Tropical Japonica Rice Research Articles

Identification of stable restorer lines developed through inter‐sub‐specific hybridization in rice (Oryza sativa) using multi‐trait stability index

AbstractInter‐sub‐specific hybridization between indica and tropical japonica rice germplasm is the most efficient approach for broadening the genetic base of hybrid rice parental lines and enhancing the heterotic potential of hybrids in a tropical country like India. In the present study, 106 indica/tropical–japonica derived lines were developed through inter‐sub‐specific hybridization and screened using functional markers with respect to the major fertility restorer genes, Rf3 and Rf4, and the wide compatibility gene, S5n. The fertility restoration ability of newly developed restorers was validated through test cross nursery performance. The functional markers were observed to accurately predict the trait of fertility restoration. From the present study, the decreasing order of efficiency of different gene combinations on fertility restoration ability are as follows: Rf4/S5n > Rf4/Rf3/S5n > Rf4 > Rf4/Rf3 > Rf3/S5n > Rf3. Based on multi‐trait stability index (MTSI) analysis, the four newly identified restorers, that is, RP6388‐90, RP6382‐49, RP6375‐81 and RP6368‐38, were selected as the top best performing genotypes with high stability for multiple traits, and these genotypes will be useful for the development of superior rice hybrids in India.

Optimization of in vitro culture system in tropical Japonica and Indica rice (Oryza sativa L.) genotypes

Optimization of in vitro culture system in tropical Japonica and Indica rice (Oryza sativa L.) genotypes

Registration of a blast‐resistant premium medium‐grain rice germplasm Eclipse

AbstractEclipse (Reg. no. GP‐149, PI 701081) is a blast‐resistant and ‘Calrose’ type medium‐grain‐quality rice (Oryza sativa L.) germplasm that was developed by the USDA‐ARS Dale Bumpers National Rice Research Center, Stuttgart, AR. It was selected from a backcross between a blast‐resistant tropical japonica rice cultivar ‘Katy’ and a temperate japonica medium‐grain rice cultivar ‘M‐202’. Eclipse was evaluated in uniform regional rice nurseries in the southern United States during 2019–2020 and further characterized in Arkansas fields during 2020–2021. Blast resistance was determined under greenhouse and field conditions. Under greenhouse conditions, Eclipse was resistant to races IA45, IB1, IB49, IB54, IC17, IE1, IG1, and IH1, similar to that of Katy. Under naturally infected field conditions in Louisiana and Puerto Rico, Eclipse was resistant to leaf and panicle blast infections, similar to that of Katy. Eclipse has Pi‐ta and Ptr genes and lacks Pi‐b, Pi‐k, and Pi‐z. Eclipse is a semidwarf glabrous type of medium‐grain rice and has a low amylose content, similar to M‐202, and quality of Calrose rice. In the southern United States, Eclipse has an average height of 98.5 cm and yields 6,710 kg grain ha−1. It reaches 50% heading at 84 d after emergence with a lodging incidence of 28.5 and 59% head rice yield. Eclipse is useful for breeding for improving disease resistance and grain quality and can be used directly by rice growers for premium medium‐grain rice production.

Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.

Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.

Fine mapping and target gene identification of qSE4, a QTL for stigma exsertion rate in rice (Oryza sativa L.).

The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (qSE4DaS)]. Populations were segregated into 2,143 individuals of BC3F2 and BC4F2, and the stigma exsertion quantitative trait locus (QTL) qSE4 was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of LOC_Os04g43910 (ARF10) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of ARF10 in DaS was significantly higher than in D50. After knocking out ARF10 in the DaS background, it was found that the SER of arf10 (the total SER of the arf10-1 and the arf10-2 were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that arf10 had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that LOC_Os04g43910 is mostly likely the target gene of qSE4, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production.

Population Structure of a Worldwide Collection of Tropical Japonica Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type

Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in indica rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.

Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality.

Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio.

Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.

Model‐based evaluation of climate change impacts on rice grain quality in the main European rice district

AbstractCrop simulation models are used to forecast the impacts of climate change on yield levels and to identify adaptation strategies. Nevertheless, crop quality has been almost neglected in available studies, despite its relevance on the economic and nutritional value of agricultural products. We present here a modeling study to evaluate the future trends of rice quality in the main European rice district, placed in Northern Italy. A rice growth model was coupled with a library of models of rice milling and cooking suitability, using current farmer management and baseline/future climatic scenarios as input for the simulations. Four general circulation models (NOResm, MIROC‐ESM, HadGEM2‐ES, and GISS‐ES) and two CO2 representative concentration pathways (2.6, 8.5) were used to generate 20‐year future climatic data centered on 2030 and 2070. Spatially distributed simulations were run at 2 × 2 km spatial resolution considering a Japonica (Loto) and a Tropical Japonica (Gladio) rice cultivar. The results depicted an overall decline in rice quality, especially for Loto (−5% of milling suitability considering GISS‐ES‐2.6 in all time frames; −8% in 2030 and −20% in 2070 under HadGEM2‐ES‐8.5). While the revenues of millers are expected to decrease of about 50 € t−1 in 2030 and 100 € t−1 in 2070 for Loto, minor changes are projected on Gladio milling and cooking suitability, except in the worst scenario in 2070 (−10 to −5% of cooking suitability, corresponding to −30 to −72 € t−1). Despite the need of reducing models uncertainty, this study provides variety‐specific indications on rice grain quality ready‐to‐use for crop specialists, farmers, and millers and that could raise the interest of different stakeholders of the agri‐food sector, including food scientists, geneticists, and policy makers.

