ArticlePloS one2022
Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 17 citations in OpenAlex.
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations.The plant genome · 2026Article
- A GWAS-machine learning framework reveals protein-synthesis pathway signals for yield in Theobroma cacao after population-structure correction.Scientific reports · 2026Article
- Longitudinal genomic prediction of cacao disease resilience identifies robust witches' broom disease targets.Frontiers in plant science · 2026Article
- Integrated phenotypic analysis, predictive modeling, and identification of novel trait-associated loci in a diverse Theobroma cacao collection.BMC plant biology · 2025Article
- Forastero cacao bean extract gel decreases IL-6 positive osteoblasts, osteoclasts, and osteocytes on OIRR model: A primitive study.Journal of Taibah University Medical Sciences · 2025Article
- Bioactive Compounds, Antioxidant, and Antimicrobial Activity of Seeds and Mucilage of Non-Traditional Cocoas.Antioxidants (Basel, Switzerland) · 2025Article
- Genome-wide association study for yield-related traits in faba bean (Frontiers in plant science · 2024Article
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Authors and funding
9 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
A genome-wide association study (GWAS) was undertaken to unravel marker-trait associations (MTAs) between SNP markers and phenotypic traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. A Mixed Linear Model (MLM) in TASSEL was used for the GWAS and followed by confirmatory analyses using GAPIT FarmCPU. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P ≤ 8.17 × 10-5 (-log10 (p) = 4.088)) MTAs of interest, including six that pertained to yield-related traits, were identified using TASSEL MLM. The latter accounted for 5 to 17% of the phenotypic variation expressed. The highly significant association (P ≤ 8.17 × 10-5) between seed length to width ratio and TcSNP 733 on chromosome 5 was verified with FarmCPU (P ≤ 1.12 × 10-8). Fourteen MTAs were common to both the TASSEL and FarmCPU models at P ≤ 0.003. The most significant yield-related MTAs involved seed number and seed length on chromosome 7 (P ≤ 1.15 × 10-14 and P ≤ 6.75 × 10-05, respectively) and seed number on chromosome 1 (P ≤ 2.38 × 10-05), based on the TASSEL MLM. It was noteworthy that seed length, seed length to width ratio and seed number were associated with markers at different loci, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in the flanking regions of the significantly associated SNPs and in linkage disequilibrium with them. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (genomic estimated breeding values (GEBV)) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.
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