Host response of Oryza glaberrima and O. sativa rice genotypes to the rice root-knot nematode Meloidogyne graminicola in a hydroponic system under growth chamber

The host response of 25 rice genotypes belonging to Oryza glaberrima and Oryza sativa to Meloidogyne graminicola infection was examined in a hydroponic system. The M. graminicola can build up high population densities in a hydroponic system. Resistance to this nematode species was found in O. glaberrima genotypes which supported significantly lower nematode numbers per plant and per unit root than O. sativa genotypes. The M. graminicola-infected O. sativa genotypes showed a higher root galling index than the O. glaberrima genotypes. The hydroponic system is efficient and reliable method to examine the host response of rice genotypes to M. graminicola infection, and can be useful for the fast screening of high numbers of rice genotypes for the selection of M. graminicola-resistant rice germplasm for breeding purposes.     

Abundance of 24-methylenecholesterol in traditional African rice as an indicator of resistance to the African rice gall midge, Orseolia oryzivora Harris & Gagné

Rice production is of great importance to food security in Nigeria. The African rice gall midge (AfRGM), Orseolia oryzivora Harris & Gagné, is a major pest of lowland rice in Nigeria and many other Africa countries. Current management efforts are directed at integrating host plant resistance with biological agents. The type and abundance of some phytochemicals are known to affect resistance in host plants, so in this study we measured rice culm hardness, rice culm stickiness and the type and quantity of phytosterols in rice cultivars, and investigated the effects of these factors on resistance to the AfRGM. The study was conducted at 24 ± 2°C, 60 ± 5% relative humidity, and a 12 h light : 12 h dark photoperiod. Three rice cultivars were studied: one Oryza glaberimma cultivar, Tog 7442 (resistant), and two O. sativa cultivars, Cisadane (tolerant) and ITA 306 (susceptible). We found no significant differences in culm hardness and stickiness among the cultivars tested. Using gas chromatography (flame ionization detection) analysis, we identified four major phytosterols: campesterol, 24‐methylenecholesterol, stigmasterol and β‐sitosterol. 24‐Methylenecholesterol was the most abundant sterol in the resistant O. glaberimma cultivar (79.20 μg), whereas β‐sitosterol was most abundant in the two susceptible O. sativa cultivars (Cisadane, 71.27 μg; ITA 306, 66.37 μg). The comparatively high concentration of 24‐methylenecholesterol in this cultivar of O. glaberimma may be an indicator of resistance to AfRGM.     

Cytological studies of African cultivated rice,Oryza glaberrima

African cultivated rice, Oryza glaberrima Steud., was cytologically characterized by using both karyotype analysis and molecular cytology. The somatic chromosomes resemble those of Asian cultivated rice, Oryza sauva L., in general morphology, although some minor differences were noted. Multicolor fluorescence in situ hybridization (McFISH) with chromosomes detected one 45s (17s-5.8s-25s) ribosomal RNA gene locus (45s rDNA) and one 5s ribosomal RNA gene locus (5s rDNA) in the chromosome complement. The 45s rDNA and 5s rDNA loci were physically mapped to the distal end of the short arm of chromosome 9 and to the proximal region of the short arm of chromosome 11 respectively, as in O. sativa. Based on the cytological observations and the physical map of the rDNA loci, the chromosomal organization of O.glaberrima and O. sativa seems to be very similar.     

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.     

Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis

Here we present the genomic sequence of the African cultivated rice, Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice, Oryza sativa. We obtained gene‐enriched sequences of O. glaberrima that correspond to about 25% of the gene regions of the O. sativa (japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes of O. glaberrima generally showed a larger synonymous–nonsynonymous substitution ratio, suggesting that O. glaberrima has undergone a genome‐wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes of O. sativa experienced changes at splice sites after the divergence from O. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes of O. glaberrima and O. sativa. Although tri‐nucleotide repeats were most common among the SSRs and were overrepresented in the protein‐coding sequences, we found that selection against indels of tri‐nucleotide repeats was relatively weak in both African and Asian rice. Our genome‐wide sequencing of O. glaberrima and in‐depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species.     

