Cultivated Rice Species Research Articles

Genome evolution and diversity of wild and cultivated rice species

Genome evolution and diversity of wild and cultivated rice species

Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes

Differential gene expression analysis is a widely used approach to identify relevant genes and functional mechanisms that influence plant tolerance to abiotic stresses. In this study, we evaluated the transcriptional responses of contrasting rice genotypes to prolonged aluminum (Al) exposure, in cultivated (Oryza sativa) and wild (Oryza glumaepatula) rice species, through RNA-Seq experiments. After comparing transcriptional responses under control and Al treatment conditions, differentially expressed genes (DEGs) were identified for each genotype. Additionally, the transcription levels of six DEGs were validated by quantitative real-time PCR. Functional analyses of the identified DEGs provided insights into the coordinated action of both exclusion and detoxification mechanisms associated with Al responses in rice. Furthermore, we report a group of 28 genes that were differentially expressed in all analyzed species and genotypes, pinpointing a core set of mechanisms that are triggered by Al exposure. Likewise, 14 DEGs were identified only in Al-tolerant genotypes, representing potential key elements for the understanding of the successful adaptive response to toxic conditions adopted by tolerant genotypes. Given that many of these identified genes have not been previously reported or characterized, they could be considered novel regulators linked with Al tolerance responses, and promising candidates for the generation of agronomically improved rice varieties.

Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species

Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.

Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice

Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F1 of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding.

Evolutionary Relationship and Structural Analysis of Blast Resistance Associated Novel Osvwa36 and Osvwa37 Genes in Cultivated and Wild Species of Rice

Rice blast is a dreadful disease that causes enormous losses in rice production worldwide. To develop blast resistant rice cultivars, it is necessary to identify resistance and defence regulator genes and the underlying mechanism of resistance. A novel von Willebrand factor domain A containing genes OsvWA36 and OsvWA37 in Tetep cultivar of rice regulate response to Magnaporthe oryzae infection and provides significant resistance. Owing to the important role of these genes, their evolutionary relationship has been studied in cultivated and wild species of rice. There is significant diversity in the protein sequence of these genes among the relative wild rice species. The size of OsvWA36 protein varies from 501 aa to 698 aa whereas size of OsvWA37 protein varies from 295 aa to 1004 aa. The, OsvWA36 gene is evolutionarily more conserved than OsvWA37 among the different rice species indicating its critical role. Besides the global variation in protein sequence, the region of vWA domain is highly conserved among all the species. Interestingly, both the genes in Oryza barthii are fused to form a single gene encoding a large protein that indicates their origin in other species from a single gene. The good quality tertiary structures of both OsvWA36 and OsvWA37 proteins in cultivated germplasm cv. Tetep were also generated which can be utilized for protein structural and docking studies.

Removing Harmful Pericarp Character of Weedy Rice as the First Step of Domestication towards Direct-Seeding Rice Using CRISPR/Cas9-Targeted Mutagenesis

With the scarcity of fresh water resources and the increase in labor prices, rice cultivation is changing from transplanting to direct seeding. Weedy rice is a malignant weed with strong drought tolerance in seed germination in direct-seeding rice fields. As the same species of cultivated rice (Oryza sativa L.), weedy rice (Oryza sativa f. spontanea) has the potential of domestication into direct-seeding rice with strong drought tolerance in seed germination by changing a few unfavorable traits. The red pericarp, one of the harmful traits of weedy rice, seriously affects the quality and commercial value of cultivated rice. The recently developed CRISPR/Cas9 (Clustered Regular Interspaced Short Palindromic Repeats) technology can accurately edit the function of genes, providing a possibility for the directed evolution. Weedy rice (WRL-162) with red pericarp was used as a mutant material. Two mutation sites, upstream and downstream of the 14 bp differential fragment of exon 6 of Rc gene, were designed using the CRISPR-Cas9 gene-editing technique. Consequently, three mutant types in T1 generation weedy rice with CRISPR-Cas9 vector changed from red to white pericarp. One mutant type in T1 generation weedy rice with CRISPR-Cas9 vector maintained red pericarp. Comparing the wild type of weedy rice and rice variety control (Nipponbare), mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly improved the drought resistance in seed germination. In addition, there was no significant difference in panicle number, seed setting rate per plant, grain length and width between wild type and T3 generation mutant weedy rice without CRISPR-Cas9 vector. Comparing the wild type, some mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly decreased plant height, decreased spikelet number per main panicle, decreased plump seed number per main panicle, and increased 1000-grain weight. Our results showed that the Rc gene editing using CRISPR/Cas9 technology can not only remove the harmful pericarp character of weedy rice, but also improve drought tolerance in seed germination. This study might provide new insights for the utilization of weedy rice as germplasm resources for direct-seeding rice by precisely editing genes to remove unfavorable traits.

Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus Oryza.

Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus Oryza. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species Oryza sativa has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for DIR genes' evolution in Oryza, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that OsjDIR genes respond to a wide range of environmental factors, and most OsjDIR genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of OsjDIR genes to the undersupply of mineral elements, the excess of heavy metals and the infection of Rhizoctonia solani. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of DIR genes in rice.

Rice Phytoalexins: Half a Century of Amazing Discoveries; Part I: Distribution, Biosynthesis, Chemical Synthesis, and Biological Activities

Cultivated rice is a staple food for more than half of the world's population, providing approximately 20% of the world's food energy needs. A broad spectrum of pathogenic microorganisms causes rice diseases leading to huge yield losses worldwide. Wild and cultivated rice species are known to possess a wide variety of antimicrobial secondary metabolites, known as phytoalexins, which are part of their active defense mechanisms. These compounds are biosynthesized transiently by rice in response to pathogens and certain abiotic stresses. Rice phytoalexins have been intensively studied for over half a century, both for their biological role and their potential application in agronomic and pharmaceutical fields. In recent decades, the growing interest of the research community, combined with advances in chemical, biological, and biomolecular investigation methods, has led to a notable acceleration in the growth of knowledge on rice phytoalexins. This review provides an overview of the knowledge gained in recent decades on the diversity, distribution, biosynthesis, chemical synthesis, and bioactivity of rice phytoalexins, with particular attention to the most recent advances in this research field.

Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species

Seeds are continuously exposed to a wide variety of microorganisms in the soil. In addition, seeds contain large amounts of carbon and nitrogen sources that support initial growth after germination. Thus, seeds in the soil can easily promote microbial growth, and seeds are susceptible to decay. Therefore, seed defense against microorganisms is important for plant survival. Seed-microbe interactions are also important issues from the perspective of food production, in seed quality and shelf life. However, seed-microbe interactions remain largely unexplored. In this study, we established a simple and rapid assay system for the antibacterial activity of rice seed crude extracts by colorimetric quantification methods by the reduction of tetrazolium compound. Using this experimental system, the diversity of effects of rice seed extracts on microbial growth was analyzed using Escherichia coli as a bacterial model. We used collections of cultivated rice, comprising 50 accessions of Japanese landraces, 52 accessions of world rice core collections, and of 30 wild Oryza accessions. Furthermore, we attempted to find genetic factors responsible for the diversity by genome-wide association analysis. Our results demonstrate that this experimental system can easily analyze the effects of seed extracts on bacterial growth. It also suggests that there are various compounds in rice seeds that affect microbial growth. Overall, this experimental system can be used to clarify the chemical entities and genetic control of seed-microbe interactions and will open the door for understanding the diverse seed-microbe interactions through metabolites.

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.

Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding.

Temperate japonica/geng (GJ) rice yield has significantly improved due to intensive breeding efforts, dramatically enhancing global food security. However, little is known about the underlying genomic structural variations (SVs) responsible for this improvement. We compared 58 long-read assemblies comprising cultivated and wild rice species in the present study, revealing 156 319 SVs. The phylogenomic analysis based on the SV dataset detected the putatively selected region of GJ sub-populations. A significant portion of the detected SVs overlapped with genic regions were found to influence the expression of involved genes inside GJ assemblies. Integrating the SVs and causal genetic variants underlying agronomic traits into the analysis enables the precise identification of breeding signatures resulting from complex breeding histories aimed at stress tolerance, yield potential and quality improvement. Further, the results demonstrated genomic and genetic evidence that the SV in the promoter of LTG1 is accounting for chilling sensitivity, and the increased copy numbers of GNP1 were associated with positive effects on grain number. In summary, the current study provides genomic resources for retracing the properties of SVs-shaped agronomic traits during previous breeding procedures, which will assist future genetic, genomic and breeding research on rice.

