Global demand for rice genetic resources

The International Rice Research Institute (IRRI) holds in trust the world's largest collection of rice diversity, with more than 130,000 accessions of cultivated rice and wild species. Between 2012 and 2018, a total of 2174 requests for rice germplasm were received from more than 1000 unique requestors. We documented and analyzed how genebank users made use of germplasm from IRRI. As we address food and nutrition security challenges in a changing context, we are motivated by the need to enhance the conservation, management, and use of rice genetic resources

Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections

Direct seeding saves time and labour in the cultivation of rice. However, seedling establishment is often unstable, and yields are lower than in transplanting. Anaerobic germination (AG) is a key trait for improvement of direct seeding of rice. We established a simple and reliable method of evaluating AG in rice breeding. We germinated seeds in distilled water or deoxygenated water and measured coleoptile length several days later; compared the results of each method with survival rate in flooded soil; and used the anoxic water method for QTL analysis and for testing cultivars. Coleoptile elongation in anoxic water and survival rate in flooded soil were significantly correlated (r = 0.879, P < 0.01). A significant QTL, likely to be a major gene (AG1), was found in chromosome segment substitution lines and in a backcrossed F2 population derived from tolerant and sensitive lines. Diverse rice genetic resources were classified into tolerant or sensitive accession groups reflecting their ecotypes. Our study revealed that anoxic water evaluation method saves space and time in a stable environment compared with flooded soil evaluation. It is applicable to QTL analysis and isolation of genes underlying anaerobic germination

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

2016 Africa-wide Breeding Task Force Trials for Rainfed Lowland - MET

In 2010, the Africa-wide Rice Breeding Task Force was launched by AfricaRice involving National Agricultural Research System (NARS) from about 30 countries. The objectives of the network are to evaluate the stability of traits incorporated in breeding processes and to identify varieties best fit to growth conditions in target regions and to markets. The Task Force also accumulates data on performance of new elite lines, thereby facilitating varietal release procedures. Furthermore, by exposing breeders from NARS and farmers to these elite lines during the testing phase, dissemination will be facilitated. The activities conducted by the Task Force consists of a series of consecutive trials. Promising breeding lines developed by AfricaRice or by national and international partners, such as IRRI, CIAT and the NARS are nominated for evaluation in one or several rice cultivation environments: rainfed lowland, irrigated lowland, rainfed upland, high elevation and mangrove. All nominated lines should be fixed and accompanied by supporting data on traits incorporated during the breeding process and with information on yield performance. These characteristics are checked at AfricaRice before incorporation into the network. The first phase (MET, Multi-Environment Testing) consists of an initial evaluation of about 100 lines selected from the nominated lines. Each national partner evaluates these lines at sites in his/her country. Such sites may be at an experimental station under optimal management to evaluate yield potential, or may be ‘hot spots’ to check the performance of the nominations in a stressed growth environment. Trials are replicated three times and include at least a common and a local check. The second phase (PET,Participatory Evaluation Trial) serves to evaluate and confirm the performance of the selected lines. These lines are cultivated using the same experimental design with 3 replications. An important feature of PET is that farmer and other stakeholders such as miller and traders are invited to participate in varietal selection and their opinion on the performance of all entries (i.e. participatory varietal selection, PVS) collected. Based on the data collected, observations by the breeders and the opinion of stakeholder groups, NARS partners select up to 10 lines. Further, NARS evaluated these lines in at least three sites per country and during one or more growing seasons, depending on varietal release requirements. All stakeholders are again invited to get acquainted with the new lines and voice their opinion to help select lines for further advancement. Among the 10 lines, farmers are invited to select three lines and cultivate these in their own fields, together with a common check and their own variety

