Pathmanathan Umaharan

Distribution and diversity of geminiviruses in trinidad and tobago.

ABSTRACT Seven crop and eight weed species from 12 agricultural locations in Trinidad and Tobago were assayed for the presence of whitefly-transmitted geminiviruses (WTGs) by using dot blot hybridization and polymerase chain reaction (PCR) amplification of the N-terminal coat protein sequence with degenerate primers. The amplified fragments were cloned and analyzed by restriction enzyme digestion to determine fragment length polymorphism among the cloned fragments. Representative clones were then sequenced and subjected to phylogenetic analysis to determine the sequence similarity to known WTGs. WTGs were found in every location sampled and in 10 of the 15 species investigated: Lycopersicon esculentum(tomato), Capsicum annuum (pepper), Capsicum frutescens (sweet pepper), Abelmoschus esculentus (okra), Phaseolus vulgaris (beans), Alternanthera tenella, Desmodium frutescens, Euphorbia heterophylla, Malva alceifolia, and Sida acuta. The geminiviruses infecting these plants were closely related to potato yellow mosaic virus from Venezuela (PYMV-VE) and tomato leaf curl virus from Panama (ToLCV-PA). However, in pepper, sweet pepper, okra, Alternanthera tenella, Euphorbia heterophylla, Des-modium frutescens, and in one sample of tomato, a PYMV-VE-related virus was found in mixed infections with a virus related to pepper huasteco virus. Full-length infectious DNA-A and DNA-B of a tomato-infecting geminivirus from Trinidad and Tobago were cloned and sequenced. DNA-A appears to be a recombinant derived from PYMV-VE or ToLCV-PA, and Sida golden mosaic from Honduras. The implications of these findings in the control of WTGs are discussed.

Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.

The relic Criollo cacao in Belize – genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

Cacao (Theobroma cacao L.) was domesticated in Mesoamerica and is native to the South American rainforest. Belizean Criollo is a group of relic landraces that are thought to be similar to those used by the Olmecs and Mayans during early domestication. Knowledge of genetic diversity is essential for efficient conservation and use of these relic landraces. Using 30 microsatellite markers, we characterized genetic diversity in 77 Belize Criollo accessions collected from the Maya Mountains in Belize, and assessed their relationship with 62 cacao accessions including 25 Trinitario accessions. Genetic diversity and heterozygosity were low in Belizean Criollo germplasm. Eleven distinctive genotypes were identified among the Belizean germplasm. Results of ordination and cluster analysis supported their putative ancestral contribution to the Trinitario cacao. However, results of Bayesian assignment and parentage analysis both suggested that the contribution of Criollo cacao to the Imperial College Selections Trinitario is small. Our preferred hypothesis for the genesis of Trinitario cacao is that a limited population of Criollo £ Forastero hybrids emanated from the introduced Forastero population of Trinidad. The present study provides new insights into the origin of the Trinitario cacao, which will be useful in the ex situ and in situ conservation of cacao landraces from Mesoamerica.

Inheritance of foliar resistance to Phytophthora palmivora (butler) Butler in cacao (theobroma cacao L.)

The genetic nature of resistance in leaves of cacao (Theobroma cacao L.) to Phytophthora palmivora (Butler) Butler was investigated in a 3 × 8 and a 4 × 4 mating design. Leaf resistance was assessed at the penetration and post-penetration stages of infection. Wide variability was observed among the 32 families examined for lesion frequency (penetration resistance) and lesion size / spread (post-penetration resistance). Segregation within families showed a continuous distribution for both forms of resistance, suggesting that resistance is polygenic. The poor association between resistance at the penetration stage and that at the post-penetration stage suggested that they were independently inherited and could be selected independently with the aim of accumulating genes for resistance. Genetic complementation between the two forms of resistance and transgressive segregation were evident within the families studied. The additive effects were predominant for lesion size, while both additive and non-additive effects were important in the inheritance of lesion frequency. The narrow sense heritabilities obtained from North Carolina Model II analysis were as high as 0.61 and 0.40 for lesion size and lesion frequency respectively. Possible breeding strategies based on these findings are discussed.

Genetic analysis of yield and its components in vegetable cowpea (Vigna unguiculata L. Walp)

The F2 and backcrosses of a cross between two vegetable cowpea (Vigna unguiculata L. Walp) varieties with contrasting characteristics were evaluated for pod yield and its components, with the aim of understanding the genetic basis of these characteristics. A four-parameter model incorporating the additive, dominance and additive × additive genetic components fitted the data for pod yield and clusters per plant. The additive and additive × additive effects were positive and were larger than the dominance component. The relatively large additive and the predominantly positive dominant effects suggest that selection would be effective. Pod weight had high broad (84%) and narrow sense heritability (75%) and can be effectively selected for in the early generations. The study suggested that vegetable cowpea improvement programs should focus on selecting for clusters per plant and average pod weight in the early generations, while selection for dry pod yield could be delayed to later generations. It was concluded that pods per plant may be a useful selection criterion in multi-location trials aimed at selecting for stability of yield.

