African Rice Research Articles

The importance of farm management training for the African rice Green Revolution: Experimental evidence from rainfed lowland areas in Mozambique

The effectiveness of basic farm management training (e.g., seed selection, nursery bed setup, field leveling, bund construction, and transplanting) for the African rice Green Revolution has not been fully examined. This study evaluated a randomized controlled trial (RCT) of such training in the remote rainfed lowland areas of Mozambique. The training taught these practices without introducing modern varieties or inorganic fertilizers. The intention-to-treat (ITT) effect on paddy yield was 447–546 kg/ha (29 %–36 % of the control group average yield), with statistical significance at 7 %–8%. The results indicate that the adoption of these basic practices alone can improve paddy yield without relying on modern purchased inputs, which are usually not readily available in remote local markets or affordable to cash-constrained farmers. Complementarity among these basic practices is also suggested in that the yield increase had the highest statistical significance when all five practices were adopted.

Physiological Response of Selected Rice Accessions to Salinity and In Silico Analysis of DREB1A Gene Among Diploid Oryza Species

The responses of selected rice accessions to variant salt concentrations and in-silico analysis of DREB1A gene among diploid Oryza species were evaluated. Ten (10) rice accessions were selected based on their popularity in farmer's fields. Seedlings of each variety (one per pot) were watered with variant salt concentrations of 0mM, 100mM and 200mM for 21 days. The morpho-physiological characters (plant height, number of tillers, root length and dry weight) were evaluated using a standard evaluation system for rice. The reference sequences of OsDREB1A and AtDREB1A were used as queries to search against the 10 diploid Oryza species in the BLASTN of the PlantEnsembl database to reveal DREB1A orthologs. The retrieved DREB1A orthologs were used to compute the physicochemical properties of their proteins, gene motifs, intron-exon architecture and phylogenetic relationship. The studied accessions showed significant differences (p<0.05) in morpho-physiological responses to salinity. The accessions Zaqama, Yar-Garnaki, Yar-Yuti, Samira and Chana-Beru performed better under salt stress and there was no significant difference (p>0.05) between the control and salt-treated groups. Additionally, the in-silico analysis of DREB1A gene identified 10 orthologs with conserved single transcript, AP2 domain and unstable protein (characteristics of TFs) across the 10 diploid Oryza species. Phylogenetic analysis revealed 3 clusters of African rice and its progenitor, Asian rice and their relatives and O. brachyantha/O. punctata complex, similar to the evolution of rice species. Conclusively, salt stress affects rice in a concentration-dependent manner and DREB1A gene is a conserved plant transcription factor (TF) across diploid Oryza species.

Deepwater response in the African cultivated rice Oryza glaberrima

ABSTRACT Partial submergence of Oryza sativa deepwater rice elicits enhancement of internodal elongation, referred to as deepwater response, conferred by three types of genes, SNORKEL1/2 (SK1/2), SEMIDWARF1 (SD1), and ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1). We investigated the presence and expression of these genes in the African cultivated rice Oryza glaberrima and the relationship between these genes and the deepwater response of O. glaberrima. In 49 of the 50 accessions tested, one or two SK genes were identified, which could be divided into three types of SK1 and four types of SK2. The accessions with the SK2 type whose expression was induced by submergence demonstrated rapid internodal elongation under submergence. In most of these accessions, submergence also increased the expression of SD1 and ACE1 genes. However, the accessions did not possess the haplotype of SD1 that is associated with high deepwater response in O. sativa. In contrast, they possessed the type of ACE1 gene similar to that in O. sativa deepwater rice. These results indicate that the molecular mechanisms underlying induction of deepwater response in O. glaberrima are similar to that found in deepwater rice of O. sativa and suggest that most O. glaberrima cultivars, including upland cultivars, can exhibit rapid internodal elongation under submergence.

Evolution of flowering time genes in rice: From the paleolithic to the anthropocene.

The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipatingor delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?

