Cultivated Rice Accessions Research Articles

Identification of African rice genotypes with early morning flowering trait to avoid heat stress

Abstract Early morning flowering (EMF) is a desirable trait in rice to avoid heat stress as temperatures in early morning hours are low compared to afternoon and flowering is the most sensitive stage to heat exposure. Cultivated rice accessions including both Oryza glaberrima and O. sativa were phenotyped for an EMF trait in 2016–2018 in two locations viz. Cotonou in Benin Republic and Ibadan in Nigeria. The initial screening was done in Cotonou in three phases in 2016 dry season, 2017 wet season and 2017 dry season, respectively. The 2093 accessions used in initial screening were subdivided into three groups based on flowering duration ensuring that each accession was grown under conditions which were best suited to their flowering duration. Further screening was done in Ibadan in 2018 dry season and 2018 wet season. Out of 2093 accessions taken in the initial screening only 1754 accessions germinated out of which only 64 accessions exhibited EMF phenotype consistently across the cultivated years, seasons and locations. Among the 64 accessions exhibiting EMF phenotype, 15 accessions also showed an early peak in spikelet opening time (EPSOT) trait, more than 80% flowering before 09:00 h. We conclude that 15 O. glaberrima accessions identified possessing both the EMF and EPSOT traits are suitable donors for use in breeding for heat escape in rice.

Association mapping of mesocotyl and coleoptile length in rice using various genome‐wide association study models

AbstractThe mechanized direct seeding of rice (Oryza sativa L.) is a major trend nowadays. The elongation of rice mesocotyl and coleoptile can facilitate the rapid emergence of seedlings under deep mechanized sowing. Currently, most of the cultivated rice accessions have short mesocotyls or coleoptiles, with only a few related genes cloned. However, understanding and enhancing the ability of rice seedlings to rapidly emerge from deep sowing depths is crucial. Herein, we assessed 745 core rice germplasm accessions sown under a soil cover depth of 10 cm and found few long mesocotyl and coleoptile germplasms. We conducted genome‐wide association study using six models to obtain three or more multi‐model co‐localization candidate regions and calculated Fst between the phenotypes of extreme samples to determine genetic differences. The candidate regions associated with mesocotyl and coleoptile lengths were identified by integrating Fst and multi‐model localization results. This multi‐model localization method may accelerate the mining of genes related to the mesocotyl and coleoptile, providing valuable targets for functional validation and marker‐assisted selection in rice breeding programs.

Genetic Variation in Tolerance to Iron Deficiency among Species of Oryza

Transplanted rice cultivation has caused groundwater depletion in several regions globally. Direct-seeded rice under aerobic conditions is a water-saving alternative. However, under aerobic conditions, iron in the soil is oxidized from the ferrous to ferric forms, which are not easily available to rice crops, resulting in iron-deficiency-induced chlorosis (IDIC) and causing significant reductions in yield. Cultivated rice accessions have limited variations in IDIC tolerance, while the wild Oryza germplasm could be a potential source of IDIC tolerance. In this study, 313 Oryza accessions were evaluated for IDIC tolerance at the tillering stage under aerobic conditions and 20 IDIC-tolerant lines were identified. The twenty lines showed no signs of chlorosis and had high levels of iron content and SPAD values, while the eight cultivated controls exhibited varying degrees of chlorosis symptoms and low levels of SPAD and iron content. To confirm their tolerance, the selected lines were evaluated again in a subsequent year, and they showed comparable levels of tolerance, indicating that these lines were efficient in iron uptake and utilization, resulting in maintained high chlorophyll and leaf area index. These accessions may be useful for developing IDIC-tolerant cultivars for aerobic rice cultivation and future studies of the molecular basis of IDIC tolerance.

Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome.

Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.

