SummaryWe report here evidence of the role that the isoform of the eukaryotic translation initiation factor 4G (eIF(iso)4G) plays in naturally occurring resistance in plant/virus interactions. A genetic and physical mapping approach was developed to isolate the Rymv1 locus controlling the high recessive resistance to Rice yellow mottle virus (RYMV) in the rice (Oryza sativa) variety Gigante. The locus was mapped to a 160-kb interval containing a gene from the eIF(iso)4G family. The stable transformation of a resistant line with the cDNA of this gene, derived from a susceptible variety, resulted in the loss of resistance in transgenic plants. The allelic variability of this gene was analysed in three resistant and 17 susceptible varieties from different cultivated rice species or subspecies. Compared with susceptible varieties, resistant varieties present specific alleles, characterized by either amino acid substitutions or short amino-acid deletions in the middle domain of the protein. The structure of this domain was modelled and showed that the substitutions were clustered on a small surface patch. This suggests that this domain may be involved in an interaction with the virus.

African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.

Rice yellow mottle virus (RYMV) is the most damaging rice-infecting virus in Africa. However, few sources of high resistance and only a single major resistance gene, RYMV1, are known to date. We screened a large representative collection of African cultivated rice (Oryza glaberrima) for RYMV resistance. Whereas high resistance is known to be very rare in Asian cultivated rice (Oryza sativa), we identified 29 (8%) highly resistant accessions in O. glaberrima. The MIF4G domain of RYMV1 was sequenced in these accessions. Some accessions possessed the rymv1-3 or rymv1-4 recessive resistance alleles previously described in O. glaberrima Tog5681 and Tog5672, respectively, and a new allele, rymv1-5, was identified, thereby increasing the number of resistance alleles in O. glaberrima to three. In contrast, only a single allele has been reported in O. sativa. Markers specific to the different alleles of the RYMV1 gene were developed for marker-assisted selection of resistant genotypes for disease management. In addition, the presence of the dominant susceptibility allele (Rymv1-1) in 15 resistant accessions suggests that their resistance is under different genetic control. An allelism test involving one of those accessions revealed a second major resistance gene, i.e., RYMV2. The diversity of resistance genes against RYMV in O. glaberrima species is discussed in relation to the diversification of the virus in Africa.

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.

Ndjiondjop, M. N., Albar, L., Fargette, D., Fauquet, C., and Ghesquière, A. 1999. The genetic basis of high resistance to rice yellow mottle virus (RYMV) in cultivars of two cultivated rice species. Plant Dis. 83:931-935.Three cultivars of Oryza sativa (IR64, Azucena, and Gigante) and four cultivars of O. glaberrima (Tog5681, Tog5673, CG14, and SG329) were evaluated for their resistance to two isolates of rice yellow mottle virus (RYMV) by enzyme-linked immunosorbent assay (ELISA) and symptomatology. Cultivars Tog5681 and Gigante were highly resistant, and no symptoms were observed when either virus isolate was inoculated at 10 or 20 days postgermination and assayed by ELISA at 7, 14, 22, 35, 50, or 64 days postinoculation. Azucena showed a partial resistance, whereas the other cultivars were susceptible. Symptom appearance was associated with increase in ELISA absorbance in the systemically infected leaves. The best discrimination among the cultivars occurred when the plants were inoculated at 10 days postgermination. Crosses were made between the highly resistant (Gigante and Tog5681) and the susceptible (IR64) cultivars to determine the genetic basis of resistance to RYMV. Evaluation of F1 hybrids and interspecific progenies, as well as the segregation of resistance in F2 and F3 lines of the IR64 × Gigante cross, provided results consistent with the presence of a single recessive resistance gene common to Tog5681 and Gigante.

Oryza glaberriina is an endemic African cultivated rice species. To provide a tool for evaluation and utilisation of the potential of O. glaberrinia in rice breeding, we developed an interspecific O. glaberri-inaxOryza sativa genetic linkage map. It was based on PCR markers, essentially microsatellites and STSs. Segregation of markers was examined in a backcross (O. sativalo. glaberrimal10. sativa) population. Several traits were measured on the BC, plants, and major genes and QTLs were mapped for these traits. Several of these genes correspond well to previously identified loci. The overall map length was comparable to those observed in indicaxjaponica crosses, indicating that recombination between the two species occurs without limitation. However, three chromosomes show discrepancies with the iizdicaxjaponica maps. The colinearity with intraspecific maps was very good, confirming previous cytological observations. A strong segregation-distortion hot spot was observed on chromosome 6 near the waxy gene, indicating the presence of sl o. a sporo-gametophytic sterility gene previously identified by Sano (1990). The main interests of such a PCR-based map for African rice breeding are discussed, including gene and QTL localisation, marker-assisted selection, and the development of interspecific introgression lines. Key words O. glaberrirna . O. sativa. Rice . Genetic maps . Microsatellites . Sequence-tagged sites . Interspecific hybridisation . GenelQTL mapping+ Segregation distortion Communicated by H.F. Linskens M. Lorieux (€33) . M.-N. Ndjiondjop . A.

Global efforts have seen the world’s plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended

The very high resistance to Rice yellow mottle virus observed in the two rice varieties Gigante ( Oryza sativa) and Tog 5681 ( O. glaberrima) is monogenic and recessive. Bulked segregant analysis was carried out to identify AFLP markers linked to the resistance gene. Mapping of PCR-specific markers, CAPS and microsatellite markers on 429 individuals of an IR64 x Gigante F(2) population pinpointed this resistance gene on the long arm of chromosome 4 in a 3.7-cM interval spanned by PCR markers. These markers also flanked the resistance gene of the O. glaberrima accession Tog 5681 and confirmed previous allelism tests. The rarity of this recessive natural resistance was in line with a resistance mechanism model based on point mutations of a host component required for cell-to-cell movement of the virus. Preliminary data on the genetic divergence between the two cultivated rice species in the vicinity of the resistance locus suggested that two different resistance alleles are present in Gigante and Tog 5681. A large set of recombinants is now available to envisage physical mapping and cloning of the gene.