African Rice Research Articles

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs.

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.

IMPACTS OF DELAYED FIELD CURING ON RICE SEED QUALITY IN A TROPICAL ENVIRONMENT

SUMMARYThree upland rice species, viz. Oryza sativa, Oryza glaberrima and an O. sativa × O. glaberrima interspecific hybrid, were grown in Ghana, harvested, and field cured under open (wet) and within ventilated but rainproof containers (dry) conditions for 5 weeks. Seeds from both environments were assessed weekly for physical, physiological and pathological quality. The relationships between air temperature and relative humidity, and seed moisture content (MC) and water activity differed between curing environments but within curing environments, relationships between seed MC and water activity were comparable among species. Prolonged field curing resulted in structural damage evidenced by the formation of multiple cracks in the endosperm; these were more frequent in wet cured seeds. Diverse fungal species were isolated from wet (22 species) and dry (23 species) cured seeds with a number of soil-borne species in the wet environment. Curing environment did not influence levels of fungal infection in O. glaberrima seeds but dry curing was associated with higher levels of fungal infection in O. sativa and O. sativa × O. glaberrima. Seed germinability in all the three species was higher in the dry cured seeds although vigour was relatively lower than wet cured seeds. Field curing the seeds of these three species within a dry environment could potentially improve subsequent seed viability, aid in moisture management and minimize structural damage to the endosperm; however, research on how fungal infection could be curbed under such conditions is needed.

English

Rice (Oryza sativa) is a salt-sensitive species and improvement of salt resistance is a major goal for plant breeders. Some species of Oryza genus may constitute an interesting source of genes involved in stress resistance for cultivated rice improvement. The African rice Oryza glaberrima is poorly described for its response to salt stress. Twenty-five accessions of O. glaberrima were exposed during 2 weeks to 0 or 60 mM NaCl in nutrient solution. Morphological and physiological parameters were recorded and used to perform principal component analysis allowing us to consider three contrasting groups (salt-resistant, medium, and salt-sensitive). Most of the tested lines appeared more salt-sensitive than the moderately salt-resistant cultivar I Kong Pao from O. sativa. Salt-sensitivity index was higher for roots than for shoots and O. glaberrima was poorly efficient for regulation of Na+ translocation from the root to the shoot. Some accessions such as TOG5307 however were able to maintain a high net photosynthesis under salt conditions and exhibited a high level of tolerance to accumulated Na+ ions and a high capacity for osmotic adjustment. It is concluded that these salt-tolerant accessions constitute a promising material for rice improvement through inter-specific crosses with O. sativa. Key words: African rice, NaCl, Oryza glaberrima, salinity, salt stress.

Utilization of New African Rice Varieties for Breeding Egyptian Cultivars Tolerant to Water Deficit

Utilization of New African Rice Varieties for Breeding Egyptian Cultivars Tolerant to Water Deficit

Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice

Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima-derived allele (denoted S1g) on the S1 locus causes preferential abortion of gametes with its allelic alternative (denoted S1s) in S1g/S1s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S1mut, which does not confer sterility in the S1mut/S1g and S1mut/S1s hybrids. We found that the causal mutation of the S1mut allele was a deletion in the peptidase-coding gene (denoted "SSP") in the S1 locus of O. glaberrima No orthologous genes of SSP were found in the O. sativa genome. Transformation experiments indicated that the introduction of SSP in carriers of the S1s allele did not induce sterility. In S1mut/S1s heterozygotes, the insertion of SSP led to sterility, suggesting that SSP complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the SSP gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a "neutral" allele, which facilitates interspecific hybridization for breeding programs.