A first interspecific Oryza sativa×Oryza glaberrima microsatellite-based genetic linkage map

Oryza glaberrima is an endemic African cultivated rice species. To provide a tool for evaluation and utilisation of the potential of O. glaberrima in rice breeding, we developed an interspecific O. glaberrima×Oryza sativa genetic linkage map. It was based on PCR markers, essentially microsatellites and STSs. Segregation of markers was examined in a backcross (O. sativa/O. glaberrima//O. sativa) population. Several traits were measured on the BC₁ 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 indica×japonica crosses, indicating that recombination between the two species occurs without limitation. However, three chromosomes show discrepancies with the indica×japonica 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 s ₁₀ , 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. Received: 1 June 1991 / Accepted: 22 June 1999     

A universal core genetic map for rice

To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (<500 individuals). We chose anchors that were evenly distributed across the rice chromosomes, with spacing between 2 and 3.5 Mbp (except in the telomeric regions, where spacing was 1.5 Mbp). Anchor selection was performed using in silico tools and data: the O. sativa cv. Nipponbare rice genome sequence, the CHARM tool, information from the Gramene database and the OrygenesDB database. Sixteen AA-genome accessions of the Oryza genus were used to evaluate polymorphisms for the selected markers, including accessions from O. sativa, O. glaberrima, O. barthii, O. rufipogon, O. glumaepatula and O. meridionalis. High levels of polymorphism were found for the tested O. sativa × O. glaberrima or O. sativa × wild rice combinations. We developed Paddy Map, a simple database that is helpful in selecting optimal sets of polymorphic SSRs for any cross that involves the previously mentioned species. Validation of the UCGM was done by using it to develop three interspecific genetic maps and by comparing genetic SSR locations with their physical positions on the rice pseudomolecules. In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation.     

Identification of a second major resistance gene to Rice yellow mottle virus, RYMV2, in the African cultivated rice species, O. glaberrima

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.     

African Rice (<Emphasis Type="Italic">Oryza glaberrima</Emphasis> Steud.): Lost Crop of the Enslaved Africans Discovered in Suriname<Superscript>1</Superscript>

African Rice ( Oryza glaberrima Steud.): Lost Crop of the Enslaved Africans Discovered in Suriname. African rice (Oryza glaberrima Steud.) was introduced to the Americas during the slave trade years and grown by enslaved Africans for decades before mechanical milling devices facilitated the shift towards Asian rice (O. sativa L.). Literature suggests that African rice is still grown in Guyana and French Guiana, but the most recent herbarium voucher dates from 1938. In this paper, evidence is presented that O. glaberrima is still grown by Saramaccan Maroons both for food and ritual uses. Saramaccan informants claim their forefathers collected their first “black rice” from a mysterious wild rice swamp and cultivated these seeds afterwards. Unmilled spikelets (grains with their husk still attached) are sold in small quantities for ancestor offerings, and even exported to the Netherlands to be used by Maroon immigrants. Little is known of the evolution of O. glaberrima, before and after domestication. Therefore, more research is needed on the different varieties of rice and other “lost crops” grown by these descendants of enslaved Africans who escaped from plantations in the 17th and 18th centuries and maintained much of their African cultural heritage in the deep rainforest.     

An extensive analysis of the African rice genetic diversity through a global genotyping

Key message

We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species.

Abstract

Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.     

Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> cv. IR64) × <Emphasis Type="Italic">O. glaberrima</Emphasis> under Lowland Moisture Stress

Drought is a major abiotic stress that limits rice productivity in rain-fed and upland ecosystems. African rice, Oryza glaberrima, has low yields but is tolerant to drought and other stresses. We evaluated 513 BC₂F₃ progenies from alien introgression lines (AILs) that were derived from crosses of Oryza sativa (IR64) × O. glaberrima. They were assessed for yield and other traits when grown under drought at two locations. Such conditions reduced grain production by 59% compared with the recurrent parent (IR64). However, 33 AILs had higher yields, thus demonstrating their potential as genetic material for transferring drought-related traits from O. glaberrima to O. sativa. A set of 200 AILs was selectively genotyped with 173 simple sequence repeat and sequenced tagged site markers. Molecular analysis showed that a mean of 4.5% of the O. glaberrima genome was introgressed in BC₂F₃ AILs. Our analysis revealed 33 quantitative trait loci (QTLs; including 10 novel) for different traits. O. glaberrima contributed 50% of the alleles to those newly identified QTLs, with one for grain yield per plant (ypp9.1) being new. A QTL at RM208 on chromosome 2 positively affected yield under stress, accounting for 22% of the genetic variation. Our identification of drought-related QTLs for yield and yield components will be useful to future research efforts in marker-assisted selection.     

