Rice Landraces Research Articles

Effects of Parboiling on Chemical Properties, Phenolic Content and Antioxidant Capacity in Colored Landrace Rice

Parboiling influences chemical compositions in rice grains. The objectives of this study were to evaluate the change in chemical content, total phenolic content and antioxidant capacity of landrace rice genotypes under parboiling conditions and to identify the genotypes suitable for production of parboiled rice. Landrace rice varieties used in this study consisted of Glam Feang, Glam Tonkeaw, Kawgum, Glam Luem Phua, Medmakham, Deang Sakonnakhon, Sang Yod, Kawniewd-eang, Mali Deang, KDML105 and RD6. Parboiling reduced fiber content, total phenolic content and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity in rice grains. Fiber contents were 1.46% in brown rice (unpolished rice) and 1.40% in parboiled rice (24 h of soaking and 48 h of incubation). Total phenolic contents were 205.67 mg/100 g seed in brown rice and 35.34 mg/100 g seed in parboiled rice. Antioxidant capacity (DPPH) reduced from 68.45% in brown rice to 26.23% in parboiled rice. Ash content and protein content were not significantly affected by the parboiling process. Medmakham cv. had the highest total phenolic content and antioxidant capacity in brown rice and parboiled rice. Gum Leamphea cv. and Medmakham cv. were the best genotypes for ash content, protein content, total phenolic content and antioxidant capacity (DPPH) in brown rice and parboiled rice. Glam Feang cv. had the highest protein contents in brown rice and parboiled rice although it had low total phenolic content and antioxidant capacity. Cluster analysis further showed variation among genotypes, revealing distinct groupings in brown rice and parboiled rice based on chemical properties, phenolic content and antioxidant capacity. This research significantly contributes to a better understanding on how parboiling affects rice compositions and nutritional values. It emphasizes the importance of nuanced comprehension of how different rice varieties respond to parboiling, aiding informed decisions in rice processing and selection to meet specific nutritional needs.

Independent genetic differentiation between upland and lowland rice ecotypes within japonica and indica subspecies during their adaptations to different soil‐nitrogen conditions

AbstractThe soil‐nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH4+) and dry fields (mainly in the form of nitrate, NO3−), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE‐related traits among rice landraces as well as the genetic differentiation between NUE‐associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE‐related traits such as the absorption ability for NH4+ and NO3−. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH4+ or NO3− or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO3−. We identified 76 QTLs for 25 measured traits using genome‐wide association analysis. The highly differentiated NUE‐associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil‐nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil‐nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil‐nitrogen conditions and have implications for the improvement of NUE.

Effect of Selected Rice Landraces on the Fecundity and Survival of Rice Leaf Folder <i>Cnaphalocrocis Medinalis</i> (Guenee)

The rice leaf folder, Cnaphalocrocis medinalis (Guenee) is a significant pest causing outbreaks. This study focuses on the impact of selected rice landraces on the survivability of C. medinalis, aiming to identify potential sources for IPM and future breeding programs. The research encompassed 35 landraces, categorized as resistant, moderately resistant and susceptible based on net house screenings along with standard resistant check (TKM6) and susceptible check (TN1). The study evaluated fecundity, larval emergence, survival rates, and adult emergence on these genotypes. Results showed that resistant and moderately resistant genotypes significantly reduced the pest’s fecundity and survival across various lifestages compared to susceptible ones. The findings indicated the possible existence of antibiosis factors in resistant genotypes.

Genetic Diversity studies in Elite Rice Landraces of North Western Himalayas

Genetic Diversity studies in Elite Rice Landraces of North Western Himalayas

Diversity of Indian rice cultivars and landraces for seedling vigour and their association for yield related traits

Diversity of Indian rice cultivars and landraces for seedling vigour and their association for yield related traits

Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To address this issue, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that enable the user to (1) explore the local environments of traditional rice varieties (landraces) in South-East Asia and (2) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We demonstrate the value of these resources by identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior quantitative trait locus analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits, including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

Delineating Local Rice Landraces of Kashmir Valley for Cooking Quality and Physico-Chemical Traits

Crop plant improvement depends on genetic diversity. The regional collections contain a variety of genes, some of which are useful despite the shifting socioeconomic and environmental/climatic circumstances. Plant breeders can produce new and enhanced cultivars with desirable features by utilizing the diversity of available plant genetic resources. Twenty five traditional rice (Oryza sativa L.) landraces from the NorthWest Himalayan region of Kashmir were assessed for cooking quality and physic-chemical characteristics. The majority of the cooking quality traits, such as kernel length before and after cooking, kernel breadth before and after cooking, amylose content gel, consistency, and alkali spreading value, showed a wide range of variability in the rice landraces under study. Extensive genetic variety across the landraces under investigation, which may be used for agricultural development programs, was suggested by the wide variation among the morphological and other cooking quality parameters.

