Prevalence of plant-parasitic nematodes associated with tomatoes in three agro-ecological zones of Ghana

A study was conducted between August 2014 and May 2015 to identify plant-parasitic nematodes taxa associated with tomato (Solanum lycopersicum L.) and to assess the knowledge, perceptions and experiences of growers of the crop on occurrence and management of the parasites on their farms in nine communities within the semi-deciduous forest, the forest/savanna transitional and the savanna agro-ecological zones of Ghana. Semi-structured questionnaires were designed and administered to 54 randomly selected growers from the nine communities. Composite rhizosphere soil and tomato root samples were collected from two farms in each of the nine communities, and nematodes extracted, identified and recorded. The study revealed that many growers (73%) could not distinguish between nematode infestation, nutrient deficiency and moisture stress and, therefore, lacked knowledge on nematode control. Most of the growers (63%) continually cropped their land to tomato for periods of 4 –7 years without fallowing. All growers applied only inorganic fertilizer to their crops. Symptoms of nematode infestation were widespread in fields with high yield losses. Tomato was a host to Helicotylenchus spp. (11.5% in soil), Hoplolaimus spp. (1.0 % in soil), Meloidogyne spp. (37.4% in soil and 69.3% in roots), Pratylenchus spp. (20.6% in soil and 13.7% in roots), Rotylenchulus spp. (11.0% in soil and 12.2% in roots), Scutellonema spp. (9.5% in soil and 4.9% in roots), Tylenchus spp.(7.6% in soil) and Xiphinema spp.(1.4% in soil) across the nine communities surveyed. Semi-deciduous forest and Savanna agro-ecological zones had the highest and least population densities of nematodes, respectively. These nematodes, if not managed efficiently, could also serve as constraint to tomato production in the country

Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome

One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes

Principal Component Analysis and Molecular Characterization of Reniform Nematode Populations in Alabama

U.S. cotton production is suffering from the yield loss caused by the reniform nematode (RN), Rotylenchulus reniformis. Management of this devastating pest is of utmost importance because, no upland cotton cultivar exhibits adequate resistance to RN. Nine populations of RN from distinct regions in Alabama and one population from Mississippi were studied and thirteen morphometric features were measured on 20 male and 20 female nematodes from each population. Highly correlated variables (positive) in female and male RN morphometric parameters were observed for body length (L) and distance of vulva from the lip region (V) (r = 0.7) and tail length (TL) and c′ (r = 0.8), respectively. The first and second principal components for the female and male populations showed distinct clustering into three groups. These results show pattern of sub-groups within the RN populations in Alabama. A one-way ANOVA on female and male RN populations showed significant differences (p ≤ 0.05) among the variables. Multiple sequence alignment (MSA) of 18S rRNA sequences (421) showed lengths of 653 bp. Sites within the aligned sequences were conserved (53%), parsimony-informative (17%), singletons (28%), and indels (2%), respectively. Neighbor-Joining analysis showed intra and inter-nematodal variations within the populations as clone sequences from different nematodes irrespective of the sex of nematode isolate clustered together. Morphologically, the three groups (I, II and III) could not be distinctly associated with the molecular data from the 18S rRNA sequences. The three groups may be identified as being non-geographically contiguous