Enigmatic double-stranded RNA in Japonica rice

We have found a linear, 16 kb, double-stranded RNA (dsRNA) in symptomless Japonica rice (Oryza sativa L.) that is not found in Indica rice (Oryza sativa L.). The dsRNA was detected in every tissue and at every developmental stage, and its copy number was approximately constant (about 20 copies/cell). Double-stranded RNA was also detected in two strains of Oryza rufipogon (an ancestor of O. sativa). Hybridization experiments indicated that the dsRNA of O. rufipogon was homologous but not identical to that of O. sativa. The sequence of about 13.2 kb of the dsRNA was determined and two open reading frames (ORFs) were found. The larger ORF (ORF B) was more than 12 351 nucleotides long and encoded more than 4 117 amino acid residues.     

Evolution in indigenous west African rice

The genus Oryza contains two cultivated species,O. sativa L., the Asiatic rice, andO. glaberrima Steud. which is limited to Africa. Despite much taxonomic work on the relationships of the wild species of the genus, they are still imperfectly known and there has not been unanimous agreement on nomenclature. Most of the species group into complexes the delimitation of which is a matter of opinion. This paper presents results from experimental work, and a theory for the evolution of African cultivated rice is put forward based on taxonomic studies.     

The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the ‘Oryza Map Alignment Project’ (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project’s finished reference genome – O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara – thought to be the progenitor of modern cultivated rice.     

SUB1A‐dependent and ‐independent mechanisms are involved in the flooding tolerance of wild rice species

Crop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood‐tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A‐genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance‐related SUB1A‐1 and the intolerance‐related SUB1A‐2 alleles were found in tolerant and sensitive accessions, respectively. Flooding‐tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C‐genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence‐induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A‐1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C‐genome group, which show instead a SUB1A‐independent response to submergence.     

Experimental studies on the origin of cultivated rice

1) Contributions to the origin of cultivated rice made by the author and his colleagues were briefly reviewed under several headlines.—2) Two parallel series of evolution of cultivated species, the Asian form of Oryza perennis to O. sativa and O. breviligulata to O. glaberrima, were pointed out compared.—3) In both the two series, a continuous array of intergrades between wild and cultivated species is found in a particular region. The pattern of character variations among those intermediate plants was considered as indicating the evolutionary path, and the monophyletic origin of the Indica and Japonica types of O. sativa was discussed.—4) The conditions of establishment of a weedy form of O. perennis found in India were discussed. It was noticed that cultivation by man in itself works as a selective agent for cultivated types.     

Contrasting physiological responses by cultivars of Oryza sativa and O. glaberrima to prolonged submergence

Background and Aims Oryza glaberrima

is widely grown in flood-prone areas of African river basins and is subject to prolonged periods of annual submergence. The effects of submergence on shoot elongation, shoot biomass, leaf area and CO₂ uptake were studied and compared with those of O. sativa.

Methods

A wide selection of lines of O. sativa and O. glaberrima, including some classified as submergence tolerant, were compared in field and pot experiments. Plants were submerged completely for 31 d in a field experiment, and partially or completely for 37 d in a pot experiment in a growth chamber.

Key Results

Leaf elongation and growth in shoot biomass during complete submergence in the field were significantly greater in O. glaberrima than in O. sativa. So-called submergence-tolerant cultivars of O. sativa were unable to survive prolonged complete submergence for 31–37 d. This indicates that the mechanism of suppressed leaf elongation that confers increased survival of short-term submergence is inadequate for surviving long periods underwater. The O. sativa deepwater cultivar ‘Nylon’ and the ‘Yélé1A’ cultivar of O. glaberrima succeeded in emerging above the floodwater. This resulted in greatly increased shoot length, shoot biomass and leaf area, in association with an increased net assimilation rate compared with the lowland-adapted O. sativa ‘Banjoulou’.

Conclusions

The superior tolerance of deepwater O. sativa and O. glaberrima genotypes to prolonged complete submergence appears to be due to their greater photosynthetic capacity developed by leaves newly emerged above the floodwater. Vigorous upward leaf elongation during prolonged submergence is therefore critical for ensuring shoot emergence from water, leaf area extension above the water surface and a subsequent strong increase in shoot biomass.Key words: Flooding, leaf area, net assimilation rate, Oryza glaberrima, O. sativa, photosynthesis, rice, stress adaptation, submergence escape