2017 Africa-wide Breeding Task Force Trials for Rainfed Lowland

Objective and Requirement of MET by Breeding Task Force: In 2010, Rice Breeding Task Force in Africa was established aimed at accelerating the breeding process, especially in the later phase of evaluation of promising breeding lines in multi-locations throughout Africa. Breeding lines included in the multi-environment trials (MET) are developed by various institutions such as IRRI, CIAT, NARS in Africa and AfricaRice. The objective of the MET is to identify lines that are suitable for cultivation under an ecological environment in the target region in Africa. To reduce noise and to acquire real genetic differences among test lines through MET, the following conditions must be met for the MET: 1. Experimental field is uniform in soil fertility; 2. Experimental field is very well leveled before seeding or transplanting, to facilitate uniform water and fertilizer management; 3. Fertilizer is evenly applied to every plot, and ideally every plant within a plot; 4. Weed control, either by applying herbicide or hand weeding, is carried out uniformly across the whole trial, and finished in one day per time; 5. Any other operations, whatever necessary for a trial, are “uniformly done across the whole trial”. The MET serves as a part of a national testing program. In other words, the MET conducted by BTF is integrated into the corresponding national testing system. Data collected from the MET will be recognized and used by the Varietal Testing and Release Committee of a country where the MET is conducted. This is a measure to shorten breeding cycle and to increase genetic gains. Structure of varietal evaluation series has been changed since the season of 2017. Explanations of the changes 1. The number of entries is reduced to ensure better conduct of the trials and higher quality data. 1.1 For each sub-region (WCA and ESA), a maximum of 29 new entries per production system (irrigated lowland, rainfed lowland, rainfed upland, mangrove and high-elevation) is considered to enter the BTF (Phase I, former MET) each year. 1.2 After evaluation and data analysis, a maximum of 10 entries is selected for further evaluation (Phase II, former PET). 1.3 After evaluation and data analysis, a maximum of 3 entries is selected for further evaluation (Phase III, former PAT). 2. Materials from Phase I, II and III are combined into a single trial (up to 42 test entries every year). 3. Participatory varietal selection (PVS) may be conducted in the single trial (one replication may be chosen for the PVS). 4. The single trial is conducted in three different locations in each participating country and in priority in the Hubs. 5. The Farmers Adoption Trial (FAT) and Validation AfricaRice Trial (VAT) is removed from the BTF scheme. Where required, further testing of selected entries in farmers’ fields will be ideally handled by NARS with the assistance of Rice Agronomy Task Force. <br

2015 Africa-wide Breeding Task Force Trials for Rainfed Lowland - PET

In 2010, the Africa-wide Rice Breeding Task Force was launched by AfricaRice involving National Agricultural Research System (NARS) from about 30 countries. The objectives of the network are to evaluate the stability of traits incorporated in breeding processes and to identify varieties best fit to growth conditions in target regions and to markets. The Task Force also accumulates data on performance of new elite lines, thereby facilitating varietal release procedures. Furthermore, by exposing breeders from NARS and farmers to these elite lines during the testing phase, dissemination will be facilitated. The activities conducted by the Task Force consists of a series of consecutive trials. Promising breeding lines developed by AfricaRice or by national and international partners, such as IRRI, CIAT and the NARS are nominated for evaluation in one or several rice cultivation environments: rainfed lowland, irrigated lowland, rainfed upland, high elevation and mangrove. All nominated lines should be fixed and accompanied by supporting data on traits incorporated during the breeding process and with information on yield performance. These characteristics are checked at AfricaRice before incorporation into the network. The first phase (MET, Multi-Environment Testing) consists of an initial evaluation of about 100 lines selected from the nominated lines. Each national partner evaluates these lines at sites in his/her country. Such sites may be at an experimental station under optimal management to evaluate yield potential, or may be ‘hot spots’ to check the performance of the nominations in a stressed growth environment. Trials are replicated three times and include at least a common and a local check. The second phase (PET,Participatory Evaluation Trial) serves to evaluate and confirm the performance of the selected lines. These lines are cultivated using the same experimental design with 3 replications. An important feature of PET is that farmer and other stakeholders such as miller and traders are invited to participate in varietal selection and their opinion on the performance of all entries (i.e. participatory varietal selection, PVS) collected. Based on the data collected, observations by the breeders and the opinion of stakeholder groups, NARS partners select up to 10 lines. Further, NARS evaluated these lines in at least three sites per country and during one or more growing seasons, depending on varietal release requirements. All stakeholders are again invited to get acquainted with the new lines and voice their opinion to help select lines for further advancement. Among the 10 lines, farmers are invited to select three lines and cultivate these in their own fields, together with a common check and their own variety