Increasing Accuracy and Throughput in Large-Scale Microsatellite Fingerprinting of Cacao Field Germplasm Collections

In this study we report on increasing the rate and accuracy of microsatellite fingerprinting of accessions in Theobroma cacao L. field germplasm collections with a medium-throughput capillary sequencing system. We examined the use of a reduced number of microsatellite loci to decrease the time and materials required for fingerprinting and determined the best available microsatellite loci for accurately separating accessions. A subset of nine informative loci that could separate sixty accessions into the same genetic groupings as a complete set of 37 loci was found. Stringent probability of identity values (i.e. chance of unique accession) was highly influenced (r = −0.996; P < 0.001) by the number of alleles utilised in the fingerprinting set but the composition of the primer set was more important when choosing discriminatory loci. DNA pooling to reduce the number of samples was also investigated. There was a relatively high level of mixture within plots (59% of 54 plots examined) of the field genebank, which opposed the use of a pooling strategy to fingerprint the multiple trees of an accession plot in the collection.

Cacao resistance to Phytophthora: Effect of pathogen species, inoculation depths and pod maturity

Two species of Phytophthora (P. palmivora and P. capsici) and inoculations at two depths (3 mm and 9 mm) were tested each on 10 clones of Theobroma cacao to determine their effects on pod resistance. Ripe and unripe pods were also assessed to determine the influence of physiological status of the pod on the expression of resistance. The two pathogens tested (P. palmivora and P. capsici) differed significantly in their reactions on pods, with P. palmivora being more aggressive than P. capsici. However, the lack of interaction between clones and pathogen species and the similarity in the ranking of clones based on lesion size suggested that selection for resistant clones can be based on one of the two pathogens, preferably the more aggressive one. Pod reactions differed between inoculation depths (3 mm and 9 mm), and between pod maturity stages (ripe and unripe pods) with relatively larger lesions being recorded at 9 mm depth and on unripe pods as compared to those observed at 3 mm depth and on unripe pods, respectively. The magnitude of increase in lesion sizes, however, varied with genotypes, indicating that inoculation depth and pod maturity stage should be standardized in screening cacao germplasm for resistance to Phytophthora.

A study of genotype-isolate interaction in cacao (Theobroma cacao L.): resistance of cacao genotypes to isolates of Phytophthora palmivora

The resistance of cacao (Theobroma cacao. L)leaves to 10 isolates of Phytophthora palmivora(Butler) Butler was investigated in 18 genotypes of cacao in three experiments. Tissue-paper-mount and punch-inoculation methods were used to distinguish between resistance at the penetration and post-penetration levels based on lesion frequency and size, respectively. There was a 5–6 fold difference in aggressiveness among isolates collected from different locations in the islands of Trinidad and Tobago for both types of resistance. However, host genotype ×isolate interaction effects were not significant for resistance at both the penetration and post-penetration levels. A strong positive relationship (r = 0.8) was observed in the abilities of isolates to effectively breach the two types of resistance. This suggests that the same isolate can be used in screening for both types of resistance. No significant relationship was found between resistance at the penetration and post-penetration levels suggesting that the resistance mechanisms were different. Subsequent experiments using a wider range of cacao genotypes from the International Germplasm Collection, Trinidad, confirmed the initial results. These experiments indicate that resistance found using one isolate would be equally valid using other isolates of Phytophthora palmivora. The implications of the findings are discussed.

Effect of short-term waterlogging applied at various growth phases on growth, development and yield in Vigna unguiculata

The effects of short-term waterlogging during the vegetative, reproductive and total growth phases were investigated in four cultivars of cowpea ( Vigna unguiculata L. Walp) in relation to their controls in a pot experiment conducted at the University of the West Indies, St. Augustine, in 1989. All cultivars were able to recover completely and produce near to normal yields, when waterlogging was confined to the vegetative period. Recovery growth was affected in cultivars waterlogged during the total growth phase and the plants were significantly smaller ( P < 0·05) in vegetative dry matter (60–80% of the size of their respective controls) even at maturity. Recovery growth was affected, to a greater extent, in cultivars possessing a small mainstem[ratio ]branch ratio. Yield development in the waterlogged plants was affected by accelerated leaf senescence and consequent reduction in the reproductive period. As a result, yields in all the cultivars tested were significantly smaller ( P < 0·05) than their respective controls and varied between 54 and 60% of the controls. Plants waterlogged during the reproductive phase were not significantly different ( P < 0·05) in vegetative dry matter from the controls, but showed root degeneration and accelerated leaf senescence in all but one cultivar (Local Red). Yield reduction, however, was significant ( P < 0·05) only in IT-83S-898. Possible criteria for selecting plants tolerant to waterlogging are discussed.

Microsatellite-aided detection of genetic redundancy improves management of the International Cocoa Genebank, Trinidad

Cacao (Theobroma cacao L.), the tree from which cocoa butter and chocolate is derived, is conserved in field genebanks. The largest of these ex situ collections in the public domain is the International Cocoa Genebank, Trinidad (ICG,T). Reduction of genetic redundancy is essential to improve the accuracy and efficiency of genebank management. This study examined the pedigree and genetic diversity in a subset of 387 accessions in this collection. Sibship reconstruction of this subset revealed 56 full-sib families nested within 189 half-sib families. Sixteen centers of interconnectivity were identified, which suggested a high level of genetic redundancy in the collection. Generally, consistent phylogenetic trees were obtained using different genetic distance measures. However, a principal coordinate analysis of the Dest differentiation measure elicited the best representation of accession group clustering, and we recommend this approach when probing fine-scale genetic differentiation among cacao accessions. The composite genetic diversity of 414 cacao accessions was contained in a core set of 59 unique accessions. These results have significant implications in the conservation of genetic resources of the ICG,T and other cacao genebanks. The approach developed in this study is recommended as a strategy to curators in guiding conservation management practices of cacao and other similar ex situ genebanks.