Technological, physicochemical and culinary characterization of African rice accessions (Oryza glaberrima)

Thanks to its contribution to human nutrition, rice is a vital issue, mainly based on its quality. While O. glaberrima is abandoned in favor of Asian rice, this study was carried out in identification process of best grain quality of African rice, in order to make them more competitive and valorous in systems of varietal improvement. Principal components analysis method has been used for characterization of 215 African rice accessions, based on their technological, physicochemical and cooking parameters. The results showed on average a high amylose content (28.82%), a cooking time of 20.20 min, machining yield of 62.71% and score of 5 for gelatinization. Three clusters have been identified. Essentially, Cluster 1 is specifically characterized by a low chalkiness (10.29%), cluster 2 is characterized by a low broken rate (25%) and good machining yield (64%) while the cluster 3 of accessions is characterized by high index of « Volume expansion » and « water uptake » during cooking. These accessions represent a solution approach to meet the different requirements in terms of improving varieties integrating nutritional properties and food processing for the development of African rice.

An α/β hydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice

Ongoing soil salinization drastically threatens crop growth, development, and yield worldwide. It is therefore crucial that we improve salt tolerance in rice by exploiting natural genetic variation. However, many salt-responsive genes confer undesirable phenotypes and therefore cannot be effectively applied to practical agricultural production. In this study, we identified a quantitative trait locus for salt tolerance from the African rice species Oryza glaberrima and named it as Salt Tolerance and Heading Date 1 (STH1). We found that STH1 regulates fatty acid metabolic homeostasis, probably by catalyzing the hydrolytic degradation of fatty acids, which contributes to salt tolerance. Meanwhile, we demonstrated that STH1 forms a protein complex with D3 and a vital regulatory factor in salt tolerance, OsHAL3, to regulate the protein abundance of OsHAL3 via the 26S proteasome pathway. Furthermore, we revealed that STH1 also serves as a co-activator with the floral integrator gene Heading date 1 to balance the expression of the florigen gene Heading date 3a under different circumstances, thus coordinating the regulation of salt tolerance and heading date. Notably, the allele of STH1 associated with enhanced salt tolerance and high yield is found in some African rice accessions but barely in Asian cultivars. Introgression of the STH1HP46 allele from African rice into modern rice cultivars is a desirable approach for boosting grain yield under salt stress. Collectively, our discoveries not only provide conceptual advances on the mechanisms of salt tolerance and synergetic regulation between salt tolerance and flowering time but also offer potential strategies to overcome the challenges resulted from increasingly serious soil salinization that many crops are facing.

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.

Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa).

The cAMP-dependent protein kinase A, cGMP-dependent protein kinase G and phospholipid-dependent protein kinase C (AGC) perform various functions in plants, involving growth, immunity, apoptosis and stress response. AGC gene family is well described in Arabidopsis, however, limited information is provided about AGC genes in rice, an important cereal crop. This research studied the AGC gene family in the AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula and Oryza longistaminata were searched and classified into six subfamilies, and it was found that these species have similar numbers of members. The analysis of gene duplication and selection pressure indicated that the AGC gene family expanded mainly by segmental or whole genome duplication (WGD), with purifying selection during the long evolutionary period. RNA-seq analysis revealed that OsAGCs of subfamily V were specifically highly expressed in leaves, and the expression patterns of these genes were compared with that of photosynthesis-related genes using qRT-PCR, discovered that OsAGC9, OsAGC20, and OsAGC22 might participate in photosynthesis. These results provide an informative perspective for exploring the evolutionary of AGC gene family and its practical application in rice.

