues with the screening method for the latter and an oligogenic mechanism of resistance for the former. The negligible overlap of DNA tags for fruit morphology, agronomic fruit traits, economic seed traits and disease resistance indicate that multiple loci are required to identify cacao plants with superior holistic trait expression.