Insights into genomic variations in rice Hsp100 genes across diverse rice accessions

The Hsp101 gene is present across all sequenced rice genomes. However, as against Japonica rice, Hsp101 protein of most indica and aus rice contain insertion of glutamic acid at 907th position. The understanding of the heat stress response of rice plants is important for worldwide food security. We examined the presence/absence variations (PAVs) of heat shock proteins (Hsps)/heat shock transcription factor (Hsf) genes in cultivated rice accessions. While 53 Hsps/Hsfs genes showed variable extent of PAVs, 194 genes were the core genes present in all the rice accessions. ClpB1/Hsp101 gene, which is critically important for thermotolerance in plants, showed 100% distribution across the rice types. Within the ClpB1 gene sequence, 40 variation sites consisting of nucleotide polymorphisms (SNPs) and short insertion/deletions (InDels) were discerned. An InDel in ClpB1 leading to an in-frame insertion of 3 nucleotides (TCC) thereby an additional amino acid (glutamic acid) at 907th amino acid position was noted in most of the indica and aus as against japonica rice types. Three rice types namely Moroberekan (japonica), IR64 (indica) and N22 (aus) were further analyzed to address the question of ClpB1 genomic variations and its protein levels with the heat tolerance phenotype. The growth profiling analysis in the post heat stress (HS) period showed that N22 seedlings were most tolerant, IR64 moderately tolerant and Moroberekan highly sensitive. Importantly, the ClpB1 protein sequences of these three rice types showed distinct differences in terms of SNPs. As the ClpB1 protein levels accumulated post HS were generally higher in Moroberekan than N22 seedlings in our study, it is proposed that some additional gene loci in conjunction with ClpB1 regulate the overall rice heat stress response.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice.

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

A Culture-dependent Study of Bacteria Associated with the Roots of Organically and Inorganically Cultivated Rice Accessions

Rice is one of the most important staple foods consumed by the maximum human population in the world. India possesses a large number of traditionally maintained rice landraces which are cultivated using traditional practices or minimal fertilizer input. Such landraces may be associated with unique microbial flora adapted to various biotic and abiotic stresses. This work aimed to study the diversity of bacteria associated with roots of 18 randomly selected landraces from Jawhar, Maharashtra, grown under organic cultivation practices, and the cv. Indrayani from Mulshi, Maharashtra, grown using conventional cultivation practices. The cultivation-based approach yielded a total of 40 bacterial isolates. Isolates were purified and identified by sequencing the 16S rDNA region. Isolates were tested for plant growth-promoting characteristics such as nitrogen fixation, phosphate solubilization, IAA production, etc. 22 isolates tested positive for nitrogen fixation either by acetylene reduction or the presence of nifH gene, 27 had phosphate solubilization and 39 had IAA production ability. Bacterial diversity demonstrated the dominance of phylum Proteobacteria and isolates belonging to 11 genera and 23 species e.g., Stenotrophomonas sp., Bradyrhizobium sp. etc. PCA showed a clear difference between bacterial diversity associated with landraces and cv. Indrayani. Our findings provide a basis for further investigations into the role and impact of microbial communities in plant growth promotion. Rice is one of the most important staple foods consumed by the maximum human population in the world. India possesses a large number of traditionally maintained rice landraces which are cultivated using traditional practices or minimal fertilizer input. Such landraces may be associated with unique microbial flora adapted to various biotic and abiotic stresses. This work aimed to study the diversity of bacteria associated with roots of 18 randomly selected landraces from Jawhar, Maharashtra, grown under organic cultivation practices, and the cv. Indrayani from Mulshi, Maharashtra, grown using conventional cultivation practices. The cultivation-based approach yielded a total of 40 bacterial isolates. Isolates were purified and identified by sequencing the 16S rDNA region. Isolates were tested for plant growth-promoting characteristics such as nitrogen fixation, phosphate solubilization, IAA production, etc. 22 isolates tested positive for nitrogen fixation either by acetylene reduction or the presence of nifH gene, 27 had phosphate solubilization and 39 had IAA production ability. Bacterial diversity demonstrated the dominance of phylum Proteobacteria and isolates belonging to 11 genera and 23 species e.g., Stenotrophomonas sp., Bradyrhizobium sp. etc. PCA showed a clear difference between bacterial diversity associated with landraces and cv. Indrayani. Our findings provide a basis for further investigations into the role and impact of microbial communities in plant growth promotion.

