Spatial multivariate cluster analysis for defining target population of environments in west Africa for yam breeding

Yam (Dioscorea spp.) is a major staple crop with high agricultural and cultural significance for over 300 million people in West Africa. Despite its importance, productivity is miserably low. A better understanding of the environmental context in the region is essential to unlock the crop’s potential for food security and wealth creation. The article aims to characterize the production environments into homologous mega-environments, having operational significance for breeding research. Principal component analysis (PCA) was performed separately on environmental data related to climate, soil, topography, and vegetation. Significant PCA layers were used in spatial multivariate cluster analysis. Seven clusters were identified for West Africa; four were country-specific; the rest were region-wide in extent. Clustering results are valuable inputs to optimize yam varietal selection and testing within and across the countries in West Africa. The impact of breeding research on poverty reduction and problems of market accessibility in yam production zones were highlighted

Sample preservation and plant sex prediction in white guinea yam (Dioscorea rotundata Poir.)

Open Access Article; Published online: 11 Jul 2020Introduction: Yam (Dioscorea spp.) is an economically important staple food in tropical regions, especially for people in West Africa. Understanding of the flowering behavior of the crop to determine potential manipulation available to accomplish crop improvement at early stage remain key challenge in the yam breeding. The methods that reliably yield quality DNA and distinguishing sex type at the early stage of growth have been a challenge in yam genetics and breeding studies. This study assessed the effect of sample preservation methods on DNA quantity and quality during extraction and potential of DNA marker to diagnose plant sex at the early seedling stage in white Guinea yam. Materials and Methods: Five sample preservation methods were assessed for quality DNA extraction during field leaf tissue collection, namely liquid nitrogen, dry ice, silica gel, 95% ethanol, and oven drying. The predicted sex at the seedling stage using the molecular marker was further validated with the visual score for the sex phenotype at the flowering stage. Results: According to the findings of the present study, the DNA extracted from leaf samples preserved in liquid nitrogen, silica gel, dry ice, and oven drying methods were higher in molecular weights than samples stored in ethanol solution. Yam plant sex diagnosis with the DNA marker (sp16) identified a higher proportion of ZW genotypes (female or monoecious phenotypes) than the ZZ genotypes (male phenotypes) in the studied materials with 74% prediction accuracy. Conclusions: The results from this study provided valuable insights on suitable sample preservation methods for quality DNA extraction and the potential of DNA marker sp16 to predict sex in white Guinea yam

Variation in tuber dry matter content and starch pasting properties of white Guinea yam (Dioscorea rotundata) genotypes grown in three groecologies of Nigeria

Open Access Journal; Published online: 28 Sep 2021The primary objective of this study was to assess the effects of genotype (G), location (L), and G × L interaction on tuber quality traits (dry matter content and starch pasting parameters) in white Guinea yam (Dioscorea rotundata Poir.). Variability in tuber dry matter and starch pasting properties was examined using 18 advanced breeding lines and two dominant landrace cultivars of white Guinea yam grown in three different agroecological zones (forest‒savanna transition, southern Guinea savanna, and rainforest) in Nigeria. The starch pasting properties were evaluated using a Rapid Visco Analyser. Our results show that the G × L interaction effect was low compared to the genotype and growing location effects on the variability of key starch properties. In addition, the repeatability of trait performance across locations was high and relatively uniform for key traits, suggesting that any of the three locations used in this study can be employed for their evaluation. Furthermore, TDr1100873 had a higher dry matter content than the dominant landrace cultivars (Amula and Meccakusa) but was similar to them in starch pasting properties. Hence, TDr1100873 is considered a suitable variety for future breeding activities

Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)

Open Access Journal; Published online: 22 Sept 2020White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam

Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers

Open Access Journal; Published online: 06 Aug 2020Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops

Cytological and molecular characterization for ploidy determination in yams (Dioscorea spp.)

Open Access Journal; Published online: 22 Sep 2021Yam (Dioscorea spp.) is a monocotyledonous herbaceous vine plant grown in the tropics and subtropics. It is a multi-species plant with varied intra- and interspecific ploidy levels. Of the 600 species, 11 are cultivated supporting the livelihood of over 300 million people. The paucity of information on ploidy and the genomic constitution is a significant challenge to the crop’s genetic improvement through crossbreeding. The objective of this study was to investigate the ploidy levels of 236 accessions across six cultivated and two wild species using chromosome counting, flow cytometry and genotyping-based ploidy determination methods. Results obtained from chromosome counting and genotyping-based ploidy determination were in agreement. In majority of the accessions, chromosome counting and flow cytometry were congruent, allowing future rapid screening of ploidy levels using flow cytometry. Among cultivated accessions, 168 (71%) were diploid, 50 (21%) were triploid, and 12 (5%) were tetraploid. Two wild species included in the study were diploids. Resolution of ploidy level in yams offers opportunities for implementing successful breeding programmes through intra- and interspecific hybridization

Application of predictive breeding in yam improvement for west Africa

Open Access Journa

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.publishersversionPeer reviewe

High-Resolution Melting Analysis as a Powerful Tool to Discriminate and Genotype Pseudomonas savastanoi Pathovars and Strains

Pseudomonas savastanoi is a serious pathogen of Olive, Oleander, Ash, and several other Oleaceae. Its epiphytic or endophytic presence in asymptomatic plants is crucial for the spread of Olive and Oleander knot disease, as already ascertained for P. savastanoi pv. savastanoi (Psv) on Olive and for pv. nerii (Psn) on Oleander, while no information is available for pv. fraxini (Psf) on Ash. Nothing is known yet about the distribution on the different host plants and the real host range of these pathovars in nature, although cross-infections were observed following artificial inoculations. A multiplex Real-Time PCR assay was recently developed to simultaneously and quantitatively discriminate in vitro and in planta these P. savastanoi pathovars, for routine culture confirmation and for epidemiological and diagnostical studies. Here an innovative High-Resolution Melting Analysis (HRMA)-based assay was set up to unequivocally discriminate Psv, Psn and Psf, according to several single nucleotide polymorphisms found in their Type Three Secretion System clusters. The genetic distances among 56 P. savastanoi strains belonging to these pathovars were also evaluated, confirming and refining data previously obtained by fAFLP. To our knowledge, this is the first time that HRMA is applied to a bacterial plant pathogen, and one of the few multiplex HRMA-based assays developed so far. This protocol provides a rapid, sensitive, specific tool to differentiate and detect Psv, Psn and Psf strains, also in vivo and against other related bacteria, with lower costs than conventional multiplex Real-Time PCR. Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants