Oryza Species Research Articles

Reexploring Rice Germplasm: Enlightening a New Path Towards Abiotic Stress-resilient Crop

Oryza sativa, the commonly cultivated rice, is one of the most important crops for human consumption, but is also a crop whose production system is increasingly threatened by the current climate changes. Due to its intensive water requirement rice faces a lot of challenges due to abiotic stresses like drought, heat stress, salinity, flooding etc. Drought is the major abiotic stress to rice grain production under unpredictable and changing environmental conditions. Traits supporting drought resistance are limited in cultivars, while wild rice species like O. glaberrima, O. longistaminata, O. rufipogon and O. meridonalis represent an important reservoir of useful genes for this trait which can be exploited to develop varieties tolerant to drought. Similarly O. australiensis, O. coarctata and O. rufipogon serve as an important sources for salinity-tolerant genes. O. rufipogon, O. meridonalis, O. australiensis comprise a collection of accessions that are reservoirs for heat-tolerant genes. Although many efforts have resulted in breeding rice varieties that are relatively tolerant to their local environments; climate change and population growth are expected to soon require a new, rapid generation of stress-tolerant rice germplasm. Diversity studies suggest that the current diversity within rice varieties may not be sufficient for generation of highly resistant or tolerant varieties for the unfavorable growing conditions. All the efforts to design an ideotype to increase production and productivity has been attempted previously, rice self-sufficiency can be attained only if high production and productivity is coupled with a high degree of tolerance and resistance to biotic and abiotic stress factors. Since it has been found that wild rice relatives serve as a hub for many desirable genes conferring tolerance or resistance to specific stresses, the present article is focused on provide an overview of different wild ancestors of rice which can be exploited to identify suitable donors for gene of interest, their ecological and genomic diversity and the variation observed in wild Oryza species for different stress tolerance traits. Such identified traits can be incorporated in modern day breeding programmes through marker assisted breeding to develop cultivable varieties with desired tolerance to abiotic stresses or transfer such traits to modern day cultivars through backcross breeding.

Origin of the presence/absence variation of the LTIA1/LTIA2 mini-ribonuclease III genes required for low-temperature growth in rice

A rice low temperature-induced albino variant was determined by the recessive ltia1 and ltia2 genes. LTIA1 and LTIA2 encode highly conserved mini-ribonucleases III located in chloroplasts and expressed in aerial parts of the plant. At low temperature, LTIA1 and LTIA2 redundantly affect chlorophyll levels, non-photochemical quenching, photosynthetic quantum yield of PS II and seedling growth. LTIA1 and LTIA2 proteins are involved in splicing of atpF and the biogenesis of 16S and 23S rRNA in chloroplasts. Presence/absence variation of LTIA1, the ancestral copy, was found only in japonica but that of LTIA2 in all rice subgroups. Accessions with LTIA2 presence tended to be distributed more remote from the equator compared to those with LTIA2 absence. LTIA2 duplicated from LTIA1 at the early stage of divergence of the AA genome Oryza species but deleted againin O. nivara. In cultivated rice, absence of LTIA2 is derived from O. nivara. LTIA1 absence occurred more recently in japonica.

ERFVII-controlled hypoxia responses are in part facilitated by MEDIATOR SUBUNIT 25 in Arabidopsis thaliana.

Flooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Transcriptional responses to low oxygen are generally associated with the activation of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors. However, the exact mechanisms and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the ERFVII factors RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 cooperate with the Mediator complex subunit AtMED25 to coordinate gene expression under hypoxia in Arabidopsis thaliana. Respective med25 knock-out mutants display reduced low-oxygen stress tolerance. AtMED25 physically associates with a distinct set of hypoxia core genes and its loss partially impairs transcription under hypoxia due to decreased RNA polymerase II recruitment. Association of AtMED25 with target genes requires the presence of ERFVII transcription factors. Next to ERFVII protein stabilisation, also the composition of the Mediator complex including AtMED25 is potentially affected by hypoxia stress as shown by protein-complex pulldown assays. The dynamic response of the Mediator complex to hypoxia is furthermore supported by the fact that two subunits, AtMED8 and AtMED16, are not involved in the establishment of hypoxia tolerance, whilst both act in coordination with AtMED25 under other environmental conditions. We furthermore show that AtMED25 function under hypoxia is independent of ethylene signalling. Finally, functional conservation at the molecular level was found for the MED25-ERFVII module between A. thaliana and the monocot species Oryza sativa, pointing to a potentially universal role of MED25 in coordinating ERFVII-dependent transcript responses to hypoxia in plants.

Wild rice: unlocking the future of rice breeding.

Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild-type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars.

Bud shapes dictate tiller-rhizome transition in African perennial rice (Oryza longistaminata).

Rhizome formation of Oryza longistaminata was dependent on the bud shape. The loci qBS3.1, qBS3.2 and qBS3.3 for controlling rhizome formation were functional redundant under Oryza longistaminata background. The rhizome, a root-like underground stem, is the key organ for grasses to achieve perennial growth. Oryza longistaminata, the only rhizomatous wild Oryza species with the same AA genome as cultivated rice, is an important germplasm for developing perennial rice. Our study found that the rhizome formation of O. longistaminata was dependent on the bud shape: the dome-like axillary bud (dome bud) usually penetrated through the leaf sheaths, developing into rhizome (extravaginal branching), but the flat axillary bud (flat bud) wrapped by the leaf sheaths only developed into tiller (intravaginal branching). The genetic loci (QTL) controlling the bud shape (BS) were mapped by entire population genotyping method (F2 population from crossing O. longistaminata with Balilla (Oryza sativa) and selective genotyping mapping method (BC1F2 population from backcrossing F1 with Balilla). A total of twelve loci were identified, including four major-effect QTL: qBS2, qBS3.1, qBS3.2 and qBS3.3, and the genetic network of these twelve loci was established. The dome bud lost the potential to develop into rhizome with the increase in backcross generations under Balilla background. Considering the rapid loss of rhizome under Balilla background, the near-isogenic lines under O. longistaminata background were used to identify the effect of major-effect loci. According to the BC3F2, BC4F2 and BC5F2 under O. longistaminata background, there was some functional redundancy among qBS3.1, qBS3.2 and qBS3.3. Our results provided a new perspective for analyzing the genetic basis of perenniality and laid the foundation for fine mapping and verification of related genes.

Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

The emergence of waterlogged Oryza species ∼15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process.

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies

The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.

Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (Oryza spp.)

Tandemly organized rRNA genes are a typical example of a multigene family, where individual members evolve co-ordinately within—but independently between—species due to gene conversion and unequal crossing over. More frequently, in eukaryotic species with an interspecies hybrid origin, expression of unhomogenized rRNA genes from one progenitor is epigenetically silenced because of nucleolus dominance, and distinct rRNA genes may lose functionality and evolve faster. Interestingly, we obtained unusual ribosomal gene sequences from Oryza species that showed great diversity and did not appear in the present rice genomic sequence. The diversity of rDNA sequences indicated that the homogenization in rice is incomplete and explains the introgression of distinct rRNA gene families into ancestral rice genomes before speciation and continent separation. The divergent large subunit (LSU) ribosomal genes are expressed, some of them differentially, depending on the N fertilization of plants. Detection of differential transcripts of the rRNA genes suggested that rRNA gene families are not functionally equivalent. Phylogenetic analysis assigned Oryza species branching order to monocots, and monocot lineages probably have the same ecological origin by molecular clock calculation. Therefore, our results suggested that the geographical distances of continent-separation cause barriers to the gene flow and homogenization among Oryza species which requires further explanation.

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara.

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

Identification and evolution of a diterpenoid phytoalexin oryzalactone biosynthetic gene in the genus Oryza.

The natural variation of plant-specialized metabolites represents the evolutionary adaptation of plants to their environments. However, the molecular mechanisms that account for the diversification of the metabolic pathways have not been fully clarified. Rice plants resist attacks from pathogens by accumulating diterpenoid phytoalexins. It has been confirmed that the composition of rice phytoalexins exhibits numerous natural variations. Major rice phytoalexins (momilactones and phytocassanes) are accumulated in most cultivars, although oryzalactone is a cultivar-specific compound. Here, we attempted to reveal the evolutionary trajectory of the diversification of phytoalexins by analyzing the oryzalactone biosynthetic gene in Oryza species. The candidate gene, KSLX-OL, which accounts for oryzalactone biosynthesis, was found around the single-nucleotide polymorphisms specific to the oryzalactone-accumulating cultivars in the long arm of chromosome 11. The metabolite analyses in Nicotiana benthamiana and rice plants overexpressing KSLX-OL indicated that KSLX-OL is responsible for the oryzalactone biosynthesis. KSLX-OL is an allele of KSL8 that is involved in the biosynthesis of another diterpenoid phytoalexin, oryzalexin S and is specifically distributed in the AA genome species. KSLX-NOL and KSLX-bar, which encode similar enzymes but are not involved in oryzalactone biosynthesis, were also found in AA genome species. The phylogenetic analyses of KSLXs, KSL8s, and related pseudogenes (KSL9s) indicated that KSLX-OL was generated from a common ancestor with KSL8 and KSL9 via gene duplication, functional differentiation, and gene fusion. The wide distributions of KSLX-OL and KSL8 in AA genome species demonstrate their long-term coexistence beyond species differentiation, suggesting a balancing selection between the genes.

