Atta Ofori

The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process.

Genetic variation and combining abilities for vigour and yield in a recurrent selection programme for cacao

The low genetic diversity of cacao germplasm collections in West Africa is often cited as a limitation to further yield improvement of the crop in its major production countries. Twelve clones obtained from first cycle selection for yield and clones available in international genebanks were tested for their combining ability for key agronomic traits by using these as males in crosses with five female clones available in the Seed Gardens in Ghana. Progenies obtained from a North Carolina II (NC II) mating design and standard varieties were planted at two sites that contrast in terms of soil fertility, rainfall total and distribution. Fifty-eight progenies obtained from the 5 × 12 incomplete NC II mating design and six other progenies, of which two were standard varieties, were evaluated at the more favourable location. At the less favourable location, 44 progenies of the NC II mating design and 20 other progenies, including the two standard varieties, were planted. A randomized complete block design with four replications was used at both locations. Progenies with PA 7 as female parent had better seedling survival at the location with poorer production conditions. Low levels of genetic diversity among female clones at 86 single nucleotide polymorphism loci was reflected in larger standard errors for the additive variance due to female parents relative to that due to male parents. Non-additive genetic effects were much larger than the corresponding additive variance components for all traits at each of the two locations. Average yields over the fourth and fifth years after planting ranged from 0·23 to 1·29 t/ha/year. The standard varieties were not among the best progenies for seedling vigour, yield or yield efficiency (yield per unit trunk cross-sectional area (TCSA) per year). Narrow-sense heritability estimates were higher for three estimates of tree vigour (estimated as increase in TCSA) than for yield traits. Heritability for yield efficiency was a moderate of h 2 = 0·5 ± 0·23. The study indicates that further yield increments are attainable by selecting and crossing among the early cacao introductions into West Africa.

Broadening the Gene Pool of Cocoa (Theobroma cacao L.) Progenies with Guiana Clones: Establishment and Precocity Traits

Guiana (GU) cocoa is one of the recently identified genetic groups with high resistance to black pod diseases. The objective of this study was to estimate combining abilities of selected GU clones for traits related to establishment ease and precocity. Three tester clones were crossed with eight GU clones as males in a 3 x 8 factorial mating design to produce F1 progenies. These progenies were evaluated together with four standard varieties at two locations in Ghana for percentage survival, stem growth, jorquette height, canopy spread, flowering intensity, and pod number. The GU progenies surpassed on average the standards for all traits except for jorquette height at one location. Preponderance of additive effects was manifested as significant general combining ability (GCA) estimates of female and male clones for all traits. The specific combining ability (SCA) was significant only for flowering intensity, stem growth, and pod number. GU 341H and GU 225V contributed positively to GCA effects for all traits studied. Based on establishment and precocity traits, the Guiana population represents a suitable genetic resource for broadening the genetic base of cocoa breeding.

Genetic base-broadening of cacao for precocity and cropping efficiency

Introduction of clones from genetic groups that are underrepresented in the pedigree of commercial cacao varieties in West Africa represents an important aspect of cacao improvement strategy of broadening the genetic base to overcome current yield stagnation of the crop. The objective of the present study was to determine the combining abilities of more recently introduced cacao clones for yield and cropping efficiency in the early bearing years. Seven recently introduced clones were crossed as males to five clones commonly used in the seed gardens in Ghana using a North Carolina II design. The 35 F 1 varieties and one commercial variety were evaluated in the field from June 2010 to March 2015 for four traits: increase in trunk cross-sectional area in the juvenile, and in the pod-bearing phases, bean yield and cropping efficiency. Though both GCA and SCA variances were significant for all traits, the ratios of GCA:SCA were much smaller than unity, indicating the importance of non-additive effects in the control of the traits. Among the set of clones therefore, prediction of F 1 variety performance cannot be based on the GCA or per se (average) performance of the clones. Six varieties were more precocious, and eight had higher cropping efficiencies than the standard variety. Bean yields ranged from 0.74 to 1.05 t/ha/year in the fourth and fifth years after planting among the top six varieties. The study provides evidence of the large potential for productivity increase through the use of cacao clones beyond Pounds early introductions into West Africa.

