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. 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. 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.

Cassava, originally from South America, is the fourth most important source of calories in the developing world after the cereal crops wheat, maize, and rice. Worldwide, it feeds an estimated 700 million people directly or indirectly. Cassava production has increased steadily for the last 50 years, with 242 MT harvested in 2012. The increase is likely to continue as farmers in more than 105 countries come to recognize the crop’s advantages. A semi-perennial root crop, cassava can stay in the ground for up to 3 years. This makes it an excellent food security crop: when all other crops have been exhausted, cassava roots can still be harvested. It is naturally drought resistant and resilient to climatic changes, high temperatures, and poor soils, and in addition, cassava responds extremely well to high CO₂ concentrations, making it a very important crop for the 21st century. Africa alone accounts for more than 55 % o ...

The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative propagules) to serve as carriers of pests and pathogens (hereafter referred to as pests) and the risk of transboundary spread along with the seed movement present a high-risk factor for international germplasm distribution activities. Quarantine and phytosanitary procedures have been established by many countries around the world to minimize seed-borne pest spread by screening export and import consignments of germplasm. The effectiveness of these time-consuming and cost-intensive procedures depends on the knowledge of pest distribution, availability of diagnostic tools for seed health testing, qualified operators, procedures for inspection, and seed phytosanitation. This review describes a unique multidisciplinary approach used by the CGIAR Germplasm Health Units (GHUs) in ensuring phytosanitary protection for the safe conservation and global movement of germplasm from the 11 CGIAR genebanks and breeding programs that acquire and distribute germplasm to and from all parts of the world for agricultural research and food security. We also present the challenges, lessons learned, and recommendations stemming from the experience of GHUs, which collaborate with the national quarantine systems to export and distribute about 100,000 germplasm samples annually to partners located in about 90 to 100 countries. Furthermore, we describe how GHUs adjust their procedures to stay in alignment with evolving phytosanitary regulations and pest risk scenarios. In conclusion, we state the benefits of globally coordinated phytosanitary networks for the prevention of the intercontinental spread of pests that are transmissible through plant propagation materials.

Globalization and changing climates are aggravating the occurrence and impacts of transboundary pests, and driving the emergence of new threats. Most of the low- and middle-income countries in Africa, Asia and Latin America are not fully prepared in terms of surveillance, diagnostics, and deployment of plant health solutions due to several factors: adequate investment is lacking; knowledge is inadequate; and connections from the local to global, and global to local are insufficient. Effectively countering the current and emerging threats to plant health requires a holistic approach that includes: 1) globally coordinated diagnostic and surveillance systems; 2) epidemiological modelling, risk assessment, forecasting and preparedness for proactive management and containment; and 3) implementation of context-sensitive, eco-friendly, gender-responsive and socially inclusive integrated disease and pest management approaches to reduce the impacts of devastating transboundary pests and diseases. Despite several success stories where major pests and diseases have been brought to control through integrated approaches, further multi-institutional and multi-disciplinary efforts are necessary. Plant health management requires stronger interface between the biophysical and social sciences, and empowerment of local communities. These reflections derive from the proceedings of a webinar on “Transboundary Disease and Pest Management,” organized by CGIAR (Consultative Group on International Agricultural Research) on March 3, 2021, in recognition of the United Nations designated International Year of Plant Health.