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.

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.

Morphological and genetic diversity of cacao (Theobroma cacao L.) in Uganda.

Cocoa is among the top foreign exchange earners in Uganda's agriculture sector and has benefitted the livelihood of farmers involved in production. Although cacao cultivation was adopted in the early 1900s, little is known about the on-farm diversity of the crop. A total of 125 cacao landraces were surveyed from eight districts in the Central and Western Regions to evaluate the morphological and genetic diversity of cacao in Uganda. Passport data included site, tree, fruit and seed information. Trees were genotyped using 96 single nucleotide polymorphism markers on a Fluidigm platform. Low heterozygosity was detected in the germplasm in both the Central [observed heterozygosity (H o ) = 0.295, expected heterozygosity (H e) = 0.334] and Western Regions (H o = 0.317, H e = 0.322). Genetic variation in both regions was generally comparable but the regions could be differentiated from each other. Inbreeding was noted in the Central Region while a greater sharing of genetic material was observed in the Western Region. The morphological and genetic data indicated that the Ugandan collection was an interspersed group with low to moderate variation with some separation of the Central from Western regions. Ancestry analysis indicated that the majority of the accessions were hybrids of Marañon lineage but also had Amelonado and Iquitos genetic backgrounds. These findings are consistent with the history of the movement of cacao into Uganda. A core collection of 18 individuals to represent the genetic diversity as well as 12 additional trees with possible advantageous traits is proposed.