Root K+ homeostasis and signalling as a determinant of salinity stress tolerance in cultivated and wild rice species

Cytosolic K+ retention is an important determinant of salinity tolerance in many crops. However, it remains unclear whether this trait is also crucial for wild rice species. In this work, contrasting pairs of cultivated (Oryza sativa L.) and wild (Oryza alta; Oryza punctata) rice species were used to understand the mechanistic basis of salinity stress tolerance in rice and the role of K+ retention in this process. Non-invasive Microelectrode Ion Flux Measuring (MIFE) measurements showed that NaCl and ROS-induced K+ efflux from the elongation root zone were significantly (2–3-fold) higher in the wild rice species compared with their cultivated counterparts. Cultivated rice group showed relatively lower K+ efflux but greater H+ efflux in response to NaCl and ROS treatments. Pharmacological experiments revealed that tetraethylammonium chloride (TEA) and gadolinium chloride (GdCl3) markedly suppressed NaCl and ROS-induced K+ efflux (>80 % inhibition), suggesting the involvement of GORK and NSCC channels in stress-induced K+ efflux. Sodium orthovanadate suppressed H+ efflux (>90 % inhibition), suggesting the role of H+-ATPase as a major source in salt-induced H+ efflux in salt tolerant cultivars. Collectively, our results indicate that, while possessing high root K+ retention ability in the mature zone, wild rice species show higher sensitivity to NaCl and ROS in the elongation zone. It is suggested that stress-induced K+ efflux in this zone may operate as a "metabolic switch" by inhibiting energy consuming anabolic reactions and allowing energy to be saved for adaptations and repairs, which may provide an advantage to wild rice in conditions with high salinity.

Comparing Essentiality of SOS1-Mediated Na+ Exclusion in Salinity Tolerance between Cultivated and Wild Rice Species.

Soil salinity is a major constraint that affects plant growth and development. Rice is a staple food for more than half of the human population but is extremely sensitive to salinity. Among the several known mechanisms, the ability of the plant to exclude cytosolic Na+ is strongly correlated with salinity stress tolerance in different plant species. This exclusion is mediated by the plasma membrane (PM) Na+/H+ antiporter encoded by Salt Overly Sensitive (SOS1) gene and driven by a PM H+-ATPase generated proton gradient. However, it is not clear to what extent this mechanism is operational in wild and cultivated rice species, given the unique rice root anatomy and the existence of the bypass flow for Na+. As wild rice species provide a rich source of genetic diversity for possible introgression of abiotic stress tolerance, we investigated physiological and molecular basis of salinity stress tolerance in Oryza species by using two contrasting pairs of cultivated (Oryza sativa) and wild rice species (Oryza alta and Oryza punctata). Accordingly, dose- and age-dependent Na+ and H+ fluxes were measured using a non-invasive ion selective vibrating microelectrode (the MIFE technique) to measure potential activity of SOS1-encoded Na+/H+ antiporter genes. Consistent with GUS staining data reported in the literature, rice accessions had (~4–6-fold) greater net Na+ efflux in the root elongation zone (EZ) compared to the mature root zone (MZ). Pharmacological experiments showed that Na+ efflux in root EZ is suppressed by more than 90% by amiloride, indicating the possible involvement of Na+/H+ exchanger activity in root EZ. Within each group (cultivated vs. wild) the magnitude of amiloride-sensitive Na+ efflux was higher in tolerant genotypes; however, the activity of Na+/H+ exchanger was 2–3-fold higher in the cultivated rice compared with their wild counterparts. Gene expression levels of SOS1, SOS2 and SOS3 were upregulated under 24 h salinity treatment in all the tested genotypes, with the highest level of SOS1 transcript detected in salt-tolerant wild rice genotype O. alta (~5–6-fold increased transcript level) followed by another wild rice, O. punctata. There was no significant difference in SOS1 expression observed for cultivated rice (IR1-tolerant and IR29-sensitive) under both 0 and 24 h salinity exposure. Our findings suggest that salt-tolerant cultivated rice relies on the cytosolic Na+ exclusion mechanism to deal with salt stress to a greater extent than wild rice, but its operation seems to be regulated at a post-translational rather than transcriptional level.

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.

