Genus Oryza Research Articles

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species.

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25717 (green) and 25215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual-color oligo-FISH was used to characterize diverse chromosomal abnormalities. Oligo-FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo-FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.

Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata.

Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC3F1 population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC3F2 plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC3F2 population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. longistaminata in the mapping populations of 94, 88, 70, and 95 BC3F4 plants. qATL3, qATL5, and qATL6.1 likely contributed to anther length by cell elongation, whereas qATL6.2 likely contributed by cell multiplication. The QTLs were confirmed again in an evaluation of the W1508ILs. In several chromosome segment substitution lines without the four validated QTLs, the anthers were also longer than those of T65, suggesting that other QTLs also increase anther length in W1508. The cloning and diversity analyses of genes conferring anther length QTLs promotes utilization of the genetic resources of wild species, and the understanding of haplotype evolution on the differentiation of annuality and perenniality in the genus Oryza.

Identification, distribution and comparative analysis of microsatellites in the chloroplast genome of Oryza species

Chloroplast genome is important because of its maternally inherited, conserved within species and stable in structure. This allows elucidation of inter-specific comparison, identification and establishment of evolutionary relationship among different species. Different classes of DNA elements were present in chloroplast genome of Oryza species, among them chloroplast microsatellites were supposed to be highly variable. In this study, a total of 102 sequences of chloroplast genome of 23 species of Oryza genus belonging to ten different genome types were downloaded from NCBI nucleotide database. The chloroplast DNA length varied from 134,401bp to 136,133bp. Microsatellite analysis revealed that total SSR number varied from 268 in O. coarctata to 281 in O. granulata. Comparative analysis of repeat type revealed that mononucleotide and trinucleotide were least present, while penta and hexa nucleotide motif were the most common type among all the Oryza species. Frequency analysis of the repeat revealed that T repeat among mono, AT among di, AAT among tri, AATA among tetra, AATTC among penta and AAAGAA among hexa nucleotide repeat was found to be common among most of the Oryza species. Total of five set of SSR markers flanking to penta and hexa nucleotide repeat types were developed which uniquely present among species, namely, O. barthi, O. sativa Japonica, O. cocarctata, O. rhizomatis and O. ridley. Phylogeny based on SSR markers indicate separate evolution of different SSR markers among individual species.

Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae.

Genome amplification and sequence divergence provides raw materials to allow organismal adaptation. This is exemplified by the large expansion of the ubiquitin-26S proteasome system (UPS) in land plants, which primarily rely on intracellular signaling and biochemical metabolism to combat biotic and abiotic stresses. While a handful of functional genomic studies have demonstrated the adaptive role of the UPS in plant growth and development, many UPS members remain unknown. In this work, we applied a comparative genomic study to address the functional divergence of the UPS at a systematic level. We first used a closing-target-trimming annotation approach to identify most, if not all, UPS members in six species from each of two evolutionarily distant plant families, Brassicaceae and Poaceae. To reduce age-related errors, the two groups of species were selected based on their similar chronological order of speciation. Through size comparison, chronological expansion inference, evolutionary selection analyses, duplication mechanism prediction, and functional domain enrichment assays, we discovered significant diversities within the UPS, particularly between members from its three largest ubiquitin ligase gene families, the F-box (FBX), the Really Interesting New Gene (RING), and the Bric-a-Brac/Tramtrack/Broad Complex (BTB) families, between Brassicaceae and Poaceae. Uncovering independent Arabidopsis and Oryza genus–specific subclades of the 26S proteasome subunits from a comprehensive phylogenetic analysis further supported a diversifying evolutionary model of the UPS in these two genera, confirming its role in plant adaptation.

