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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 defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.

Although Moringa oleifera Lam. (Moringaceae) is a multipurpose tree with remarkable nutritional and therapeutic benefits, it is undervalued and neglected in Kenya, as the local people associate it with famine and poverty. The present study aims to assess and document the traditional knowledge on use and management as well as production constraints of the species among the Mijikenda community in Kilifi County, Kenya. We found that the plant is locally used as food and medicine for various ailments, including diabetes, high blood pressure, ulcers, stomach aches, and body pains. In addition, the plant is used for fencing and as a source of fuel. Watering and pruning were found to be the main management practices of the plant. Slightly more than half (51.3%) of the respondents reported pests as a constraint in growing the plant, while the bitter taste (60.5%) and small leaves (36.8%) were deterrents to its consumption and harvesting, respectively. More than half (55.3%) of the respondents had between one and five trees in their compounds, indicating a low preference for the plant compared to major crops. The plant species is undervalued compared to locally grown major crops, highlighting the need for concerted efforts to raise awareness of its potential benefits and address the production challenges. [ABSTRACT FROM AUTHOR]

Abstract: Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses [...]

Sesbania sesban (L.) Merr. is a multipurpose legume tree grown primarily for fodder and forage in the tropical and subtropical world. In this study, the Sesbania sesban collection maintained in the International Livestock Research Institute (ILRI) forage Genebank was studied using genome-wide markers generated on the DArTseq platform. Genotyping produced 84,673 and 60,626 SNP and SilicoDArT markers with a mean polymorphic information content of 0.153 and 0.123, respectively. From the generated markers, 7587 and 15,031 highly informative SNP and SilicoDArT markers, respectively, were filtered and used for genetic diversity analysis and subset development. Analysis of molecular variance (AMOVA) revealed higher variability 'within' (52.73% for SNP markers and 67.36% for SilicoDArT markers) than 'between' accessions. Hierarchical cluster analysis showed the presence of four main clusters in the collection. Mantel correlation analysis showed a lack of relationship between genetic variation of the germplasm and their geographical origin. A representative subset of 34 accessions containing germplasm from diverse origins and agro-ecologies was developed using SNP markers. The genetic diversity information generated in this study could be used for marker-assisted screening for stress tolerance, gap analysis and identification and acquisition of new distinct genotype(s) to broaden the genetic basis of the collection for future improvement programs to develop high-yielding, stress-tolerant varieties for enhancing food and environmental security in crop–livestock-based production systems. [ABSTRACT FROM AUTHOR]

Canarium tramdenum occurs naturally in subtropical and tropical regions of Indochina and China. The wood is used for making high quality furniture and the fruit and leaves are used in traditional medicine. However, a lack of information on genetic diversity and population structure has handicapped the genetic conservation and domestication of this high-value species. This study evaluated genetic variation within and among four C. tramdenum populations. Sixty individuals were collected from four natural populations in Vietnam in the provinces of Ninhbinh, Bacgiang, Nghean, and Backan. Genetic diversity and genetic structure were determined using 20 ISSR markers. A total of 192 DNA fragments with sizes ranging from 110 bp to 3,000 bp were detected, of which 154 segments (80.2%) were polymorphic and 38 segments (19.8%) were monomorphic. The ISSR data indicated a moderate degree of genetic diversity for the species (h = 0.252). The four populations were separated into three genetic clusters with low levels of genetic distance between them. AMOVA result showed that most (78%) of the genetic variation was within the populations. The moderate to high genetic diversity of C. tramdenum and the low genetic differentiation among populations suggested that all existing natural populations in the particular regions needed to be preserved to protect the genetic diversity of this species. [ABSTRACT FROM AUTHOR]