Evaluation of resistance and tolerance of rice genotypes from crosses of Oryza glaberrima and O. sativa to the rice root-knot nematode, Meloidogyne graminicola

Resistance and tolerance to Meloidogyne graminicola infection of introgressed rice genotypes derived from crosses between M. graminicola-resistant Oryza glaberrima genotype CG14 and -susceptible O. sativa genotype IR64 were evaluated in an indoor growth chamber and outdoor raised beds. None of the 44 introgressed genotypes: 24 first backcross F2 generation (BC1F2) and 20 first backcross F3 generation (BC1F3) evaluated did express the same level of resistance as the resistant O. glaberrima reference genotypes included in the experiments for comparison. Lower nematode multiplication factor on the BC1F3 genotypes suggests that M. graminicola resistance trait segregated among the 3rd generation progeny of the backcross population. The majority of the introgressed genotypes were susceptible and sensitive to M. graminicola infection, some genotypes were susceptible but tolerant and few were both resistant and tolerant to nematode infection. Several genotypes with resistance and/or tolerance to M. graminicola were identified that could either be further developed into advanced breeding lines to produce resistant and/or tolerant cultivars or in the short-term developed into M. graminicola-resistant and/or –tolerant cultivars for use by resource-poor farmers.

How Can West African Rice Compete in Urban Markets? A Demand Perspective for Policymakers

SummaryIn West Africa, rice produced locally falls short of meeting the demand and preferences of urban consumers. We analyzed the challenges facing local rice in urban markets and identified policies that can be implemented to improve the competitiveness of the regional rice sector. We argue that without addressing the demand side of the value chain, efforts on the supply side might fall short in reducing import dependency. Evidence suggests that while imported rice has easy access to urban markets, local rice faces more challenges in reaching urban consumers. The low market share of local rice in urban markets is in part due to consumers’ dislike of local rice as it is perceived as being of inferior quality relative to imported rice. Local rice also tends to fetch lower prices. The experimental studies reviewed suggest, however, that urban consumers are willing to pay price premiums for local rice if its quality is upgraded. We propose a two‐stage policy sequence: (i) encouraging investment in quality upgrading; (ii) gradually increasing the Common External Tariff (CET) from 10 to 35 per cent to increase cost‐competitiveness of West African rice relative to imported rice. To stabilise and finance the sector, we further advocate the establishment of a flat‐rate levy on the value of rice imports.

Characterization of OglDREB2A gene from African rice (Oryza glaberrima), comparative analysis and its transcriptional regulation under salinity stress.

In this study, AP2 DNA-binding domain-containing transcription factor, OglDREB2A, was cloned from the African rice (Oryza glaberrima) and compared with 3000 rice genotypes. Further, the phylogenetic and various structural analysis was performed using in silico approaches. Further, to understand its allelic variation in rice, SNPs and indels were detected among the 3000 rice genotypes which indicated that while coding region is highly conserved, yet noncoding regions such as UTR and intron contained most of the variation. Phylogenetic analysis of the OglDREB2A sequence in different Oryza as well as in diverse eudicot species revealed that DREB from various Oryza species were diversed much earlier than other genes. Further, structural features and in silico analyses provided insights into different properties of OglDREB2A protein. The neutrality test on the coding region of OglDREB2A from different genotypes of O. glaberrima showed the lack of selection in this gene. Among the different developmental stages, it was upregulated at tillering and flag leaf under salinity treatment indicating its positive role in seedling and reproductive stage tolerance. Real-time PCR analysis also indicated the conserve expression pattern of this gene under salinity stress across the three different Oryza species having different degree of salinity tolerance.

Host response of rice genotypes from crosses of high-yielding and drought-tolerant Oryza sativa advanced breeding lines to the rice root-knot nematode Meloidogyne graminicola

The host response to Meloidogyne graminicola infection of 30 advanced breeding lines developed from crosses between high-yielding and drought-tolerant Oryza sativa genotypes was evaluated in outdoor raised beds. None of the advanced breeding lines showed resistance to M. graminicola comparable to the M. graminicola-resistant African rice (O. glaberrima) genotype TOG5674. However, rice genotype IR86815-23-4-1-2 was identified tolerant which showed no yield reduction even when infected with M. graminicola. IR82635-B-B-143-1, IR85733-19-4-1-1, IR85733-19-4-2-4, IR85,735-42-1-4-1 and IR 85735-42-1-4-4 were less sensitive to M. graminicola infection with less than 20% yield reduction compared to other rice genotypes. These rice genotypes could alleviate yield losses in M. graminicola-infested rice fields in regions with limited resources to control M. graminicola and when resistant cultivars are not available.

Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress

Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs. We also used smallRNAseq data of NCBI of O. glaberrima to discover additional 246 known miRNAs. Totally, 29 known and 32 novel miRNAs were differentially regulated under salinity stress. Gene ontology and KEGG analysis indicated several targets were involved in vital biological pathways of salinity stress tolerance. Expression of selected miRNAs as indicated by Illumina data were found to be coherent with real time-PCR analysis. However, target gene expression was inversely correlated with their corresponding miRNAs. Finally based upon present results as well as existing knowledge of literature, we proposed the miRNA-target modules that were induced by salinity stress. Therefore, the present findings provide valuable information about miRNA-target networks in salinity adaption of O. glaberrima.

Genetic Variability Assessment in Irrigated Rice (&amp;lt;i&amp;gt;Oryza sativa&amp;lt;/i&amp;gt; and &amp;lt;i&amp;gt;Oryza glaberrima&amp;lt;/i&amp;gt;) by PCR-SSR in Mali

Rice species (<i>Oryza sativa, L</i>. and <i>Oryza glaberrima, Steud</i>) provide 20% energy of world’s food. Knowledge of genetic variability is important to remove duplicate materials for gene bank management and conservation. In this study, 59 microsatellite markers were used to assess the genetic diversity of 54 intraspecific (<i>Oryza sativa</i>) and interspecific (<i>Oryza sativa X Oryza glaberrima</i>) irrigated rice varieties by PCR-SSR. A total of 250 alleles were detected with an average of 4.24 alleles per SSR. Genetic diversity was ranged from 0.0713 (RM333, RM3744) to 0.8937 (RM251) to with an average of 0.4325. Polymorphism Information Content (PIC) varied from 0.0688 (RM333, RM3744) to 0.8854 (RM251) with an average of 0.3940. Rice genotypes were shared between five Groups based on their similarity with majority of them (64.81%) under Group V. Variety SK 7-8 within Group III was highly dissimilar to other varieties. Malian varieties were shared out between Groups II, III, VI and V. Strong genetic variability was observed within cluster V2 of Group V among the most cultivated and appreciated rice varieties such as Kogoni 91-1, Adny11 and BG90-2. Allelic variability observed among rice varieties could help breeding programs to identify cultivars with good agronomic traits for crop improvement.

Screening African Rice (Oryza glaberrima) for Tolerance to Abiotic Stresses: II. Lowland Drought

ABSTRACTDrought is a major constraint to rice (Oryza spp.) production in sub‐Saharan Africa. Oryza glaberrima Steud., the cultivated rice species that originated from West Africa, is well‐adapted to its growing ecologies. This study was initiated to identify promising O. glaberrima accessions tolerant to lowland drought stress from the 2106 accessions held at the AfricaRice Genebank. Screening was done over a 3‐yr period in West Africa using standardized protocol and involved evaluating for grain yield under drought and/or irrigated conditions, selecting the high‐yielding lines, and repeating the testing with the newly selected lines. Four accessions (TOG 7400, TOG 6520, TOG 6519‐A, and TOG 7442‐B) with consistently higher grain yield under drought stress and irrigated conditions were selected. These four accessions originated from three countries in West Africa, namely, Ghana, Liberia, and Nigeria. The selected O. glaberrima accessions could be used as donors in breeding for drought tolerance in rice.

Neutral alleles at hybrid sterility loci of Oryza glaberrima from AA genome relatives in Genus Oryza.

Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Neutral alleles at each locus have the potential to overcome the sterility between the two cultivated rice species. In this study, an O. sativa cultivar Dianjingyou 1 (DJY1) and its near-isogenic lines (NILs) harboring the single sterility allele S1-glab, S19-glab, S20-glab, S37-glab, S38-glab and S39-glab as the tested lines were crossed with O. glaberrima, O. rufipogon, O. nivara, O. glumaepatula, O. barthii, O. meridionalis and O. sativa so as to detect the neutral alleles of these loci. Pollen fertility was investigated in the paired F1s based on two seasons’ result and genotypic segregation was also analyzed in some F2 populations to confirm the results of pollen fertility investigation. The neutral alleles of S38-n and S39-n were identified based upon the pollen fertility and genotypic segregation analysis for the first time. The neutral alleles of sterility loci detected from present report have the potential to know of the nature of interspecific hybrid sterility, and to overcome the interspecific hybrid sterility between O. sativa and O. glaberrima.

Fine mapping of a major quantitative trait locus, qgnp7(t), controlling grain number per panicle in African rice (Oryza glaberrima S.).

Grain number per panicle is a major component of rice yield that is typically controlled by many quantitative trait loci (QTLs). The identification of genes controlling grain number per panicle in rice would be valuable for the breeding of high-yielding rice. The Oryza glaberrima chromosome segment substitution line 9IL188 had significantly smaller panicles compared with the recurrent parent 9311. QTL analysis in an F2 population derived from a cross between 9IL188 and 9311 revealed that qgnp7(t), a major QTL located on the short arm of chromosome 7, was responsible for this phenotypic variation. Fine mapping was conducted using a large F3 population containing 2250 individuals that were derived from the F2 heterozygous plants. Additionally, plant height, panicle length, and grain number per panicle of the key F4 recombinant families were examined. Through two-step substitution mapping, qgnp7(t) was finally localized to a 41 kb interval in which eight annotated genes were identified according to available sequence annotation databases. Phenotypic evaluation of near isogenic lines (NIL-qgnp7 and NIL-qGNP7) indicated that qgnp7(t) has pleiotropic effects on rice plant architecture and panicle structure. In addition, yield estimation of NILs indicated that qGNP7(t) derived from 9311 is the favorable allele. Our results provide a foundation for isolating qgnp7(t). Markers flanking this QTL will be a useful tool for the marker-assisted selection of favorable alleles in O. glaberrima improvement programs.

Comparative assessment of insect pests population densities of three selected cucurbit crops

Comparative assessment of insect pests population densities of three selected cucurbit crops

A Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa).

Meloidogyne graminicola is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata; however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and, here, we report for the first time the histological and genetic characterization of the resistance to M. graminicola in Zhonghua 11, an O. sativa variety. Bright-light microscopy and fluorescence observations of the root tissue of this variety revealed that the root cells surrounding the nematode displayed a hypersensitivity-like reaction with necrotic cells at early stages of infection when nematodes are migrating in the root's mesoderm. An accumulation of presumably phenolic compounds in the nematodes' neighboring root cells was also observed. In addition, at a later stage of infection, not only were few feeding sites observed but also the giant cells were underdeveloped, underlining an incompatible interaction. Furthermore, we generated a hybrid O. sativa population by crossing Zhonghua 11 with the susceptible O. sativa variety IR64 in order to describe the genetic background of this resistance. Our data suggested that the resistance to M. graminicola infection was qualitative rather than quantitative and, therefore, major resistance genes must be involved in this infection process. The full characterization of the defense mechanism and the preliminary study of the genetic inheritance of novel sources of resistance to Meloidogyne spp. in rice constitute a major step toward their use in crop breeding.

Why did farmers stop cultivating NERICA upland rice varieties in central Benin?

