Genetic Diversity in Cocoa (Theobroma cacao L.) Germplasm Collection from Ghana

Opoku, SY; Bhattacharjee, Ranjana; Kolesnikova-Allen, Maria; Motamayor, Juan Carlos; Schnell, Raymond J.; Ingelbrecht, Ivan; Enu-Kwesi, Lewis; Adu‐Ampomah, Y.

doi:10.1300/j411v20n01_04

Cited by 18 publications

(6 citation statements)

References 16 publications

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“…The cocoa progenies that are cultivated currently in most of the cocoa growing countries come from a narrow genetic base of the Upper Amazon gene pool, comprising mainly the Naney, Iquitos, Parinari, and Scavina (Aikpokpodion et al, 2009;Bekele et al, 2008;Opoku et al, 2007). The resistance of these varieties to P. megakarya the causative pathogen of the most virulent form of black pod disease is poor (Nyadanu et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

“…The cacao progenies currently cultivated in most of the cacao-growing regions in West Africa are predominantly of Upper Amazon origin (Aikpokpodion et al, 2009;Opoku et al, 2007). They were evaluated under forest conditions with high soil fertility and overhead shade trees and selected on the basis of yields and tolerance to Cacao swollen shoot virus (CSSV) (Brunt, 1975).…”

Section: Crop Sciencementioning

confidence: 99%

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Field evaluation of cacao progenies derived from Guiana clones for yield and black pod disease resistance

2020

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Phytophthora spp. is a major disease of cacao (Theobroma cacao L.), and there is a need to develop cultivars that are resistant to this disease. Among the various genetic groups of cacao, the Guiana (GU) has received little attention in developing varieties even though they are known to be tolerant to black pod disease. The objective of this study was to estimate combining abilities and heritability of selected GU clones for bean yield and black pod resistance. Twenty‐four F1 progenies were derived by crossing three seed garden parental clones with eight GU clones as males in a three‐by‐eight North Carolina II (NC II) complete factorial mating design. These were evaluated together with four standard varieties over a 4‐yr period in a randomized complete block design with four replications at two contrasting locations in Ghana. Progeny, year, and location effects were significant (p < .01) for all traits, whereas progeny × location was significant for only number of beans per pod. The general combining ability (GCA) effects of females and males and specific combining ability (SCA) of female × male were significant (p < .01) for all traits, indicating that both additive and dominant effects are important in the inheritance of the traits. Heritability ranged from 0.14–0.51 for broad sense and 0.10−0.37 for narrow sense. The best general combiners identified—GU 125/C, GU 144/C, and GU 290/H—were involved in crosses that combines high bean yield with high black pod resistance. They could be added to parental clones currently used in producing cacao varieties in areas with high black pod incidence.

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Section: Discussionmentioning

confidence: 99%

Section: Crop Sciencementioning

confidence: 99%

Field evaluation of cacao progenies derived from Guiana clones for yield and black pod disease resistance

2020

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“…Sequence data of 65 plants with high membership to the 10 cacao ancestry genetic groups [6], were downloaded and used as reference plants for SNP-based analyses. Using these data, Cornejo et al [16] had already classified these plants as: Amelonado (10), Contamana (7), Criollo (4), Curaray (5), Guiana (7), Iquitos (6), Marañon (10), Nacional (4), Nanay (8) and Puru ´s (4) (S3 Table ). Only 3 of these plants were also references for SSR genotyping.…”

Section: Plant Materialsmentioning

confidence: 99%

“…Other studies have also exploited SSR markers for various applications in cacao including: off-type detection, genetic diversity assessment and parentage analysis [8][9][10]. A set of 15 SSR markers was assumed as international standard microsatellites for cacao DNA fingerprinting [11,12] and it has been widely used for population analysis and cacao clone genetic classification, although carrying some disadvantages associated with SSR genotyping such as: allele size estimation, reproducibility and cost [13].…”

Section: Introductionmentioning

confidence: 99%

Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping

Ramirez-Ramirez,

Bidot-Martínez,

Mirzaei

et al. 2024

PLoS ONE

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Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.

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“…In the short term, one mechanism for increasing the genetic diversity of cocoa stands is the use of 'seed gardens', as has been used in Africa (Opoku et al 2007) and Brazil (Monteiro et al 2009). In a seed garden a selection of compatible out-crossing accessions are grown together to allow cross-pollination, the resulting seeds can be used to produce planting material.…”

Section: Climate Smart Breeding In Cocoamentioning

confidence: 99%

Climate adaptation in a minor crop species: is the cocoa breeding network prepared for climate change?

Farrell

Rhiney

Eitzinger

et al. 2018

Agroecology and Sustainable Food Systems

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Climate adaptation in a minor crop species: is the cocoa breeding network prepared for climate change? The International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications.

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Genetic Diversity in Cocoa (Theobroma cacao L.) Germplasm Collection from Ghana

Cited by 18 publications

References 16 publications

Field evaluation of cacao progenies derived from Guiana clones for yield and black pod disease resistance

Field evaluation of cacao progenies derived from Guiana clones for yield and black pod disease resistance

Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping

Climate adaptation in a minor crop species: is the cocoa breeding network prepared for climate change?

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