Monitoring System of Rice Plant Growth Using Microcontroller Sensor

Rice is one of the species belonging to the genus Oryza L, which covers approximately 25 species and is spread in the tropics and subtropical regions. Rice is a type of plant that requires care to grow. Each type of plant needs different characteristics of the growing media. The surrounding environment has an effect on the growth of rice plants for the quality of crop harvest to give maximum results. Rice productivity is largely determined by soil conditions, water level, humidity, and light intensity of the rice plant itself. Therefore rice plants must grow and develop in the hot climate with a lot of water vapor which includes rainfall, temperature, and sunlight. This rice monitoring system uses the sensors of soil moisture, air humidity, light intensity, water level, modems, Arduino Nano and Raspberry Pi. The test results were carried out only two days in 2 weeks which monitored the rice plants, especially Mekongga rice varieties by paying attention to the soil moisture, air humidity, light intensity, and water level.

Identification and Analysis of Micro-Exon Genes in the Rice Genome.

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

Increase rate of light-induced stomatal conductance is related to stomatal size in the genus Oryza.

The rapid response of stomatal conductance (gs) to fluctuating irradiance is of great importance to maximize carbon assimilation while minimizing water loss. Smaller stomata have been proven to have a faster response rate than larger ones, but most of these studies have been conducted with forest trees. In the present study, the effects of stomatal anatomy on the kinetics of gs and photosynthesis were investigated in 16 Oryza genotypes. Light-induced stomatal opening includes an initial time lag (λ) followed by an exponential increase. Smaller stomata had a larger maximum stomatal conductance increase rate (Slmax) during the exponential increase phase, but showed a longer time lag and a lower initial stomatal conductance (gs,initial) at low light. Stomatal size was, surprisingly, negatively correlated with the time required to reach 50% of maximum gs and photosynthesis (T50%gs and T50%A), which was shown to be positively correlated with λ and negatively correlated with gs,initial. With a lower gs,initial and a larger λ, small stomata showed a faster decrease of intercellular CO2 concentration (Ci) during the induction process, which may have led to a slower apparent Rubisco activation rate. Therefore, smaller stomata do not always benefit photosynthesis as reported before; the influence of stomatal size on dynamic photosynthesis is also correlated with λ and gs,initial.

Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus.

The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.

Genetic characterization of the chromosome single-segment substitution lines of O. glumaepatula and O. barthii and identification of QTLs for yield-related traits

Oryza glumaepatula and Oryza barthii are AA-genome wild species in Oryza genus. In order to effectively mine and transfer beneficial genes from these wild species in genome-wide by distant hybridization, in the present study, the chromosome single-segment substitution lines (SSSLs) were developed using O. glumaepatula and O. barthii as donors and elite indica cultivar, HJX74, as a recipient. A total of 168 homozygous SSSLs of O. glumaepatula (GLU-SSSLs) and 95 homozygous SSSLs of O. barthii (BAR-SSSLs) were developed. In 168 GLU-SSSLs and 95 BAR-SSSLs, the total lengths of the substituted segments distributing on 12 chromosomes were 3636.35 cM and 1731.65 cM, respectively. Accordingly, the mean length of each substituted segment was 21.64 cM in GLU-SSSLs and 18.23 cM in BAR-SSSLs. The total coverage lengths of the substituted segments on rice genome were 80.15% in GLU-SSSLs and 54.67% in BAR-SSSLs. To evaluate the utilization potential of these SSSLs, four yield-related traits, heading date, plant height, seed-setting rate, and 1000-grain weight, were investigated in the SSSLs over two seasons. Significant variations of the traits were observed among the SSSLs. At P ≤ 0.05 level, a sum of 28 stable QTLs in GLU-SSSLs and 53 in BAR-SSSLs were identified. Among them, the additive effects of 12 QTLs contributed averagely more than 10% for phenotypic variations, viz., qPHg1-2, qGWTg9-2, qHDb1-1, qPHb1-2, qPHb1-3, qPHb7-1, qPHb7-2, qPHb8-1, qPHb10-1, qPHb12-2, qSSb7-1, and qSSb10-2. Nine pairs of QTLs in the two donors were comparatively mapped on chromosomes 1, 5, and 10, which means the same QTLs or alleles existing in O. glumaepatula and O. barthii have been detected and transferred to SSSLs. Besides, qGWTg1-1, qGWTg4-1, and qGWTb1-1 have shown positive additive effects, implying alleles from the two wild donors of these QTLs have the potential in increasing 1000-grain weight in SSSLs. The SSSLs library of the wild species is a valuable resource for rice germplasm innovation and breeding.