The Impact of Yellow Stem Borer, Scirpophaga incertulas (Walker) on Local Rice Landraces: Screening for Resilience

Field evaluation of 50 local landraces against paddy yellow stem borer (YSB), Scirpophaga incertulas (Walker) was carried out at the College of Agriculture, V.C. Farm, Mandya during Kharif 2022. The per cent of damage by YSB on different genotypes was evaluated at 30, 60 and 90 days after transplanting (DAT). Based on the mean per cent incidence genotypes were grouped into different resistance categories using the Standard Evaluation System for Rice (SES) developed by IRRI. Results revealed ten genotypes exhibiting resistance with a damage score of 1, while 25 genotypes showed moderate resistance (score 3). Additionally, ten genotypes displayed moderate susceptibility (score 5), and five genotypes were susceptible (score 7) to YSB infestation. Notably, none of the genotypes were classified as highly resistant or highly susceptible. Promising resistant and moderately resistant genotypes, including Chinna Ponni – 5, Jeerige Sanna, Karimundaga, Kyasakki, Kariga Javele, Kari Doddi, Kari Dodi Budda, Laalya, Murkanna Sanna, and Sidda Sanna, were identified, offering potential for incorporation into breeding programs aimed at enhancing YSB resistance in rice cultivars.

Characterization, Quality Assessment and Comparison of Selected Rice Landraces (Anadi, Bhotange, and Kalo Nuniya) of Nepal

This study aimed to characterize, assess and compare the milling-, physical-, cooking-, and eating qualities of brown and milled rice landraces (Kalo Nuniya, Anadi, and Bhotange). Paddysamples (~10 kg each) were cleaned, sun-dried to bring the moisture content to about 13-14%, shelled and then milled to obtain brown (unpolished) rice and milled (white/polished) rice, respectively. Milling-, physical-, cooking-, eating-, and nutritional properties of the rices were studied. The data generated were statistically analyzed using Genstat®version 12.1 for two-way ANOVA, and MS-Excel version 2019 for the Jarque-Bera test of homogeneity, correlation, and to generate graphical presentations. Bhotangehad better brown rice recovery (BRR=76.70%) and milled rice recovery (MRR=58.91%). Anadiand KaloNuniyahad poorer BRR (71.11%) and MRR (49.97%), respectively. Classifying rice samples based on the ‘grain type’, Anadi-, Bhotange-, and KaloNuniya-white were found to be of Medium-, Long-and Medium-'grain type'. Similarly, Anadi-, Bhotange-,and KaloNuniya-brown were found to be of Medium-, Medium-and Small-'grain type', respectively. In terms of size (1000-kernel weight, TKW), Anadi, Bhotangeand KaloNuniya(all white/polished) were found to be 'Small', 'Small' and 'Tiny'. Equilibrium moisture content during soaking (EMC-S) negatively (moderate degree) correlated with apparent amylose content (AAC) for both milled-(R2=0.73) and brown rices (R2=0.70). In white-rices, apparent water uptake ratio (AWUR) showed moderate degree of positive correlation (R2=0.367) with length/breadth (l/b) ratio. But for brown rices, AWUR showed high degree of positive correlation (R2=0.793) with l/b ratio. Volume expansion ratio (VER) positively (moderate degree) correlated (R2=0.63) with AAC for milled rices. This simple correlation established between 2 parameters (assuming other factors to be the same) with few data points cannot be generalized and further investigations are needed to establish solid correlations. Both Bhotangewhite and Bhotangebrown, respectively, had better cooking properties with lower solid loss (both 1.36 ± 0.11%), cooking times (17.67±1.52 and 25.33±2.51 min), higher VER (2.78±0.03 and 2.70±0.04), and l/b ratios after cooking (3.03±0.03 and 2.59±0.03). Anadiwhite had a sticky texture shown by the least VER (2.63 ± 0.13) and the lowest AAC (15.70±1.03%). Classifying rice samples based on the ‘AAC’, Anadi-, Bhotange-,and KaloNuniya-white had Low-, Low-, and Intermediate AAC. Anadi-, Bhotange-, and KaloNuniya-brown had very Low-, Low-, and Low AAC, respectively. Classifying rice samples based on the GT, Anadi-, Bhotange-, and KaloNuniya-white had Low-, Low-, and Intermediate GT. Similarly, Anadi-, Bhotange-, and KaloNuniya-white had Intermediate-, High-, and High-GT, respectively.