Physicochemical Properties of Un-parboiled Oryza Species Cultivated in Igbemo-Ekiti, Ekiti State, Nigeria

The amounts of carbohydrate, protein, crude fat, crude fiber, ash, and mineral elements (Calcium, Magnesium, Iron, Potassium, Sodium, and Zinc) in two kinds of rice grown in Igbemo-Ekiti, Ekiti State, were determined in this study. Using Gc-Ms spectrometric analysis, the fatty acids contained in the oil of Oryza sativa and Oryza glaberrima were identified. On a dry weight basis, the estimated carbohydrate content of rice samples ranged from 71.41 ± 0.37 to 74.02 ± 0.35 %, with no significant difference in carbohydrate content amongst the examined species, with Oryza glaberrima having the highest carbohydrate content. Protein levels ranged from 7.06 ±0.35 to 7.11 ± 0.20 %, with Oryza sativa having the highest protein content. The crude fat levels in the tubers ranged from 6.26 ± 0.04 to 7.18 ±0.17 %, with Oryza sativa having the highest level. The crude fiber content ranged from 3.02 ±0.32 to 3.77± 0.38 %, with Oryza sativa having the highest level and the ash content ranging from 0.51± 0.07 to 0.92± 0.32 %. Calcium, sodium, and potassium concentrations were all fairly high in both species. The Gc-Ms chromatogram indicated a wide range of bioactive chemicals, the majority of which were fatty acids. Linolenic acid, Arachidic acid, Palmitic acid, palmitoleic acid, Myristoleic acid, and Capric acids were some of the primary chemical components detected in the Oryza sativa chromatogram, however monounsaturated and polyunsaturated fatty acids were found in lesser amounts. Linoleic acid, oleic acid, palmitoleic acid, Myristoleic acid, Elaidic acid, Linolelaidic acid, stearic acid, and Behenic acid have been discovered in Oryza glaberrima, making them more favorable in nutrition and diet. The two Oryza types were found to be high in fatty acids, protein, and mineral content.

Genetic characterization and fine mapping of qHMS4 responsible for pollen sterility in hybrids between Oryza sativa L. and Oryza glaberrima Steud.

The online version contains supplementary material available at 10.1007/s11032-022-01306-8.

Proximate and Sensory Properties of Snacks developed from African Yam Beans and African Rice Flour Blends for Household Consumption

Proximate and Sensory Properties of Snacks developed from African Yam Beans and African Rice Flour Blends for Household Consumption

Super graph-based pan-genome: Bringing rice functional genomic study into a new dawn

Rice is one of the earliest domesticated crops that has been cultivated for thousands of years. Interestingly, unlike other crops that are predominantly domesticated by a singleton event in one place, the domestication of rice is quite complicated; it independently occurred in Asia and Africa to form the Asian cultivated rice Oryza sativa and the African cultivated rice O. glaberrima, respectively. O. sativa was mainly domesticated from the Asian wild rice O. rufipogon in East/South Asia (Huang et al., 2012).

A super pan-genomic landscape of rice

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

Trends in rice research: 2030 and beyond

AbstractRice production and research have met unprecedented challenges in recent years. Yield and total production have plateaued for many years in some major producing rice‐producing countries while the demand from populations in poverty is ever increasing. For example, more than 100 million additional people became extremely poor, mostly from Asia and sub‐Saharan Africa in 2020 alone. Rice is not only the calorie source for half of the global population but also the key staple food for the world's poorest and undernourished people living in Asia and Africa. In this review, we have analysed the trends in rice research in the past three decades, particularly on the mega‐projects that attempted to revolutionize rice yield, sustainability and quality of both Asian (Oryza sativa) and African (O. glaberrima) rice, with their impact on rice cultivation. We have also analysed the trends in population growth, rice cultivation, production, price and consumption along with their projections for 2030 and beyond. Furthermore, we have analysed recent trends in variety release using Bangladesh as an example. Finally, we have identified the future challenges and priorities of rice research.

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima.

Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC1F1 population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs.

Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2–6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5–6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.

