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Rice is a major grain crop in numerous countries. In lowland areas, high iron levels in the soil severely hinder its cultivation. The current study explored high-yielding and Fe-toxicity-tolerant irrigated lowland rice (340 lines) among a population derived from a cross between Suakoko 8 and Bao Thai in Edozighi and Ibadan, Nigeria. In contrast to Ibadan, the soils in Edozighi contain a significant amount of iron. For the stated purpose, we carried out a two-year experiment using an alpha lattice design. The data showed significant differences between genotypes for the days to heading, plant height, number of tillers per plant, number of panicles per plant, panicle length, and grain yield. The results revealed that multiple characteristics had both direct and indirect effects on cultivated rice yields. There was a direct and positive influence on the number of days in the 50% heading period (0.31), a direct and negative effect on plant height (−0.94), a direct and positive effect on tiller and panicle numbers, and a direct but negative effect on panicle length (−0.56). The leaf bronzing score was adversely correlated with yield, panicle length, and plant height, while it was positively correlated with the number of panicles, tillers, and days to heading. The findings showed significant changes in yield and yield characteristics between genotypes. Grain yields ranged from 283 to 11,700 kg/ha in the absence of iron in the soil, contrary to 0 to 8230 kg/ha in soil with iron toxicity, with losses estimated between 6 and 94%, demonstrating the resulting disaster. In contrast to the elite parents and varieties used in this study, the ten top genotypes exhibited smaller losses in yield. The authors strongly recommend using these lines for further studies as donors or releasing them in farmer fields in Africa.

Abstract Background 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. Methods We examined the patterns of use of the IRRI genebank using distribution data and analyzed the results from a survey of germplasm recipients. The 2019 IRRI genebank user survey is the most recent attempt to obtain structured feedback from genebank end-users in multiple countries on their use of rice germplasm since 1995. We received 244 responses (a 35% response rate) out of the complete list of 694 respondents with valid email addresses. We also tested the relationship between the availability of germplasm information, proxied by the passport data completeness index (PDCI), and the demand for rice accessions, measured by the number of requests for each unique accession using a Negative Binomial regression model. We hypothesized that materials that are better documented are more frequently requested by users because they offer more useful information for targeted research and breeding. Results Between 2012 and 2018, requests for germplasm from outside IRRI were received from 63 countries in all regions of the world, mostly from Asia. IRRI distributed germplasm externally to requestors from universities (32%), national research programs (14%), private companies (9%), and individuals, including farmers (24%) as well as other CGIAR centers (3%). The traits sought most often were tolerances to environmental stresses, followed by tolerance or resistance to biotic stresses. The majority of survey respondents confirmed the usefulness of IRRI germplasm for research, breeding, characterization, and evaluation. The analytical model confirmed the significant positive relationship between PDCI values and the demand for those accessions. The results indicated that improving the availability of information at the accession level will enhance the use of those materials. To the best of our knowledge, this study is the first to show the empirical link between documentation and use of germplasm. Conclusions The findings demonstrate the crucial role of IRRI's genebank as a key germplasm source for global rice research and development, with important implications for the conservation and use of rice genetic diversity in the future. Public sector organizations and the scientific community in general benefit from the conservation and availability of rice genetic resources. We also show the importance of the availability of data on conserved accession to enhance their use. To sustain the benefits, continuous investment in genebanks is needed to allow them to adapt to changes in technology and agricultural context.

Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.

Climate change is expected to significantly increase submergence stress of lowland rice (Oryza sativa) production in Africa. There is a need to further improve the ability of SUB1 gene to tolerate submergence stress. Genetic control of submergence tolerance was studied in a moderately tolerant to submergence African rice landrace "TOS6454." Three mapping populations with a total of 1182 lines were developed by crossing TOS6454 with three popular rice varieties of West Africa that are high‐yielding but submergence susceptible, that is, FARO44, FARO52, and FARO60. The screening for submergence was conducted at the Africa Rice Center (AfricaRice) station in Ibadan, Nigeria during 2016–2018. The three mapping populations were genotyped with single nucleotide polymorphic markers either on the Kompetitive allele specific PCR or the DArTseq platforms. Quantitative trait locus (QTL) analysis revealed five different QTLs on chromosomes 1, 2, 3, 4, and 9. The QTLs on chromosomes 2 (qSUB2) and 9 (qSUB9) had consistent large effects and the tolerance alleles were contributed by TOS6454. The QTL on chromosome 9 (qSUB9) had a large effect on submergence tolerance in all three mapping populations. This QTL had a highest logarithm of odds (LOD) score of 30.46 and explained as much as 27.7% phenotypic variation (R2), with an additive effect of up to 9.39. The QTL on chromosome 2 (qSUB2) had a highest LOD score of 10.78 and explained up to 10.8% R2 for this trait. Furthermore, qSUB2 had positive epistasis with qSUB9 which further increased submergence tolerance. A total of 57 lines carrying both qSUB2 and qSUB9 alleles were superior to all other lines in submergence tolerance. qSUB9 co‐segregated with ART5 a marker for the SUB1 gene; thus, it is suggested that qSUB9 is the same as the well‐known SUB1 gene. Pyramiding qSUB2 with the SUB1 gene locus is expected to further improve submergence tolerance in elite rice varieties. Core Ideas: qSUB2 is a novel major effect QTL for submergence and was discovered in the African rice germplasm.qSUB2 had positive epistasis with qSUB9 which further increased submergence tolerance.qSUB2 QTL can be used in combination with SUB1 to enhance submergence tolerance of rice cultivars. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]