АНАЛИЗ ГЕНЕТИЧЕСКИХ ВЗАИМОСВЯЗЕЙ СОРТОВ РИСА ИЗ РАЗНЫХ ЭКОЛОГО-ГЕОГРАФИЧЕСКИХ ГРУПП С ИСПОЛЬЗОВАНИЕМ SSR МАРКЕРОВ

Microsatellite DNA markers are widely used in genetic research on rice: for studying the genetic diversity of genetic resources collections, iden-tifying microevolutionary processes within the genus Oryza L. and analyzing genetic relationships of gene pools from different regions of the world, as well as in gene mapping and performing marker-assisted selection in breeding. Given the size of the collection held by the All-Russian Rice Research Institute, which has a total of about 7,000 accessions, it is important to analyze its genetic structure and study genetic diversity, including the use of molecular genetic methods. The aim of the work was to clarify the genetic relationships among modern Russian rice varieties and varieties from different regions of Asia (Central Asia or East Asia) representing various ecogeographic groups using microsatellite DNA markers. The material of the study was 32 rice cultivars representing three different ecogeographic groups: Eastern, Central Asian and European. We used 10 SSR markers, which showed a level of polymorphism from 2 (RM11, RM316, RM19) to 8 alleles (RM1). For a total of ten loci, 46 alleles were identified. The average PIC was 0.45. The results of the Bayesian analysis and clustering using the UPGMA method made it possible to make a conclusion about the complex genetic structure of the set of the studied cultivars, which is consistent with the presence of cultivars from different ecogeographic groups (EGG). A number of cultivars that occupy an intermediate position between ecogeographic groups were identified, which obviously is a consequence of the active use of crosses between cultivars belonging to different EGGs in the process of breeding. Russian cultivars, which according to their morphological characteristics belong to the European ecogeographic group, were attributed to the group which also included some varieties from Central Asia and from the Eastern EGG. It was a consequence of the use of cultivars belonging to different ecogeographic groups in domestic breeding programs.

Development of introgression lines of AA genome Oryza species, O. glaberrima, O. rufipogon, and O. nivara, in the genetic background of O. sativa L. cv. Taichung 65.

To evaluate and utilize potentially valuable quantitative trait loci or genes of wild relatives in the genetic background of domesticated crop species, chromosome segment substitution lines (CSSLs) are a valuable tool. CSSLs can be constructed through the exchange of chromosome segments of AA genome species of the genus Oryza with cultivated rice, Oryza sativa L. Here we report the development of three sets of CSSLs carrying segments of AA genome species closely related to Oryza sativa—O. glaberrima (IRGC 103777 from Mali), O. rufipogon (W1962 from China), and O. nivara (IRGC 105715 from Cambodia)—in the genetic background of ssp. japonica cultivar Taichung 65 through the use of 101 to 121 simple-sequence-repeat markers in whole-genome genotyping and marker-assisted selection. The materials are available via the National Bioresource Project (Rice) Oryzabase Web page.

