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Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization., (© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd.)

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.

A proper understanding of the diversity of the available germplasm is an initial step for the genetic improvement of a crop through breeding. However, there is limited information on the diversity of Uganda's yam germplasm. The study sought to characterize the diversity of yam germplasm utilized for decades in Uganda together with germplasm recently introduced from West Africa using phenotypic traits. A germplasm collection of 291 genotypes was characterized using 28 phenotypic traits. Data were subjected to multivariate analysis using principal component analysis and cluster analysis. The traits assessed were informative and discriminating, with 62% of the total variation explained among the first six principal components. Results showed that the important phenotypic traits contributing to most of the variability among the genotypes were leaves, flowering, and tuber traits. Ugandan genotypes were identified with amorphous tuber shapes compared to West African genotypes. The study has shown that there is ample phenotypic variability within the major yam genotypes in Uganda yam germplasm that can be used for genetic improvement. More in-depth molecular and biochemical studies to further understand the diversity are recommended. The preprint was made available by research square in the following link: "https://www.researchsquare.com/article/rs-1518551/v1." [ABSTRACT FROM AUTHOR]

Taro is an ancient nutritional and medicinal crop woven into the fabric of the socio-economic life of those living in the tropics and sub-tropics. However, West Africa (WA), which has been a major producer of the crop for several decades, is experiencing a significant decline in production as a result of taro leaf blight (TLB), a disease caused by Phytophthora colocasiae Raciborski. A lack of research on taro in WA means that available innovative technologies have not been fully utilized to provide solutions to inherent challenges and enhance the status of the crop. Improvement through plant breeding remains the most economically and environmentally sustainable means of increasing the productivity of taro in WA. With this review, we provide insights into the importance of the taro crop in WA, evaluate taro research to date, and suggest how to address research gaps in order to promote taro sustainability in the region. [ABSTRACT FROM AUTHOR]

Introduction: Ninety-seven percent of yam ( Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs. Objectives: Metabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop. Methods: Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry. Results: A visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers. Conclusions: Metabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other '-omics' studies will deliver a significant advancement to yam breeding strategies. [ABSTRACT FROM AUTHOR]

Background: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results: To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions: Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. [ABSTRACT FROM AUTHOR]

Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. [ABSTRACT FROM AUTHOR]

The article presents a study which characterizes the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)-bred seed restorer lines of pearl millet plant in India. At the ICRISAT pearl millet improvement program, pollinator lines (R-lines) are developed with morphological and genetic diversity based on agronomic performance. It notes that the 114 designated restorer lines show the utilization of a wide range of germplasm and improved lines in developing R lines.

Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) targets highly diverse biotic and abiotic constraints, whilst meeting complex end-user quality preferences to improve livelihoods of beneficiaries in developing countries. Achieving breeding targets and increasing the rate of genetic gains for these vegetatively propagated crops, with long breeding cycles, and genomes with high heterozygosity and different ploidy levels, is challenging. Cheaper sequencing opens possibilities to apply genomics tools for complex traits, such as yield, climate resilience, and quality traits. Therefore, across the RTB program, genomic resources and approaches, including sequenced draft genomes, SNP discovery, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS), are at different stages of development and implementation. For some crops, marker-assisted selection (MAS) is being implemented, and GS has passed the proof-of-concept stage. Depending on the traits being selected for using prediction models, breeding schemes will most likely have to incorporate both GS and phenotyping for other traits into the workflows leading to varietal development. [ABSTRACT FROM AUTHOR]