"Breaking through the 40% adoption ceiling: Mind the seed system gaps." A perspective on seed systems research for development in One CGIAR.

Seed systems research is central to achieving the United Nations Sustainable Development Goals. Improved varieties with promise for ending hunger, improving nutrition, and increasing livelihood security may be released, but how do they reach and benefit different types of farmers? Without widespread adoption the genetic gains achieved with improved crop varieties can never be actualized. Progress has been made toward demand responsive breeding, however the draft CGIAR 2030 Research and Innovation Strategy fails to recognize the complexity of seed systems and thus presents a narrow vision for the future of seed systems research. This points to the lack of evidence-based dialogue between seed systems researchers and breeders. This perspective paper presents findings from an interdisciplinary group of more than 50 CGIAR scientists who used a suite of seed systems tools to identify four knowledge gaps and associated insights from work on the seed systems for vegetatively propagated crops (VPCs), focusing on bananas (especially cooking bananas and plantains), cassava, potato, sweetpotato, and yam. We discuss the implications for thinking about and intervening in seed systems using a combined biophysical and socioeconomic perspective and how this can contribute to increased varietal adoption and benefits to farmers. The tools merit wider use, not only for the seed systems of VPCs, but for the seed of crops facing similar adoption challenges. We argue for deeper collaboration between seed systems researchers, breeders and national seed system stakeholders to address these and other knowledge gaps and generate the evidence and innovations needed to break through the 40% adoption ceiling for modern varieties, and ensure good quality seed once the new varieties have been adopted. Without this, the achievements of breeders may remain stuck in the seed delivery pipeline.

Potential returns to yam research investment in sub-Saharan Africa and beyond.

Lack of good-quality planting materials has been identified as the most severe problem militating against increased agricultural productivity in sub-Saharan Africa (SSA) and beyond. However, investment of research efforts and resources in addressing this menace will only be feasible and worthwhile if attendant economic gains are considerable. As a way of investigating the economic viability of yam investment, this research has been initiated to address problems confronting yam productivity in eight countries of SSA and beyond: Nigeria, Ghana, Benin, Togo, Côte d'Ivoire, Papua New Guinea, Jamaica, and Columbia. Research options developed were to be deployed and disseminated. Key technologies include the adaptive yam minisett technique (AYMT), varieties adapted to low soil fertility and drought, nematode-resistant cultivars (NRC), and crop management and postharvest practices (CMPP). This article aims at estimating the potential economic returns, the expected number of beneficiaries, and poverty reduction consequent to the adoption of technology options. Estimates show that the new land area that will be covered by the technologies in the eight countries will range between 770,000 ha and 1,000,000 ha with the highest quota accounted for by AYMT. The net present value will range between US$584 and US$1392 million and was highest for the NRC. The CMPP had the lowest benefit-cost ratio of 7.74. About 1,049,000 people would be moved out of poverty by these technologies by 2037 in the region. These technologies are less responsive to changes in cost than that in adoption rate. Therefore, the realization of the potential economic gains depends on the rate and extent of adoption of these technologies. Giving the knowledge-intensive nature of some of these interventions, capacity building of potential adopters will be critical to increasing the sustainability of the yam sector, thereby enhancing food security and reducing poverty.

High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance.

Cassava bacterial blight (CBB), incited by Xanthomonas axonopodis pv. manihotis (Xam), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65 Xam strains and deduce the phylogenetic relatedness of Xam across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.

Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (Dioscorea alata).

Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Genome of the African cassava whitefly Bemisia tabaci and distribution and genetic diversity of cassava-colonizing whiteflies in Africa.

The whitefy Bemisia tabaci, a species complex consisting of many morphologically indistinguishable species divided into distinct clades, is one of the most globally important agricultural pests and plant virus vectors. Cassava-colonizing B. tabaci transmits viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Half of all cassava plants in Africa are affected by these viral diseases, resulting in annual production losses of more than US$ 1 billion. Here we report the draft genome of the cassava whitefly B. tabaci Sub-Saharan Africa - East and Central Africa (SSA-ECA), the super-abundant population that has been associated with the rapid spread of viruses causing the pandemics of CMD and CBSD. The SSA-ECA genome assembled from Illumina short reads has a total size of 513.7 Mb and a scaffold N50 length of 497 kb, and contains 15,084 predicted protein-coding genes. Phylogenetic analysis suggests that SSA-ECA diverged from MEAM1 around 5.26 million years ago. A comprehensive genetic analysis of cassava-colonizing B. tabaci in Africa was also conducted, in which a total of 243 whitefly specimens were collected from 18 countries representing all major cassava-growing regions in the continent and genotyped using NextRAD sequencing. Population genomic analyses confirmed the existence of six major populations linked by gene flow and inferred the distribution patterns of these populations across the African continent. The genome of SSA-ECA and the genetic findings provide valuable resources and guidance to facilitate whitefly research and the development of strategies to control cassava viral diseases spread by whiteflies.