Salinity tolerance in Australian wild Oryza species varies widely and matches that observed in O. sativa

BackgroundSoil salinity is widespread in rice-producing areas globally, restricting both vegetative growth and grain yield. Attempts to improve the salt tolerance of Asian rice, Oryza sativa—the most salt sensitive of the major cereal crops—have met with limited success, due to the complexity of the trait and finite variation in salt responses among O. sativa lines. Naturally occurring variation among the more than 20 wild species of the Oryza genus has great potential to provide breeders with novel genes to improve resistance to salt. Here, through two distinct screening experiments, we investigated variation in salinity tolerance among accessions of two wild rice species endemic to Australia, O. meridionalis and O. australiensis, with O. sativa cultivars Pokkali and IR29 providing salt-tolerant and sensitive controls, respectively.ResultsRice plants were grown on soil supplemented with field-relevant concentrations of NaCl (0, 40, 80, and 100 mM) for 30 d, a period sufficient to reveal differences in growth and physiological traits. Two complementary screening approaches were used: destructive phenotyping and high-throughput image-based phenotyping. All genotypes displayed clear responses to salt treatment. In the first experiment, both salt-tolerant Pokkali and an O. australiensis accession (Oa-VR) showed the least reduction in biomass accumulation, SES score and chlorophyll content in response to salinity. Average shoot Na+/K+ values of these plants were the lowest among the genotypes tested. In the second experiment, plant responses to different levels of salt stress were quantified over time based on projected shoot area calculated from visible red-green-blue (RGB) and fluorescence images. Pokkali grew significantly faster than the other genotypes. Pokkali and Oa-VR plants displayed the same absolute growth rate under 80 and 100 mM, while Oa-D grew significantly slower with the same treatments. Oa-VR showed substantially less inhibition of growth in response to salinity when compared with Oa-D. Senescence was seen in Oa-D after 30 d treatment with 40 mM NaCl, while the putatively salt-tolerant Oa-VR had only minor leaf damage, even at higher salt treatments, with less than a 40% increase in relative senescence at 100 mM NaCl compared to 120% for Oa-VR.ConclusionThe combination of our two screening experiments uncovered striking levels of salt tolerance diversity among the Australian wild rice accessions tested and enabled analysis of their growth responses to a range of salt levels. Our results validate image-based phenotyping as a valuable tool for quantitative measurement of plant responses to abiotic stresses. They also highlight the potential of exotic germplasm to provide new genetic variation for salinity tolerance in rice.

Comparative Evaluation of Rice SSR Markers on Different Oryza Species

The growing number of rice microsatellite markers permit a comprehensive comparison of allelic variation among the markers developed using different methods, with diverse repeat motifs and at variable genomic regions. Under this study, comparison between a set of 67 microsatellite markers representing the whole (twelve) rice chromosomes was done over worldwide collections of nine species of the genus Oryza. These SSR markers were evaluated for the genetic parameters such as; number of alleles amplified per primers, observed heterozygosity, gene diversity, rare allelic frequency and Polymorphic Information Content (PIC) values.

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.

Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes

Oryza coarctata (KKLL; 2n = 4x = 48, 665 Mb) also known as Porteresia coarctata is an extreme halophyte species of genus Oryza. Using Illumina and Nanopore reads, we achieved the assembled genome size of 569.9 Mb, accounting 85.69% of the estimated genome size with N50 of 1.85 Mb and 19.89% repetitive region. We also found 230,968 simple sequence repeats (SSRs) and 5,512 non-coding RNAs (ncRNAs). The functional annotation of predicted 33,627 protein-coding genes and 4,916 transcription factors revealed that high salinity adaptation of this species is due to the exclusive or excessive presence of stress-specific genes as compared to rice. We have identified 8 homologs to salt-tolerant SOS1 genes, one of the three main components of salt overly sensitive (SOS) signal pathway. On the other hand, the phylogenetic analysis of the assembled chloroplast (134.75 kb) and mitochondrial genome (491.06 kb) favours the conservative nature of these organelle genomes within Oryza taxon.