The effect of environmental parameters and fertilization practices on yield and soil microbial diversity in a Kenyan paddy rice field

Rice is gaining importance for nutrition in sub-Saharan Africa, but domestic production can only cover a fraction of the actual needs. Suboptimal fertilization limits production and affordable solutions are needed. It is, however, of utmost importance to minimize negative impacts on the environment and on soil health, which is largely determined by microbial processes.An agronomic field trial was conducted at the KALRO Mwea research site (Central Kenya) to compare mineral and organic fertilization effects on rice plant parameters and on soil microbial abundance and diversity. Abundance of fungi and bacteria was quantified by ddPCR and the community composition was determined by amplicon sequencing of the ITS2- and 16S-regions, respectively. Mineral fertilizer had a strong positive effect on panicle number, spikelet number, grain yield and straw dry weight, but fertilizer type did not significantly influence soil microbial community abundance or composition. The rice development stage shaped fungal communities with differences between the vegetative and the reproductive stages, whereas the bacterial communities were mainly influenced by soil depth in a range from 0 to 30 cm. Additionally, spatial effects between rows of the experimental field were observed, resulting in row-specific differences in soil organic carbon, total nitrogen and certain fungal taxa, notwithstanding that the field was manually ploughed to a depth of 30 cm before the experiment. This study is the first census of soil fungal and bacterial communities in an African paddy rice field and provides insights into similarities and differences to paddy rice fields in other regions. To increase local African rice production, manure application alone might not be sufficient due to the poor nutrient status of traditional farm-yard manure, yet it can be part of a sustainable and more efficient fertilization strategy.

AgReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species.

Simple SummaryIn breeding research, the investigation of regulatory SNPs (rSNPs) is becoming increasingly important due to their potential causal role for specific functional traits. Especially for crop species, there is still a lack of systematic analyses to detect rSNPs and their predicted effects on the binding of transcription factors. In this study, we present agReg-SNPdb-Plants, a database storing genome-wide collections of regulatory SNPs for agricultural plant species which can be queried via a web interface.Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.

Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud.

Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.

Assessment of Genetic Diversity among Intra- and Interspecific Lowland Rice using Morpho-agronomic Traits and SSR Markers

Rice is staple food in many countries of Africa and a major part of the diet in many others. However, Africa’s demand for rice exceeds production with the deficit of 40% being imported. One way to improve Africa’s rice production is through breeding high yielding varieties suitable for the different environment conditions. This study was conducted to assess the genetic variability and stability performance of 48 lowland rice genotypes including 37 interspecific (Oryza glaberrima × Oryza sativa ssp. indica) and 11 intraspecific (O. sativa ssp. indica × O. sativa ssp. indica) in 12 environments in Nigeria, Benin Republic and Togo using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype+ Genotype x Environment (GGE) biplot models. The combined analysis of variance revealed significant differences (P<0.01) among the genotypes, environments, and genotypes x environment interaction. Both the AMMI and GGE models identified NERICA-L8 and NERICA-LI2 as the best genotypes for cultivation across environments. Ouedeme environments in Benin Republic were the most stable and ideal for rice cultivation, while Ibadan sites were the most unstable. TOG 5681 had the least yield and was the most unstable across seasons. Genetic diversity was analyzed using 22 important morpho-agronomic traits and 50 simple sequence repeat (SSR) markers and the results were subjected to principal components analysis (PCA). The results revealed that the first eight PC axes (PC1–8) accounted for 75.13% of the total variation, while PC1–4 accounted for 50.39% of the total variation among rice genotypes. However, 10 of the 50 SSR markers were polymorphic and generated 49 alleles (average = 4.9 alleles per locus), suggesting moderate to substantial genetic diversity among the rice genotypes. The polymorphic information content (PIC) ranged from 0.24 to 0.65, with an average PIC value of 0.45. Two structured populations were observed which clustered into five heterotic groups and an outgroup, respectively. This suggests that heterosis could be exploited in the next hybridization program by crossing one of the genotypes in any SSR marker-defined cluster, with the rice accession TOG 5681 in cluster I. The results of this study suggest that morpho-agronomic traits should be used to compliment SSR data in rice diversity studies, especially if a few polymorphic SSR markers are to be used.