Mounirou Sow

Morpho-agronomic and molecular characterisation of Oryza glaberrima germplasm from Mali

In order to exploit the important agronomic traits that make Oryza glaberrima Steud suitable for harsh growing conditions, 79 Riz Africain du Mali (RAM) including four checks of known cultivated rice species (Oryza sativa and O. glaberrima) were used for both field evaluation over two seasons (2007 and 2008) and assessment of molecular diversity. The molecular characterization showed all the 37 SSR markers used amplified and were polymorphic. The average heterozygosity of the accessions were relatively higher (0.18) than some earlier studies. The population from Mopti and Gao had a higher genetic diversity than other populations. Clustering of individuals showed no clear pattern of grouping based on either location or growing condition; this is due to the higher gene flow (Nm = 7.83) that may occur between different growing condition within location. Moreover, populations from different locations were highly differentiated (fst = 0.06) as compared to populations from different growing conditions (fst = 0.03). The dendrogram based on populations from different growing conditions revealed more similarity among populations with relatively similar growing conditions. Accessions such as, RAM116, RAM100 and RAM122, performed better under drought with a grain weight advantage of 40, 16 and 6.7% respectively over the best performing check. Key words: Genetic diversity, SSR markers, drought tolerance, Oryza glaberrima.

De novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices

Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.

Genetic diversity, population structure and differentiation of rice species from Niger and their potential for rice genetic resources conservation and enhancement

Rice genetic resources conservation and evaluation is crucial to ensure germplasm sources for further crop breeding. We conducted a wide collection of Oryza species in Niger and characterize its diversity with microsatellites (or simple sequence repeats, SSR). The aims of this research were to get a better understanding of the extent of genetic diversity, its structure and partition within rice eco-geographical zones of Niger. There were 264 accessions found in farmers’ and other fields: 173 O. sativa (Asia’s rice), 65 O. glaberrima (Africa’s rice), 25 O. barthii, and 1 O. longistaminata (weedy perennial rice), which were genotyped with 18 SSR. A total of 178 alleles were detected, with a mean of 9.89 alleles per locus. The polymorphism information content was 0.65 and heterozygosity was estimated as 0.14. Two main well-differentiate genotypic groups, which correspond to Asian and African rice species, were identified. The SSR set divided the Asia’s rice group (solely indica) into irrigated and floating rice, with rainfed lowland rice in between. The African rice species group was composed of O. glaberrima, O. longistaminata and O. barthii accessions, but without any clear genetic differentiation among them likely due admixtures within the samples of O. barthii. Five accessions that could be natural interspecific hybrids were too admixed for assigning them to any of the two well-differentiated groups. The partitioning of the overall diversity showed that maximum variation was within genotypic groups and subgroups or cropping ecologies, rather than between eco-geographical zones. The eco-geographical distribution of the diversity suggests germplasm exchange in Niger. Next-steps for conserving rice and crop wild relatives in Niger could be taken using the findings of this research.

QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders.

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.

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.

Interactions Between Rice yellow mottle virus (RYMV) Isolates and Rice Germplasm from Niger

Rice yellow mottle virus (RYMV) is the most damaging virus in Niger’s rice agrosystems. We analysed host plant-RMYV interactions using 175 accession from the rice germplasm collection of Niger and 52 accessions from Mali. Five different virus isolates from Niger (three), Benin (one) and Burkina Faso (one) were used for inoculation. The assessment was based on visual disease symptom scoring, and secondary disease-related traits such as leaf chlorophyll content and plant height. Most rice accessions were susceptible to RMYV but a few African rice accessions displayed a level of resistance to some virus isolates, which was similar to that of the highly resistant TOG5681. Their host plant resistance was characterised by the absence of symptoms, low chlorosis and limited plant height reduction. Examining alleles using primers derived from the RYMV1 resistance gene revealed that one of these accessions has the rymv1-3 allele and other two accessions bear the rymv1-4 allele. We could not identify any known allele in one highly resistant accession, suggesting the presence of another resistance gene. The RYMV isolate BF1 from Burkina Faso was more aggressive than the three isolates from Niger, which were in turn found to be more aggressive than the isolate from Benin.

Farmers’ rice knowledge and adoption of new cultivars in the Tillabéry region of western Niger

BackgroundTillabéry is the main rice growing region of Niger, and it includes both irrigated and lowland rice. Rice production has stagnated due to several factors this research investigated through farmers’ eyes.MethodsSemi-structured group discussions were carried out in 14 villages in which 153 farmers, after giving their informed consent, were individually subjected to a questionnaire, and farmers’ fields and storage facilities were visited.ResultsFields were larger in private irrigation and lowland agrosystems compared to those in public irrigation schemes. The local farmers’ union was the only formal seed dissemination system. Farmers exchanged seed as well as did re-seeding of leftovers from the previous harvest. They indicated Rice yellow mottle virus (RYMV) and bacterial leaf blight (BLB) as the most prevalent biotic stresses in the irrigated agrosystems, but the RYMV-susceptible cultivars IR1529 and ‘Waihidjo’ are still the most popular varieties. Floods, birds, and hippopotamuses were the most damaging agents in lowland agrosystems where the landrace ‘Degaulle’/D5237 was the preferred cultivar.ConclusionsRice farmers in the region of Tillabéry were aware of the RYMV, could provide good descriptions of its symptoms, but could not establish the real causes of the disease nor its relationship with insects’ prevalence and other cultural practices. However, traditional management strategies were implemented to reduce RYMV epidemics. This situation showed that farmers in the region of Tillabéry were willing to face RYMV epidemic outbreaks while growing their preferred rice cultivars. Good seed availability and absence of seed policy at the time of this study were also detected as bottlenecks in rice production increase in Tillabéry.