ABSTRACTNew Rice for Africa (NERICA) was developed by the Africa Rice Center by crossing high-yielding Asian rice (Oryza sativa L.) with locally adapted African rice (Oryza glaberrima Steud.). Community-based seed production of NERICA varieties was introduced in a village in central Benin in 2006 through seed dissemination projects. It was reported that high-adoption rates of these varieties were mainly due to high demand by development projects for seed dissemination, and to incentives (i.e. selling the rice seed at a higher than local market price to a local extension service) for farmers to grow NERICA varieties. A follow-up survey was undertaken after the seed dissemination projects ended to examine the change in the cultivation of NERICA varieties. About half of the farmers had ceased cultivation of NERICA varieties in 2011. The reasons for abandonment were the combined effects of reduced seed demand and low yields, which were attributed to a lack of access to credit and training on NERICA cultivation practices. The majority of the farmers did not abandon rice cultivation, but grew other high-yielding varieties, including one aromatic variety for which there was market demand. We conclude that to avoid immediate reductions in the adoption of new varieties after projects are terminated and to enhance agricultural sustainability, the varieties should be introduced in conjunction with appropriate group training on their cultivation, and the project should target farmers who do not have off-farm businesses. Furthermore, access to credit should also be enhanced, and the marketability of the varieties should be assessed.

Effects of initial nematode population density and water regime on resistance and tolerance to the rice root-knot nematode Meloidogyne graminicola in African and Asian rice genotypes

ABSTRACTThe rice root-knot nematode (RKN), Meloidogyne graminicola, is an important pathogen affecting rice production in South and Southeast Asia. Efficacy of resistance and tolerance in selected M. graminicola-resistant African rice genotypes TOG5674, TOG5675 and CG14 and -susceptible Asian rice genotypes IR64 and UPLRi-5 were examined under a range of initial population densities (Pi) and water regimes. Resistance to M. graminicola in resistant rice genotypes was not broken with increasing pathogen pressure (Pi = 15,000 to 60,000 J2/plant). Resistant rice genotypes were even tolerant to the damage and yield loss caused by high pathogen pressure. On the other hand, increasing Pi levels caused more damage on susceptible rice genotypes. Final nematode population densities in the root systems of resistant and susceptible rice genotypes were significantly lower under flooded conditions than under upland and drought conditions. TOG5674, TOG5675 and CG14 were more tolerant to M. graminicola infection even when grown under upland and drought conditions while IR64 and UPLRi-5 were highly sensitive.

Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq.

The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97–99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1–89.2% attributable to differences within groups.

English

Rice is an important staple food crop that feeds over half of the global population and it has become the cereal that provides a major source of calories for the urban and rural poor in Africa. This research aimed to use simple sequence repeat (SSR) markers to evaluate the genetic diversity in rice (Oryza sativa and Oryza glaberrima) germplasm as breeding method. In the present study, 16 SSR markers were used across 48 genotypes or accessions obtained from Central Agricultural Research Institute (CARI), Suakoko, Liberia and Plant Genetic Resources Research Institute (PGRRI), Bunso, Ghana. DNA was extracted from 48 plants per accession without bulking to check the purity of the accession using the 16 SSR markers. Sixteen primers were acquired out of 20 primers which showed DNA amplification and polymorphism among the 48 rice accessions. The numbers of alleles detected by these 16 primers ranged from 1 to 16 with a mean of 5.25, while polymorphism information content (PIC) ranged from 0.06 to 0.66 with a mean of 0.35. The SSR markers were highly informative as generated by the power marker V3.25 software. The unweight pair group method with arithmetic averages (UPGMA) cluster dendrogram generated based on the 16 SSR markers grouped the accessions into 11 main clusters. At the similarity coefficients of 90%, the highly distance genetic diversity was found between 2 accessions; ACSS37 and ACSS1. Cluster X was the largest of all the clusters, while clusters VII and VIII were the second largest clusters with 7 accessions each. The outcome of this study should be useful to manage the gremplasm conservation and future rice genetic improvement. Key words: Germplasm, genetic diversity, molecular markers, polymorphism, sequence repeat.