Morpho-agronomic and molecular characterisation of Oryza glaberrima germplasm from Mali

In order to exploit the important agronomic traits that make Oryza glaberrima Steud suitable for harsh growing conditions, 79 Riz Africain du Mali (RAM) including four checks of known cultivated rice species (Oryza sativa and O. glaberrima) were used for both field evaluation over two seasons (2007 and 2008) and assessment of molecular diversity. The molecular characterization showed all the 37 SSR markers used amplified and were polymorphic. The average heterozygosity of the accessions were relatively higher (0.18) than some earlier studies. The population from Mopti and Gao had a higher genetic diversity than other populations. Clustering of individuals showed no clear pattern of grouping based on either location or growing condition; this is due to the higher gene flow (Nm = 7.83) that may occur between different growing condition within location. Moreover, populations from different locations were highly differentiated (fst = 0.06) as compared to populations from different growing conditions (fst = 0.03). The dendrogram based on populations from different growing conditions revealed more similarity among populations with relatively similar growing conditions. Accessions such as, RAM116, RAM100 and RAM122, performed better under drought with a grain weight advantage of 40, 16 and 6.7% respectively over the best performing check.Key words: Genetic diversity, SSR markers, drought tolerance, Oryza glaberrima

CGIAR genebank viability data reveal inconsistencies in seed collection management

Genebanks underpin global food security, conserving and distributing agrobiodiversity for use in research and breeding. The CGIAR collections include >700,000 seed accessions, held in trust as global public goods. However, the role of genebanks in contributing to global food security can only be realized if collections are effectively managed. Examination of the historical viability monitoring data from seven CGIAR genebanks confirmed that high seed viability was maintained for many decades for the various crops and forage species. However, departures from optimum management procedures were revealed, and there were insufficient data gathered to derive reliable estimates of longevity needed to better forecast regeneration requirements, estimate the size of seed lots that should be stored, and optimize accession monitoring intervals

Technical assistance to strengthen national agricultural research organizations’ capacity to use digital sequence information. A submission from CGIAR

CGIAR submitted this report in response to an open request from the Plant Treaty Secretary, for submissions regarding, a) contracting parties’ and stakeholders’ capacity building needs for accessing and using digital sequence information (DSI)/genomic sequence data (GSD) and b) ‘technical assistance’ and ‘actions taken’ by stakeholders (including CGIAR) ‘to reduce the existing gap on capacity regarding DSI/GSD’. The primary objective of this paper is to respond to the second part of the request by sharing information about how CGIAR Centers and Initiatives have been assisting organizations outside CGIAR to access, generate, share, analyse, and use DSI for the conservation of plant genetic resources for food and agriculture (PRGFA) and for the use of PGRFA in pre-breeding and breeding. This paper does not provide an exhaustive account of all of the Centers’ relevant activities, but it does provide a general overview of the kinds of activities in which the Centers have been engaged. CGIAR very much appreciates the Governing Body’s initiative, as expressed in Resolution 16/2022, to ask the Plant Treaty Secretariat to gather and synthesize information about both demand for, and supply of, capacity strengthening related to DSI linked to plant genetic resources for food and agriculture, with the overall objective of working to close the capacity gap between developed and developing countries. It is our hope that, based on the outcomes of this exercise, CGIAR will be able to further adapt and improve its own approach to capacity sharing in response to needs prioritized by the Governing Body

Digital sequence information is changing the way genetic resources are used in agricultural research and development: implications for new benefit-sharing norms

This paper analyses the ways in which CGIAR Centers use digital sequence information (DSI) in their efforts to conserve and sustainably utilize the world’s most important crop and livestock genetic diversity. The paper then reflects on which of the benefit-sharing options currently under consideration by the Contracting Parties to the CBD (and the versions of those options that must be considered by the Governing Body of the Plant Treaty and the UN FAO Commission on Genetic Resources for Food and Agriculture) would provide effective policy support for the continued use of DSI in agricultural research and development in the future

Domestication history and geographical adaptation inferred from a SNP map of African rice

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa-3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began-13,000-15,000 years ago with effective population size reaching its minimum value-3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within-300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species

Genetic relationships between interspecific lines derived from Oryza glaberrima and Oryza sativa crosses using microsatellites and agro-morphological markers

New Rice(s) for Africa (NERICA) are high yielding rice varieties mostly cultivated in Sub-Saharan Africa and developed by the Africa Rice Center. This study is aimed at investigating the proportion of introgression of parental genomic contribution of 60 lowland NERICA varieties and establishment of molecular profiling. Agro-morphological data from 17 characteristics was recorded and significant (p<0.05) to high significant (p<0.0001) differences were obtained with leaf length and width, plant height at maturity, days to heading, maturity, primary and secondary branching of panicles, and grain width and grain thickness. A total of 114 microsatellite polymorphic markers covering 2183.13 cM of the rice genome showed the proportions of alleles introgressed from the donor parent (Oryza glaberrima) into 52 lowland NERICA lines (TOG5681 and IR64) as follows: 11% for BC2, 6.07% for BC3, and 7.55% for BC4. The introgression proportions for the eight remaining lowland NERICA lines derived from other crosses ranged from 5.5 to 11.3%. The proportion recorded with the recurrent parent was 83.99%. The highest introgression proportions of the O. glaberrima allele for all 60 lowland NERICA lines were found on chromosomes 2, 6 and 12 (TOG5681/IR64) and on chromosome 3 with NERIC-L-29 (TOG5681/IR1529-680-3-2). Multivariate analyses performed using an association of agro-morphological and molecular data revealed two major groups according to the distribution of the lowland NERICAs including the lowland NERICAs released were found in cluster 1 of the dendrogram. Genetic and genomic studies, QTL identification and analysis using agro-morphologically significant traits revealed should be used to develop mega-varieties adapted in rice growth conditions in Sub-Saharan Africa