Characterization of diterpene synthase genes in the wild rice species Oryza brachyatha provides evolutionary insight into rice phytoalexin biosynthesis

Cultivated rice (Oryza sativa; Os) produces a variety of labdane-related diterpenoids; not only phytohormone gibberellins (GAs) but also phytoalexins for defense including phytocassanes, momilactones and oryzalexins. Their carbon skeleton diterpenes are constructed from geranylgeranyl diphosphate via ent-copalyl diphosphate (ent-CDP) or its diastereomer syn-CDP. These two-step reactions are successively catalyzed by homologs of the two diterpene synthases, ent-CDP synthase (ent-CPS) and ent-kaurene synthase (KS) that are responsible for the biosynthesis of GAs; e.g. OsCPS4 and OsKSL8 that are involved in the biosynthesis of oryzalexin S, a rice phytoalexin. Oryza brachyantha (Ob) is the most distant wild rice species from Os among the Oryza genus. We previously reported that the Ob genome contains ObCPS_11g, ObKSL8-a, ObKSL8-b and ObKSL8-c for specialized metabolism at a locus similar to the OsKSL8 locus on chromosome 11. These Ob genes are closely related to OsCPS4 and OsKSL8, respectively. We herein characterize the diterpene synthase genes in Ob, using functional analyses and expression analysis. Recombinant OsKSL8 and ObKSL8-a showed the same in vitro function when syn-CDP or normal-CDP were used as substrates. Nonetheless, our results suggest that Ob produces normal-CDP-related diterpenoid phytoalexins, presumably via ObKSL8-a, while Os produces a syn-CDP-related phytoalexin, oryzalexin S, via OsKSL8. This difference must be due to the kinds of CPS that are present in each species; Os has OsCPS4 encoding syn-CPS, while Ob has ObCPS_11g encoding normal-CPS. Thus, we propose the evolutionary history underlying oryzalexin S biosynthesis: the gain of a syn-CPS was a critical event allowing the biosynthesis of oryzalexin S.

Electrophoretic variation in seed proteins and interrelationships of species in the genus Oryza

Comparative studies of two cultivated and sixteen wild species of the genus Oryza were carried out using one- and two-dimensional gel electrophoresis for variation in their seed proteins for interrelationships of these species. A number of polypeptides in the range of molecular weight 13–110 kDa were seen to vary. Under reducing conditions, polypeptides spread over the regions of mol. wt. 33–40.5, 25–27 and 19–21.5 kDa exhibited maximum variation in their patterns. Two-dimensional gel electrophoresis revealed the occurrence of disulphide-linked glutelin polypeptide pairs of mol. wt. 60, 58, 52 and 25 kDa breaking into a large and a small subunit each in the range of mol. wt. 18–40.5 and 16–25 kDa respectively in Oryza sativa. The number of such polypeptide pairs varied from 2 to 6 in different species and also in O. sativa showed variation in mol. wts. of their constituent subunits. The UPGMA dendrogram revealed that most of the Oryza species occurred in different clusters and subclusters and thus did not share very close relationships. The undisputed and closest relationship observed was that of cultivated rice O. sativa with the O. rufipogon followed by that with O. nivara. The African cultivated O. glaberrima occurring on the nearest branch of the same subcluster, thereby, supporting the phylogenetic of these species suggested in earlier studies. Eight diploid species and seven tetraploid species were included in one part of the dendrogram while the remaining two species with AA genome i.e. O. glumaepatula and O. meridionalis and one with FF i.e. O. brachyantha stood separately from these as scattered in the group of seven tetraploid species with BBCC, CCDD and HHJJ genomes. The tetraploids O. alta, O. latifolia and O. grandiglumis with CCDD genomes which occurred on the farthest part were distantly related with O. sativa. The cyanogen bromide peptide maps and two dimensional gel electrophoresis also supported the closest relationship between O. sativa and O. rufipogon.

Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions.

Centromeres are dynamic chromosomal regions, and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here, we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza We report a 12.4-Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ∼15 million years ago. The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and 10 in O. brachyantha Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in O. brachyantha jumped ∼400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P < 2.2 × 10-16). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g., spreading or microrepositioning) may drive such gene loss.

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.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.