Natural variation of RGN1a regulates grain number per panicle in japonica rice.

The grain number per panicle (GNP) is an important yield component. Identifying naturally favorable variations in GNP will benefit high-yield rice breeding. Here, we performed a genome-wide association study using a mini-core collection of 266 cultivated rice accessions with deep sequencing data and investigated the phenotype for three years. Three genes, i.e., TOTOU1 (TUT1), Grain height date 7 (Ghd7), and Days to heading 7/Grain height date 7.1/Pseudo-Response Regulator37 (DTH7/Ghd7.1/OsPRR37), which regulate GNP, were found in the quantitative trait loci (QTL) identified in this study. A stable QTL, qGNP1.3, which showed a strong correlation with variations in GNP, was repeatedly detected. After functional and transgenic phenotype analysis, we identified a novel gene, regulator of grain number 1a (RGN1a), which codes for protein kinase, controlling GNP in rice. The RGN1a mutation caused 37.2%, 27.8%, 51.2%, and 25.5% decreases in grain number, primary branch number per panicle, secondary branch number per panicle, and panicle length, respectively. Furthermore, breeding utilization analysis revealed that the additive effects of the dominant allelic variants of RGN1a and DTH7 played a significant role in increasing the grain number per panicle in japonica rice. Our findings enrich the gene pool and provide an effective strategy for the genetic improvement of grain numbers.

Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication.

The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.

Genetic architecture of seed glycerolipids in Asian cultivated rice.

Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.

Global demand for rice genetic resources

BackgroundThe International Rice Research Institute (IRRI) holds in trust the world's largest collection of rice diversity, with more than 130,000 accessions of cultivated rice and wild species. Between 2012 and 2018, a total of 2174 requests for rice germplasm were received from more than 1000 unique requestors. We documented and analyzed how genebank users made use of germplasm from IRRI. As we address food and nutrition security challenges in a changing context, we are motivated by the need to enhance the conservation, management, and use of rice genetic resources.MethodsWe examined the patterns of use of the IRRI genebank using distribution data and analyzed the results from a survey of germplasm recipients. The 2019 IRRI genebank user survey is the most recent attempt to obtain structured feedback from genebank end-users in multiple countries on their use of rice germplasm since 1995. We received 244 responses (a 35% response rate) out of the complete list of 694 respondents with valid email addresses. We also tested the relationship between the availability of germplasm information, proxied by the passport data completeness index (PDCI), and the demand for rice accessions, measured by the number of requests for each unique accession using a Negative Binomial regression model. We hypothesized that materials that are better documented are more frequently requested by users because they offer more useful information for targeted research and breeding.ResultsBetween 2012 and 2018, requests for germplasm from outside IRRI were received from 63 countries in all regions of the world, mostly from Asia. IRRI distributed germplasm externally to requestors from universities (32%), national research programs (14%), private companies (9%), and individuals, including farmers (24%) as well as other CGIAR centers (3%). The traits sought most often were tolerances to environmental stresses, followed by tolerance or resistance to biotic stresses. The majority of survey respondents confirmed the usefulness of IRRI germplasm for research, breeding, characterization, and evaluation. The analytical model confirmed the significant positive relationship between PDCI values and the demand for those accessions. The results indicated that improving the availability of information at the accession level will enhance the use of those materials. To the best of our knowledge, this study is the first to show the empirical link between documentation and use of germplasm.ConclusionsThe findings demonstrate the crucial role of IRRI's genebank as a key germplasm source for global rice research and development, with important implications for the conservation and use of rice genetic diversity in the future. Public sector organizations and the scientific community in general benefit from the conservation and availability of rice genetic resources. We also show the importance of the availability of data on conserved accession to enhance their use. To sustain the benefits, continuous investment in genebanks is needed to allow them to adapt to changes in technology and agricultural context.

