Variability and genetic merits of white Guinea yam landraces in Nigeria

Open Access JournalIntroduction: Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa. Methods: A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits. Results and discussion: Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa

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

Farmers’ perspective toward a demand led yam breeding in Nigeria

Open Access JournalThis study seeks to increase the efficiency of yam breeding practice using farmers’ insight at the trait and socioeconomic levels. A three-staged multisampling procedure was employed and 792 yam farmers from four geopolitical zones, comprising 10 states and the Federal Capital Territory, Abuja in Nigeria were randomly selected. Farmer’s preference criteria and factors pertinent to improving the efficiency of yam breeding in Nigeria were documented. The data obtained were analyzed using a 5-point Likert scale to identify major traits farmers consider in the yam cultivar selection decision. Kendall’s coefficient of concordance was used to measure the degree of agreement of ranking among the farmers. Factors influencing farmers’ trait preference for yam cultivars were evaluated using a multinomial-ordered logistic regression model. The result revealed that yam varieties with high germination rates, disease-free quality, big tuber sizes, early maturity, and good pounding attributes are held in high esteem. The most critical constraint limiting the production of yam in the study area includes pest and disease attack, climate change, high cost of seed yam, high cost of staking, and weed infestation. Sex, age, access to credit, membership to yam association, total land owned, and years of experience as a yam farmer significantly influence farmers’ ability to select yam cultivars with preferred attributes. A strategic effort needs to be given to these farmers’ desired yam attributes and factored into developing improved yam varieties for increased adoption and enhanced food security in Nigeria

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

Population genomics of yams: evolution and domestication of Dioscorea species

Published online: 21 Aug 2021Yam is a collective name of tuber crops belonging to the genus Dioscorea. Yam is important not only as a staple food crop but also as an integral component of society and culture of the millions of people who depend on it. However, due to its regional importance, yam has long been regarded as an “orphan crop” lacking a due global attention. Although this perception is changing with recent advances in genomics technologies, domestication processes of most yam species are still ambiguous. This is mainly due to the complicated evolutionary history of Dioscorea species caused by frequent hybridization and polyploidization, which is possibly caused by dioecy that imposed obligate outcrossing to the species of Dioscorea. In this chapter, we provide an overview of the evolution of Dioscorea and address the domestication of yam from population genomics perspectives by focusing on the processes of hybridization and polyploidization. A review is given to the recent population genomics studies on the hybrid origin of D. rotundata in West and Central Africa, the global dispersion of D. alata through human migrations, and the whole-genome duplication of the South America species of D. trifida. In the end, we give a summary of current understanding of sex-determination system in Dioscorea

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

Diversity of water yam (Dioscorea alata L.) accessions from Cote d'Ivoire based on SNP markers and agronomic traits

Open Access Journal; Published online: 24 Nov 2021Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d’Ivoire

Diversity of white Guinea yam (Dioscorea rotundata Poir.) cultivars from Benin as revealed by agro-morphological traits and SNP markers

Open Access Article; Published online: 18 Oct 2021White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding

In vitro propagation: A biotechnological tool capable of solving the problem of medicinal plants decimation in South Africa

South Africa has a very rich plant biodiversity, many of which are medicinally useful. The rich resource is decreasing at an alarming rate as a result of over- exploitation. Plant in vitro regeneration is a biotechnological tool that offers a potential solution to this problem as it provides a means of putting the plants onto the market at lower prices. We present in this paper a review of micro propagation protocols developed for selected medicinal plants of South Africa and highlight the need for the utilization of this technology for the mass propagation of over-exploited medicinal plants in South Africa