Gene disruption by structural mutations drives selection in US rice breeding over the last century.

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.

Genetic factors enhancing seed longevity in tropical japonica rice

Seed longevity is a key trait to secure seed viability and vigor of farmer’s seed lots under the increased temperatures and humidity associated with climate change. While previous studies have found quantitative trait loci (QTL) for improved longevity in temperate japonica rice varieties, there are no available QTL identified that can potentially enhance seed longevity in tropical japonica rice, which are grown in ASEAN countries and highly vulnerable to the impact of climate change. Here, we present QTL and candidate genes identified in an F3 bi-parental QTL mapping population developed from a tropical japonica × indica cross, using 1 k single nucleotide polymorphism (SNP) markers. To accelerate seed ageing through a seed storage experiment, seed moisture content (MC) was elevated by equilibrating seeds at 60 % relative humidity (RH) and 20 °C, after which seeds were stored at 10.9 % seed MC and 45 °C for 56 days. Within a QTL identified on chromosome 2 (2.9 Mb size), there were 45 annotated genes potentially relevant to seed longevity mechanisms such as oxidative stress reduction and repair of damaged DNA. Within the QTL, the preponderance of genes expressed largely in reproductive tissues, seeds or embryo make this a dependable QTL. Based on coexpression and network analysis, we highlight eight genes as potentially important candidate genes, consistent with previous studies suggesting their role in seed germination and longevity.

An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies.

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.

Genomic history and ecology of the geographic spread of rice.

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.

Response of U.S. Rice Cultivars Grown under Non-Flooded Irrigation Management

Achieving food security along with environmental sustainability requires high yields with reduced demands on irrigation resources for rice production systems. The goal of the present investigation was to identify traits and germplasms for rice breeding programs that target effective grain production (EGP) under non-flooded field systems where the crop can be subjected to intermittent water stress throughout the growing season. A panel of 15 cultivars was evaluated over three years regarding phenological and agronomic traits under four soil moisture levels ranging from field capacity (29% volumetric water content; VWC) to just above the wilting point (16% VWC) using subsurface drip irrigation. An average of 690 ha-mm ha−1 water was applied for the 30% VWC treatment compared to 360 ha-mm ha−1 for the 14% VWC treatment. The average soil moisture content influenced several traits, including grain quality. Regression analysis identified six traits that explained 35% of the phenotypic variability of EGP. Four varieties (PI 312777, Francis, Zhe 733, and Mars) were found possessing significant slopes for 10 or more traits that respond to a range in soil moisture levels, indicating that they may offer promise for future rice breeding programs. Furthermore, based on the contrasting responses of four parent cultivars, two mapping populations were identified as potential genetic resources for identifying new quantitative trait loci/genes for improving EGP of tropical japonica rice varieties.

Colchicine and osmotic stress for improving anther culture efficiency on long grain temperate and tropical japonica rice genotypes.

Anther culture is a fast tool to obtain double haploid plant lines for breeding purposes. In rice, this procedure is commonly performed in two steps: i) induction of calli from anthers and ii) regeneration of plantlets from calli. It has been stated that genotype highly influences the anther culture efficiency, so the media used in each step should be optimized for each variety. In this study, we tested different media modifications of an efficient protocol optimized for a medium sized grain temperate japonica NRVC980385, used as a control, in a long grain temperate japonica rice variety (NRVC20120346), and two long grain tropical japonica varieties (303012 and 303013). We found that the addition of 150 mg l-1 colchicine to the induction medium worked best for all genotypes except for NRVC20120346, whose best induction was obtained with the colchicine-free medium. Referring to regeneration, increased gelling agent in the medium provided the best rates in NRVC980385, improving our former NRVC980385-optimized anther culture protocol. Sorbitol fortified regeneration medium worked the best in the case of the long grain varieties. The presence of colchicine in the induction medium was also related to a higher obtention of double haploid plantlets. This study highlights that genotype is a key factor in the performance of rice anther culture. It has set a first anther culture study on long grain japonica varieties and optimizes the anther culture protocol for temperate japonica medium grain NRVC980385 with the use of colchicine and other additives that increase osmotic stress.