Cacao Seed Purity and Genotype Influence on Seedling Growth under Peasant-Farmer Conditions in Ghana

ABSTRACT One of the reasons for the low yields of cacao (Theobroma cacao L.) in West Africa is the poor adaptation of varieties to a rapidly changing climate reflected in poor seedling survival and reduced precocity. To show the impact of cacao seed purity and genotype on seedling survival and precocity, recommended varieties being supplied to farmers were sampled from four seed gardens and compared with breeders’ varieties in one on-station and five on-farm trials in Ghana. Varieties were assessed for plant survival, stem diameter increment and pod production by 27 months after transplanting. Parentage analyses at 75 single nucleotide polymorphism (SNP) loci revealed the presence of illegitimate progeny (seedlings of unapproved parents) among the recommended varieties, with selfed progeny comprising up to 50% of seedlings from one seed garden. The selfed progeny possessed the least vigor, and had not initiated pod production by 27 months after transplanting. In general, the seed garden varieties performed poorly compared with the breeders’ varieties for all three traits. On the strength of the results of the present study, two key actions are needed to increase cacao adaptation and yields at the farm level. First, a DNA marker-auditing system of the progenies issued from the seed gardens should be operationalized as a quality-control mechanism. Second, new male parents that produce seedlings of improved vigor need to be introduced into the seed gardens to improve cacao plant survival and yield.

Assessment of Genetic Diversity in Robusta Coffee Using Morphological Characters

ABSTRACT Assessing the level of genetic variation that exist in any breeding population is important as this has significant implications for selection and variety development. The objectives of the present study were to determine the variation among 71 Robusta coffee genotypes based on 21 traits and to determine the genetic relationships between the genotypes. The 71 genotypes were established in 2013 as clones raised from single node cuttings and planted in a randomized complete block design with four blocks, with five plants per genotype per block. There was variation in all the traits assessed for the different Robusta coffee genotypes as evidenced by the coefficient of variation and frequencies of the quantitative and qualitative traits, respectively. Principal Component Analysis (PCA) was performed to obtain information on the relative importance of the morphological characters assessed, and cluster analysis was used to determine relationships among the genotypes evaluated. The first and second principal components accounted for 39.2% and 18.9% of the total variability, respectively. PCA revealed that height, stem diameter, span, number of laterals per tree, diameter of laterals, and number of nodes per lateral were the principal characters to discriminate the Robusta coffee genotypes examined. Cluster analysis grouped the Robusta coffee genotypes into five clusters as revealed by the dendrogram. The diversity among the Robusta coffee genotypes in both quantitative and qualitative traits revealed by this study can be used for trait improvement through selection and hybridization.

Variability of survival and yield traits in cacao (Theobroma cacao L.) clones under marginal field conditions in Ghana

ABSTRACT Increasing the genetic base of current parental cacao varieties grown in West Africa with clones that are able to perform well under marginal conditions could improve cacao production. Survival and yield of 30 different cocoa clones of more recent introductions were compared with five parental clones of improved cocoa varieties under natural field conditions in Ghana. A randomized complete-block design with five replications was used to evaluate the 35 clones for the following traits: percentage survival, increase in trunk cross-sectional area (TCSA), canopy spread, bean mass and bean yield. Significant (p < 0.05) clone effects for all traits and broad-sense heritability range of 0.16–0.51 were observed. Bean mass and bean yield varied from 0.90 to 1.44 g and 149 to 467 kg/ha, respectively. Bean yield and TCSA was positively and moderately correlated (r = 0.46; p < 0.01). Clones A 1/197, ICS 70 and MO 20 outperformed the best control clone for both survival and yield, which could be used in cacao breeding to improve production under marginal conditions in Ghana.