Search

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

The flavor and health benefits of coffee (Coffea spp.) are derived from the metabolites that accumulate in the mature bean. However, the chemical profiles of many C. canephora genotypes remain unknown, even as the production of these coffee types increases globally. Therefore, we used Gas Chromatography-Mass Spectrophotometry to determine the chemical composition of C. canephora genotypes in Nigeria-those conserved in germplasm repositories and those cultivated by farmers. GC-MS revealed 340 metabolites in the ripe beans, with 66 metabolites differing (p-value < 0.05) across the represented group. Univariate and multivariate approaches showed that the 'Niaouli' genotypes could be clearly distinguished from 'Kouillou' and 'Java' genotypes, while there was almost no distinction between 'Kouillou' and 'Java,'. Varietal genotyping based on bean metabolite profiling was synchronous with that based on genome-wide Single Nucleotide Polymorphism analysis. Across genotypes, the sucrose-to-caffeine ratio was low, a characteristic indicative of low cup quality. The sucrose-to-caffeine ratio was also highly correlated, indicative of common mechanisms regulating the accumulation of these compounds. Nevertheless, this strong correlative link was broken within the 'Niaouli' group, as caffeine and sucrose content were highly variable among these genotypes. These 'Niaouli' genotypes could therefore serve as useful germplasm for starting a Nigerian C. canephora quality improvement breeding program.

Coffea canephora is an important economic crop in Nigeria, however, little is known about the diversity inherent within, and the genetic relationship among coffee grown and conserved in the country. We examined the genetic diversity and relatedness among 48 Coffea genotypes which included: (a) C. arabica, C. abeokutae, C. liberica, and C. stenophylla, (b) 14 C. canephora accessions conserved in the germplasm of Cocoa Research Institute of Nigeria (CRIN), and (c) 30 farmer-cultivated genotypes collected from South-Western Nigeria. By analyzing 433048 single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing we discovered that previous characterizations of C. canephora based on morphological data were inconclusive. Here, we established the correct number of C. canephora varieties present in the CRIN genebank which was four and not six as previously described based on morphological characters. We found three distinct diversity structures within the C. canephora genepool that were dominated by a single genetic group determined from passport descriptors to most likely be of Congolese (Democratic Republic of Congo) origin. High uniformity was also found among the farmer-cultivated accessions with 99% of them representing C. canephora var. Niaouli as their ancestral background. The analysis showed that the genetic base of coffee germplasm in Nigeria is narrow compared to the large genetic diversity of C. canephora. Therefore, broadening this genetic base through future acquisition and hybridization is imperative. However, the relatively high genetic differentiation (FST estimate = 0.3037) identified between Java Robusta and Niaouli will be used as a starting point for our breeding program.

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world's production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers' fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers. [ABSTRACT FROM AUTHOR]

Introduction: Yam is an important crop for food security in East and West Africa due to its high market value and customer demand. High tuber quality with yield and disease resistance are the main traits for acceptability of yam cultivars across the tropical zone. There has been limited progress in enhancing the production and quality traits of yams, despite the significant socio-economic significance of this crop. Method: To expedite the development of high-quality yam cultivars in Uganda, traits association study was conducted to identify genomic regions associated with key traits such as disease resistance, high yields, and dry matter content. The association mapping was conducted with multi-random mixed linear model (mrMLM) to compute the associations using five genetic models. Results: A total of 16 significant single nucleotide polymorphisms (SNPs) markers were identified to be associated with the traits studied. Gene identification analysis revealed the presence of key putative genes such as Vicilin-like seed storage protein At2g28490 (ARATH)and Growth-regulating factor 1 involved in a variety of functions ranging from storage and gene regulation for disease resistance. Discussion: The results obtained from this work have significant implications for the in-depth analysis of the genetic structure underlying key traits in yam. Additionally, this study emphasizes the identification of SNP variants and genes that may be utilized for genomic-informed selection in order to enhance yield and disease resistance in yams. [ABSTRACT FROM AUTHOR]

Introduction: Yam is an important crop for food security in East and West Africa due to its high market value and customer demand. High tuber quality with yield and disease resistance are the main traits for acceptability of yam cultivars across the tropical zone. There has been limited progress in enhancing the production and quality traits of yams, despite the significant socio-economic significance of this crop. Method: To expedite the development of high-quality yam cultivars in Uganda, traits association study was conducted to identify genomic regions associated with key traits such as disease resistance, high yields, and dry matter content. The association mapping was conducted with multi-random mixed linear model (mrMLM) to compute the associations using five genetic models. Results: A total of 16 significant single nucleotide polymorphisms (SNPs) markers were identified to be associated with the traits studied. Gene identification analysis revealed the presence of key putative genes such as Vicilin-like seed storage protein At2g28490 (ARATH)and Growth-regulating factor 1 involved in a variety of functions ranging from storage and gene regulation for disease resistance. Discussion: The results obtained from this work have significant implications for the in-depth analysis of the genetic structure underlying key traits in yam. Additionally, this study emphasizes the identification of SNP variants and genes that may be utilized for genomic-informed selection in order to enhance yield and disease resistance in yams. [ABSTRACT FROM AUTHOR]