Strategies for Rice Improvement: Utilizing Genetic Resources from Wild and Cultivated Oryza Species

Strategies for Rice Improvement: Utilizing Genetic Resources from Wild and Cultivated Oryza Species

DRR Dhan 65 (IET 27641) – A High Yielding Low Soil Phosphorous Tolerant and Climate Resilient Rice Variety Developed from Wild Introgression Lines

The wild species of Oryza are an important source of genetic variability for the improvement of yield and tolerance to biotic and abiotic stresses. Phosphorus (P) is the second most important key nutrient, vital for plant growth and development at all stages. Phosphorous deficiency is one of the factors limiting rice yields and farmer’s profitability so it is necessary to identify genotypes with stable yield and tolerance to P deficiency. Keeping in view the unlimited potential of wild species for yield enhancement and stress tolerance, interspecific population between Oryza rufipogon in the back ground of Oryza sativa genotype KMR3 was developed by advanced back cross breeding strategy. DRR Dhan 65 (IET 27641) (RP Bio 4919-B-B NSR86) is an interspecific wild introgression line, a derivative of KMR 3 / O rufipogon with short bold grains which is high yielding under both normal and low soil phosphorous conditions. It has seed to seed maturity of 130- 135 days and gives an average yield of 6.5 t/ ha (under normal conditions; 60 kg/ha of P, i.e., recommended dose) and 4.7 t/ ha (under low Phosphorus; 40 kg/ha of P). It was released for cultivation in Andhra Pradesh, Telangana, Karnataka, Chhattisgarh, Jharkhand and Maharashtra states through Central Sub-committee on Crop Standards, Notification and Release of Varieties for Agricultural Crops vide S.O. 4065(E) dated 31st August, 2022 [CG-DL-E-31082022-238490].

Genetic relatedness of rice landraces in North East India with wild relatives using chloroplast markers

AbstractThe evolutionary relationship between domesticated Oryza species and their wild relatives in North East India is not well understood. To improve the understanding of the evolutionary relationship, this study investigates the genetic diversity of 68 indigenous rice landraces from North East India, ten O. rufipogon genotypes, and nine O. nivara genotypes using chloroplast variable repeat markers which, due to non-recombination and uniparental inheritance, enable better phylogenetic inference. Reference genotypes IR64 (indica) and Nipponbare (japonica) were included to characterize various phylogenetic clusters. Using distance-based hierarchical clustering, model-based structuring and principal component analysis, selected landraces from the three North Eastern Indian states of Assam, Manipur and Arunachal Pradesh were grouped into two phylogenetically different clusters that represented the IR64 and Nipponbare groupings. Interestingly, despite the fact that a cluster analysis combining North East landraces and wild relatives likewise produced two separate clusters (cluster I: Nipponbare, cluster II: IR64), the majority of the wild relatives were only clustered in the IR64 cluster. This suggests that the two distinct evolutionary histories of the rice landraces in North East India are distinguished by their genetic affinity for wild relatives and their variation in the indica and japonica pools. These results highlight chloroplast divergence influencing the genetic diversity of North East landraces with wild relatives. Further, these findings will enable in-depth studies on the functional significance of chloroplast diversity on trait adaptation in rice landraces.

Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.

Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.

Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza.

Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.

<i>In silico</i> Analysis of <i>Dreb2a</i> Gene among Diploid <i>Oryza</i> Species Reveal Gene Retrogression in Cultivated Species

The dehydration-responsive element-binding (DREB) genes are types of plant-specific transcription factors that bind to DRE/CRT elements in response to abiotic stresses. It belongs to the AP2 superfamily and contains highly conserved APETELA2 (AP2) domain. In this study, comparative analysis of DREB2A gene from diploid Oryza species was performed using BLASTN approach. The OglDREB2A sequence (KU159742.1) was used as query against 11 diploid Oryza species in the Gramene database for identification of DREB2A orthologs. Molecular characterization, subcellular localization, conserved motifs and promoter analysis were also performed using bioinformatics tools. Molecular characterization of DREB2A protein in the diploid Oryza showed an AP2 conserved domain and nuclear localized protein which is similar to putative transcription factor involved in stress responses. Motif analysis using MEME suites identified 7 significant motifs across all the diploid Oryza species with motif 2, 3, 4 and 5 as the common motifs with ~50 amino acids length. Analysis of 1kb upstream of TSS of DREB2A of the 11 diploid Oryza species revealed many CAREs associated with stress (DRE, LTRE, ERE, G-box, TCC-motif and Sp1) and hormonal regulations (ABREs, MeJA, GARE, and GC-motif) with ABRE as the common element in all the diploid species. Additionally, wild species has more number of cis elements than the cultivated species suggesting a possible role in genome evolution. Overall, the 11 DREB2A orthologs are conserved in terms of sequence homology and protein structure but cultivated species has less number of transcripts than their progenitors suggesting gene retrogression in cultivated Oryza species.

A high-quality chromosome-level wild rice genome of Oryza coarctata

Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.

Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India.

Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O. nivara (H' = 1.09) and O. rufipogon (H' = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (- 0.58) and panicle bearing tillers (- 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon's information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.