ASSESSING THE COMPETING ABILITY OF WEEDY RICE (Oryza sativa f. spontanea) WITH CULTIVATED RICE UNDER ELEVATED CO2 CONDITIONS

Climate change can adversely affect rice production, especially for weed management in the context of emergence and proliferation of newer weed species like weedy rice (Oryza sativa f. spontanea) in the rice growing tracts of Kerala. In the past decade, atmospheric carbon dioxide (CO2) has risen from 371.82 to 407.05 ppm from 2000 to 2018 which might have an impact on the competitive ability of a C3 plant like weedy rice. The competitiveness of weedy rice was studied in an open top chamber (OTC) under a CO2 concentration of 500 ppm (Chamber A), OTC without external CO2 supply (Chamber B), and open condition along with two popular cultivated rice varieties Uma and Jyothi with both air and soil temperature inside the chamber to the tune of 40-430C and 35-400C respectively. The study revealed a higher competitive potential of weedy rice in terms of tillering ability under elevated carbon dioxide as it responded well compared to cultivated rice varieties. There was a differential response of rice varieties to elevated CO2 conditions with medium duration variety responding well compared to short duration one. Compared to ambient conditions (chamber B and open condition), higher tillering was observed under elevated CO2 (chamber A) in which weedy rice tillered profusely (17.33) than cultivated rice species (9 and 11.33). There was a linear increase in plant height of weedy rice in chamber A (108.97cm) during the initial stages and in chamber B (112.77 cm) during reproductive stages. The study evidenced that in the coming future, higher CO2 levels can stimulate biomass production of C3 weed like weedy rice with a greater increase in tillering which could be an important trait affecting inter specific competition.

Field performance of heat tolerant mutant rice lines generated from Oryza sativa and Oryza glaberrima

This study evaluated mutant lines developed from two cultivated species of upland rice, Oryza sativa, and Oryza glaberrima, in field experiments conducted during the hot and dry seasons of 2014/2015 in Morogoro, Tanzania. The growth yield and yield components of 34 and 14 Gamma induced mutant upland rice lines developed from O. sativa (Kihogo red) and O. glaberrima were evaluated, respectively. The mutant lines were selected based on variable expression of heat shock protein genes (HSPs) in previously conducted heat tolerance studies. The minimum and maximum temperatures and rainfall during the field performance experiment were measured between 20 oC and 35 oC, and 32.7 mm and 155.5 mm, respectively. The data for 12 yield and yield component parameters such as days to early and 50% flowering, days to physical maturity, plant height, number of tillers, number of panicles, spikelets, filled grains, unfilled grains and 1,000 grain weights were collected and analysed using ANOVA and Principal Component Analysis. Significant differences (P≤0.05) were obtained among the mutant lines in terms of grain yield, spikelet sterility and other variables, which were further used as criteria for selection of heat and drought tolerant rice lines. Eight heat and drought tolerant mutant rice lines with high yields (over 3.5 ton/ha) and low spikelet sterility were selected for further advancement in breeding programmes

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.

What happened during domestication of wild to cultivated rice

Domestication of crops is one of the greatest inventions of the human race and has played a vital role in the progress of human civilization. Understanding the genetic mechanisms of crop domestication could shed light on its history and would advance crop breeding. Cultivated rice species, which were domesticated from wild rice species, are important food crops worldwide. Morphological traits, physiological characteristics, and ecological adaptability of cultivated rice are very different from those characters of wild rice. In this review, we summarize current knowledge of the genetic mechanisms underlying these differences between wild and cultivated rice and discuss the application of wild rice species in modern breeding.

Weedy rice (Oryza spp.): what’s in a name?

AbstractThere are two species of cultivated rice in the world—Oryza sativa L. from Asia and Oryza glaberrima Steud. from Africa. The former was domesticated from the wild progenitor Oryza rufipogon Griff. and the latter from the African wild rice species Oryza barthii A. Shiv. The first known center of rice cultivation in China generated the O. sativa subspecies japonica. The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded or dry-drill-seeded rice. Weedy rice (Oryza spp.) is the most difficult weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop de-domestication, and regionalized adaptation have resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice—Oryza sativa L. and Oryza sativa f. spontanea. Genomic data show that O. sativa L. applies to weedy rice populations derived from cultivated O. sativa, whereas O. sativa f. spontanea applies only to weedy types that primarily descended from O. rufipogon. Neither of these names applies to African weedy rice, which is of African wild rice or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp.

Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice.

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.