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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.

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.

The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization’s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks’ trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers’ acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers’ distributions of PGRFA included the extent of accession-level information, users’ capacity to identify the materials they want, and policies. The genebanks’ rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.

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.

More than 60% of phosphorus (P) taken up by rice (Oryza spp) is accumulated in the grains at harvest and hence exported from fields, leading to a continuous removal of P. If P removed from fields is not replaced by P inputs then soil P stocks decline, with consequences for subsequent crops. Breeding rice genotypes with a low concentration of P in the grains could be a strategy to reduce maintenance fertilizer needs and slow soil P depletion in low input systems. This study aimed to assess variation in grain P concentrations among rice genotypes across diverse environments and evaluate the implications for field P balances at various grain yield levels. Multi-location screening experiments were conducted at different sites across Africa and Asia and yield components and grain P concentrations were determined at harvest. Genotypic variation in grain P concentration was evaluated while considering differences in P supply and grain yield using cluster analysis to group environments and boundary line analysis to determine minimum grain P concentrations at various yield levels. Average grain P concentrations across genotypes varied almost 3-fold among environments, from 1.4 to 3.9 mg g-1. Minimum grain P concentrations associated with grain yields of 150, 300 and 500 g m-2 varied between 1.2 and 1.7, 1.3 and 1.8 and 1.7 and 2.2 mg g-1 among genotypes respectively. Two genotypes, Santhi Sufaid and DJ123, were identified as potential donors for low grain P concentration. Improvements in P balances that could be achieved by exploiting this genotypic variation are in the range of less than 0.10 g P m-2 (1 kg P ha-1) in low yielding systems, and 0.15 to 0.50 g P m-2 (1.5-5.0 kg P ha-1) in higher yielding systems. Improved crop management and alternative breeding approaches may be required to achieve larger reductions in grain P concentrations in rice.

Genetic control of yield under reproductive-stage drought stress was studied in a population of 436 random [F.sub.3]-derived lines from a cross between the upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Screening was conducted under upland conditions at IRRI during the dry seasons of 2005 and 2006. Lines were evaluated in drought stress and nonstress trials in both years to identify QTL contributing to drought resistance. For QTL detection, a set of random lines and the highest and lowest-yielding lines under both stress and nonstress conditions were genotyped by 126 SSR markers. A QTL (qtl12.1) with a large effect on grain yield under stress was detected on Chromosome 12 in both years. The whole population was genotyped for additional markers on Chromosome 12, allowing QTL localization to a 10.2 cM region between SSR markers RM28048 and RM511. Under stress conditions, the locus also increased harvest index, biomass yield, and plant height while reducing the number of days to flowering. Under nonstress conditions, qtl12.1 did not significantly affect any trait. The additive effect of this QTL on grain yield under stress was 172 kg [ha.sup.-1] per year over the 2 yr of testing, representing 47% of the average yield under stress and explaining 51% of the genetic variance. The yield-increasing allele was derived from the susceptible parent, Way Rarem, suggesting an epistatic effect. This is the first QTL reported in rice having a large and repeatable effect on grain yield under severe drought stress in the field.