Spatial control of cell division by GA-OsGRF7/8 module in a leaf explaining the leaf length variation between cultivated and wild rice.

Cellular and genetic understanding of the rice leaf size regulation is limited, despite rice being the staple food of more than half of the global population. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that remarkably differed for leaf size. Comparative transcriptomics, gibberellic acid (GA) quantification and leaf kinematics of the contrasting accessions suggested the involvement of GA, cell cycle and growth-regulating factors (GRFs) in the rice leaf size regulation. Zone-specific expression analysis and VIGS established the functions of specific GRFs in the process. The leaf length of the selected accessions was strongly correlated with GA levels. Higher GA content in wild rice accessions with longer leaves and GA-induced increase in the leaf length via an increase in cell division confirmed a GA-mediated regulation of division zone in rice. Downstream to GA, OsGRF7 and OsGRF8 function for controlling cell division to determine the rice leaf length. Spatial control of cell division to determine the division zone size mediated by GA and downstream OsGRF7 and OsGRF8 explains the leaf length differences between the cultivated and wild rice. This mechanism to control the rice leaf length might have contributed to optimizing leaf size during domestication.

Diversity of Sodium Transporter HKT1;5 in Genus Oryza

Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane (MPM) motifs in OsHKT1;5. HKT1;5 sequences from more recently evolved Oryza species (O. sativa/O. officinalis complex species) contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains, potentially governing transport characteristics, while more ancestral HKT1;5 sequences have shorter intracellular loops. We compared homology models for homoeologous OcHKT1;5-K and OcHKT1;5-L from halophytic O.coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na+. Using haplotyping, we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species (O. nivara and O. rufipogon). Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance. Within Asian rice accessions, 10 non-synonymous HKT1;5 haplotypic groups occur. More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica. Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups, corresponding to haplotypes in O. sativa salt-sensitive and salt-tolerant landraces, respectively. This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica, or from different haplotypes selected during domestication. Predominance of specific HKT1;5 haplotypes within the 3 000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes.

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication

Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BackgroundCadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.ResultsIn this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.ConclusionThe exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice.

Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination. Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, seed coat components and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy in the whole panel and five in the Japonica and Indica subpanel; expression of candidate genes within 100kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. Two candidates were validated using Quantitative Reverse Transcription (qRT)-PCR. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index, with qRT-PCR validation. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BackgroundRice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined.ResultsIn the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together.ConclusionsThis study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Genetic architecture and key genes controlling the diversity of oil composition in rice grains

Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.

Morphological characterization and genetic identity of crop wild relatives of rice (Oryza sativa L.) collected from different ecological niches of India

Crop wild relatives of rice (Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were undertaken in six states located in different agro-ecological zones of India. Forty-four accessions belonging to four wild species (Oryza rufipogon Griff., Oryza nivara Sharma et Shastry, Oryza officinalis Wall. ex Watt and Oryza sativa L. f. spontanea Roshev.) including two accessions of cultivated rice (Oryza sativa L. subsp. indica Kato) were collected from different ecological niches. The rice accessions were characterized using 28 morphological descriptors, which included 15 qualitative and 13 quantitative traits. Wild rice accessions displayed a broad range of phenotypic variation for plant height, main heading days, days to 50% flowering, flag-leaf length and width, panicle shape and size, peduncle length, awning pattern, awn length and colour, seed length and width, seed length/width ratio and 100-seed weight. Cluster analysis based on Jaccard’s similarity coefficients derived from 28 morphological traits grouped 44 accessions into three clades. DNA sequencing revealed that internal transcribed spacer (ITS) region of 18S–5.8S–28S nuclear ribosomal cistron varied from 574 to 577 bp with mean of 576.1 bp in AA-genome species. GC content was high in ITS region, which varied from 69.57 to 70.36% with mean value of 69.99%. Neighbour-joining phylogenetic tree distinguished Oryza sativa–nivara–rufipogon complex from other species of AA-genome. The wild germplasm characterized in this study could be utilized in the genetic enhancement of cultivated rice.