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Background Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.

BACKGROUND: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS: Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity.Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

Additional file 11: Figure S8. Log scale QQ-plots corresponding to association analysis performed independently on each trait and repetition. Three different models (i.e. EMMA, LFMM, MLM) taking into account relatedness and/or structure were used for association and ANOVA was used as a benchmark. For a given trait, the transformed data were used if at least one of the replicates failed to reach normality, otherwise non-transformed data were used.

Additional file 8: Figure S5. Correlations between traits and structure. For each ancestry group (A1 to A4), we made a Spearman’s rank correlation test and plotted it as a correlogram. Colors sign the intensity of the correlation and white stars were added when the correlation was significant given the threshold retained, i.e. either a p-value cutoff of 0.01 (a) or a False Discovery Rate of 5% (b).

Additional file 5: Figure S2. Genome wide Linkage disequilibrium (LD) decay.

Additional file 1: Supplemental Table 1. Composition of media (1 L) used in this study. Supplemental Table 2. Work flow of test of regeneration from callus derived from immature embryos of wild Oryza species.

Additional file 9: Figure S6. Linear scale QQ-plots corresponding to association analysis performed independently on each trait and repetition. Three different methods (EMMA, LFMM, MLM) taking into account relatedness and/or structure were used for association and ANOVA was used as a benchmark. For a given trait, the transformed data were used if at least one of the replicates failed to reach normality, otherwise non-transformed data were used.

Context Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. Results Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. Conclusions Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice. Electronic supplementary material The online version of this article (10.1186/s12870-018-1504-1) contains supplementary material, which is available to authorized users.

Background The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. Results Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. Conclusion The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0065-y) contains supplementary material, which is available to authorized users.

Rice panicle architecture is one of the most important morphological traits specifying rice yield potential, which was under selection during rice domestication. A panicle is a branched structure composed of a rachis, primary branches, higher order branches (i.e. secondary and tertiary branches) and finally spikelets. This morphology, depending on the activity of axillary meristems during its development, shows a wide diversity in both inter-specific (i.e. crops vs. wild-relatives) and intra-specific (Asian or/and African rice) levels. Several important genes/QTLs have been characterized in Oryza sativa as controlling panicle architecture by regulating meristem fate, cell division and hormone signaling. However the mechanisms related to rice panicle diversity and its evolution in the context of domestication are still largely unknown. During my PhD, I mainly investigated the histological and molecular bases of panicle diversity between the African species Oryza glaberrima and its wild-relative Oryza barthii. I analyzed the expression patterns of orthologs of O. sativa landmark genes related to panicle development and was involved in small RNA transcriptomic analysis in early stages of panicle development. This work revealed a high conservation of the spatial expression pattern of the landmarks genes studied but have highlighted a differential timing and level of the expression of these genes during the panicle development between two species. The genes promoting meristem activity were upper-accumulated over a longer period during the panicle development in the crop species, whereas the gene promoting spikelet/floret meristem fate behaved in opposite way. This work also has shown similar heterochronic alteration of the expression of members of the miR2118-triggered 21-nt phased siRNA pathway, known to be involved in male gametogenesis. Together, these findings suggest that variation of panicle complexity in African rice may rely on heterochronic changes in branching activity as well as spikelet/floret meristem determinacy., L'architecture de la panicule de riz est l'un des caractères morphologiques majeurs du potentiel de rendement, sélectionné lors de sa domestication. Une panicule est une structure ramifiée, composée d'un axe principal (rachis), de branches primaires, et d'ordres supérieurs de branchement (branches secondaires et tertiaires) et enfin les épillets. Cette structure, qui dépend de l'activité des méristèmes axillaires au cours du développement de la panicule, montre une grande diversité à la fois inter-spécifique (espèces cultivées vs espèces sauvages apparentées) et intra-spécifiques (riz asiatique et / ou africain). Plusieurs gènes/QTL importants ont été caractérisés chez Oryza sativa pour le contrôle de l'architecture de la panicule en régulant l'identité des méristèmes, la division cellulaire et la signalisation hormonale. Cependant, les mécanismes liés à la diversité de la panicule de riz et son évolution dans le contexte de la domestication sont encore largement inconnus. Durant ma thèse, j'ai principalement contribué à l'étude des bases histologique et moléculaires de la diversité de la panicule entre l'espèce africaine Oryza glaberrima et Oryza barthii, l'espèce sauvage apparentée. J'ai analysé les profils d'expression d'orthologues à des gènes de O. sativa liés au développement de la panicule et participé à l'analyse transcriptomique de petits ARN dans les premiers stades de développement de la panicule. Ce travail a révélé une différence de période d'initiation et de niveau d'expression de ces gènes au cours du développement de la panicule entre les deux espèces, conjointement avec une forte conservation de leurs domaines d'expression. Les gènes qui favorisent l'activité des méristèmes sont sur-accumulés sur une période plus longue au cours du développement de la panicule chez l'espèce cultivée, tandis que les gènes liés au développement des épillets se comportent de manière opposée. Ces travaux ont également montré une altération similaire de l'expression des membres de la voie de siRNA phasés initiés par miR2118, voie connue pour être impliquée dans la gamétogenèse mâle. L'ensemble de ces résultats suggère que la diversité de complexité de la panicule chez les riz africains reposerait sur des altérations hétérochroniques de l'activité de ramification et de déterminisme des méristèmes d'épillets.

Additional file 6: Figure S3. Structure of the population. (a) evolution of the cross-entropy criterion with increasing K, (b) bar plot of ancestries membership considering K = 4 ancestral population.

Additional file 7: Figure S4. Geographic distribution of traits. We plotted the mean value of each trait for accessions having sampling location in their passport data.

Additional file 3: Figure S1. Histograms of trait distribution and quantile-quantile plots for each non-transformed and transformed variables.

Additional file 3: Figure S1. Histograms of trait distribution and quantile-quantile plots for each non-transformed and transformed variables.

Additional file 7: Figure S4. Geographic distribution of traits. We plotted the mean value of each trait for accessions having sampling location in their passport data.