2018 Africa-wide Breeding Task Force Trials for Rainfed Lowland

In 2010, the Africa-wide Rice Breeding Task Force was launched by AfricaRice involving National Agricultural Research System (NARS) from about 30 countries. The objectives of the network are to evaluate the stability of traits incorporated in breeding processes and to identify varieties best fit to growth conditions in target regions and to markets. The Task Force also accumulates data on the performance of new elite lines, thereby facilitating varietal release procedures. Furthermore, by exposing breeders from NARS and farmers to these elite lines during the testing phase, dissemination will be facilitated. The activities conducted by the Task Force consists of a series of consecutive trials. Promising breeding lines developed by AfricaRice or by national and international partners, such as IRRI, CIAT and the NARS are nominated for evaluation in one or several rice cultivation environments: rainfed lowland, irrigated lowland, rainfed upland, high elevation and mangrove. All nominated lines should be fixed and accompanied by supporting data on traits incorporated during the breeding process and with information on yield performance. These characteristics are checked at AfricaRice before incorporation into the network. Further details are in the “2018-Rainfed Lowland-protocol.pdf

Soil-based screening for iron toxicity tolerance in rice using pots

The objective of this study was to assess the reliability of pot-based screening method for iron (Fe) toxicity tolerance in rice using soils from hot spots. Five lowland rice varieties with known reaction to Fe toxicity were grown in pots in a screen house for three seasons. Fe-toxic soils from two hot spot fields – Edozighi, Nigeria and Niaouli, Benin were used and soil from Africa Rice Center (AfricaRice) experimental farm, Cotonou, Benin was included as control. Leaf bronzing score (LBS) was determined at different stages, and grain yield was determined at maturity. Heritability was estimated using data across the three seasons. High heritability was recorded for LBS and grain yield. Grain yield reduction in stress treatment relative to control varied from 15 to 56% depending on the variety and soil. Bao Thai, Suakoko 8, and WITA 4 had better performance under Fe toxicity in terms of LBS, yield and relative yield reduction, whereas Bouake 189 and IR64 had poorer performance. Grain yield and LBS were significantly correlated but negatively at 60 days after sowing (DAS). Overall, the results found in this experiment were consistent with previous field studies. Therefore, pot screening using soils from hot spots can be used by rice breeding programs to reliably assess Fe toxicity tolerance ex situ

Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Abstract Background Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties. However, the molecular basis of the traits in NU varieties is largely unknown. Results Whole genome re-sequencing was performed of four NU lines (3, 4, 5, and 7) and for the parental Oryza sativa WAB56–104 and Oryza glaberrima CG14. The k-mer analysis predicted large genomes for the four NU lines, most likely inherited from WAB56–104. Approximately 3.1, 0.10, and 0.40 million single nucleotide polymorphisms, multi nucleotide polymorphisms, and short insertions/deletions were mined between the parental lines, respectively. Integrated analysis with another four NU lines (1, 2, 8, and 9) showed that the ratios of the donor CG14 allelic sites in the NU lines ranged from 1.3 to 9.8%. High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common. Segregation of genic segments revealed potential causal genes for some agronomic traits including grain shattering, awnness, susceptibility to bacterial leaf bright, and salt tolerance. Analysis of unmapped sequences against the reference cultivar Nipponbare indicated existence of unique genes for pathogen and abiotic stress resistance in the NU varieties. Conclusions The results provide understanding of NU genomes for rice improvement for Africa reinforcing local capacity for food security and insights into molecular events in breeding of interspecific hybrid crops

Genetic Improvement of Iron Toxicity Tolerance in Rice-Progress, Challenges and Prospects in West Africa

In sub-Saharan Africa, the demand for higher rice production continues to grow rapidly. Although there is a huge potential for increasing rice production through expansion of the rice cultivation area in wetlands, iron (Fe) toxicity tends to occur and consequently results in low rice yield. Development and deployment of varieties tolerant to Fe toxicity is one of the practical options to overcome this constraint. Several tolerant varieties have been developed through conventional breeding but progress in breeding has been generally slow mainly due to large genotype × environment interaction and field heterogeneity, which make rice selection ineffective. In addition, there are no valid managed-stress screening protocols which are highly efficient and that can predict rice performance in the diverse target environments of West Africa. Many O. glaberrima accessions have superior tolerance, but only a few of them have been utilized in breeding programs. The known quantitative trait loci (QTLs) related to Fe toxicity, have not been used for marker-assisted selection (MAS), as they gave small effects with a large confidence interval. Accelerating rice breeding efficiency for tolerance to Fe toxicity requires establishment of reliable screening protocols, use of O. glaberrima accessions as donors, identification of large-effect QTLs and MAS using such QTLs. This paper reviews the past and current efforts in West Africa to develop new varieties with superior tolerance to Fe toxicity