Registration of the Estrela × NSFTV199 Rice Recombinant Inbred Line Mapping Population

Understanding the genetic variation for yield‐related traits in tropical japonica rice (Oryza sativa L.) is extremely important to US rice breeding because most US rice is from this subpopulation. The Estrela × NSFTV199 mapping population (Reg. no. MP‐8, NSL 530337 MAP) was developed from the Rice Diversity Panel 1 accessions Estrela (GSOR 301227), an admixture of japonica, and NSFTV199 (GSOR 301190), a tropical japonica. Both accessions were characterized as phenotypically and genotypically diverse from each other. The population consists of 276 F2:9 recombinant inbred lines (RILs) and parents (GSOR 104001 through GSOR 104282), which were genotyped with 65 simple sequence repeat (SSR) markers and 256 RILs genotyped with an additional 69 SSR markers. The population was phenotyped for eight agronomic traits (days to heading, plant height, flag leaf length and width, leaf pubescence, culm habit, awn presence, and seed shattering), six panicle architecture traits (panicle length; number of primary branches, florets, seeds, and sterile florets per panicle; and percentage fertility), and nine grain traits (seed length, width, and length‐to‐width ratio with and without the hull; percentage chalk in brown rice with and without the broken kernels, and 100‐seed weight). Here within we report the evaluation of the population for eight of the traits. Quantitative trait loci associated with 22 of these 23 traits were identified. This population represents a valuable resource for basic genomic studies and applied marker‐assisted breeding efforts.

Dissection of coleoptile elongation in japonica rice under submergence through integrated genome-wide association mapping and transcriptional analyses.

Rice is unique among cereals for its ability to germinate not only when submerged but also under anoxic conditions. Rice germination under submergence or anoxia is characterized by a longer coleoptile and delay in radicle emergence. A panel of temperate and tropical japonica rice accessions showing a large variability in coleoptile length was used to investigate genetic factors involved in this developmental process. The ability of the Khao Hlan On rice landrace to vigorously germinate when submerged has been previously associated with the presence of the trehalose 6 phosphate phosphatase 7 (TPP7) gene. In this study, we found that, in the presence of TPP7, polymorphisms and transcriptional variations of the gene in coleoptile tissue were not related to differences in the final coleoptile length under submergence. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome-wide association study analysis on a panel of 273 japonica rice accessions. We discovered 11 significant marker-trait associations and identified candidate genes potentially involved in coleoptile length. Candidate gene expression analyses indicated that japonica rice genotypes possess complex genetic elements that control final coleoptile length under low oxygen.

Validation of Yield Component Traits Identified by Genome-Wide Association Mapping in a tropical japonica × tropical japonica Rice Biparental Mapping Population.

The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) studies to explore five rice ( L.) subpopulations (, , , , and ). The RDP1 was evaluated for over 30 traits, including agronomic, panicle architecture, seed, and disease traits and genotyped with 700,000 single nucleotide polymorphisms (SNPs). Most rice grown in the southern United States is and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 accessions, 'Estrela' and 'NSFTV199' are both phenotypically and genotypically diverse, thus making them excellent parents for a biparental mapping population. The objectives were to (i) ascertain the GWA QTLs from the RDP1 GWA studies that overlapped with the QTLs uncovered in an Estrela × NSFTV199 recombinant inbred line (RIL) population evaluated for 15 yield traits, and (ii) identify known or novel genes potentially controlling specific yield component traits. The 256 RILs were genotyped with 132 simple sequence repeat markers and 70 QTLs were found. Perl scripts were developed for automatic identification of the underlying candidate genes in the GWA QTL regions. Approximately 100 GWA QTLs overlapped with 41 Estrela × NSFTV199 QTL (RIL QTL) regions and 47 known genes were identified. Two seed trait RIL QTLs with overlapping GWA QTLs were not associated with a known gene. Segregating SNPs in the overlapping GWA QTLs for RIL QTLs with high values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.

Development and Characterization of a Large Mutant Population of a Rice Variety Katy for Functional Genomics Studies and Breeding

The availability of a large mutant population is an important genetic resource for functional genomic studies and breeding. Katy, a publicly available long grain tropical japonica rice variety with an excellent package of disease resistance and suitable agronomic traits, was used to develop a large mutant population. A combination of ethyl methane sulfonate (EMS), fast neutron (FN), and gamma irradiation (60Co) treatments were applied at varying dosages to develop the population. Approximately 7500 rice seeds were each treated with EMS (0.4%, 0.8%, and 1.2%) and 60Co (200 Gy), and approximately 10,000 rice seeds were exposed to 7.7 Gy, 26.3 Gy, and 49.4 Gy dosages of FN. Mutation effects were initially evaluated at the M2 generation by assessing chlorophyll biosynthesis deficiencies. The mutation effects of each line were detected at 1.04% for 0.4% EMS, 5.04% for 0.8% and 1.2% EMS, 2.9% for 26.3 Gy FN, 3.2% for 49.4 Gy FN, and 5.04% for 60Co 200 Gy for the M2 population. After seeds were advanced to M4 using a single seed breeding strategy, the genotype identity of 189 randomly selected lines was verified with nine simple sequence repeat markers and 96 randomly selected lines were evaluated for mutant morphological phenotypes. The analysis uncovered slightly higher frequencies of morphological mutants at M4 than was observed in the M2 generation. These findings suggest that the Katy putative mutant population consisting of 23,558 individuals is a potential asset for rice functional genomics studies and breeding.

Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>