Stability analysis in rice landraces grown under dry Direct seeded condition

In the present study the genotype x environment interaction and stability performances of 15 rice landraces in Rabi season during 2017-18 to 2021-22 at Agricultural Research Station, Tamil Nadu Agricultural University, Tamil Nadu, India were evaluated. Eberhart - Russel model was used for stability analysis in rice. In this model, genotype mean across environments, regression of genotype on environmental index and function of the squared deviation from the regression were determined. Mean sum of squares against environment source of variation as well as linear component of environment were significant for all the studied characters suggesting a presence of variation among the environments tested. The linear component of genotype x environment interaction was also found significant for all the traits studied which indicated presence of significant differences between the genotypes. The landraces Kallurundaikar and Kattanur responded favourably to better environments but gave poor yield in an unfavourable environment. Hence, they are suitable for favourable environments. Sivappuchithiraikar and Mysore malli recorded the highest grain yield with bi value closer to unity and non-significant deviation from regression. They were reported as stable genotypes and recommended for cultivation in southern districts of Tamil Nadu. Bangladesh J. Bot. 52(4): 941-948, 2023 (December)

Evaluation of Yield Indices and Identification of Yield Responsive Genes (Gn1a and Gs3) of Selected Rice Genotypes

This research aimed at evaluation of yield Indices and identification of yield responsive Genes (Gn1a and Gs3) of selected rice Genotypes. A total of ten rice genotypes including four improved rice (high yielding) genotypes and six local rice (landraces) genotypes obtained from Maslaha seeds limited Gusau, Zamfara State were collected. The Data was collected for plant height, tiller number, number of panicles, panicle length, panicle weight and days to 50% flowering were recorded, grain length and seed dimension was measured. The genomic DNA of the Rice accession was extracted using a standard DNA extraction Kit (Plant/Seed Miniprep kit). The PCR reaction was set using a total of 40 ul reaction mixture containing 4ul 10x dream taq green buffer, 1.0 ul of dNTPs, 2.0 ul of each primer, 0.4ul of dream taq total nucleic acid polymerase, 2ul total nucleic acid template and 28.6 ul of molecular grade water. The Data collected for grain yield attribute and seed germination was subjected to one way analysis of variance (ANOVA) using statistical analysis system (SAS Version 9.4). The results were expressed as mean + Standard Deviation (SD) of three replicates and the differences between the means were separated using Duncan’s new multiple range test (DNMRT). The result showed that significant differences exist amongst entries for plant height at maturity. Panicle length observed in this study was significantly different in all the entries with FARO67 (25.92cm) recorded the highest compared to genotype Bvfort (20.37cm) which had the lowest. PCR products revealed the presence of Gn1a and Gs3 genes in the ten rice cultivars screened. Eight rice cultivars (FARO44, FARO59, FARO67, Bvfort, Fanjim, Kamrun, Maikwalli and Jamila) have Gn1a and Gs3 gene and shows during PCR Analysis while the remaining two cultivars (FARO60 and Danruwa) have the gene but do not show during the PCR analysis. This investigation therefore, recommends that accessions like Danruwa, kamrun and FARO60 which showed desirable yield, quantitative and qualitative traits in this study should be used for further rice improvement programmes.

Nutritional Assessment and Comparison between Brown and Milled Rice Landraces (Anadi, Bhotange, and Kalo Nuniya) of Nepal

The main objective of this study was to assess and compare the nutritional quality of brown- and milled rice landraces (Kalo Nuniya, Anadi, and Bhotange) of Koshi Province. Paddy samples were cleaned to remove dockage and sun-dried until about 13-14% moisture to ensure maximum hulling- and milling recovery. Paddy samples were shelled and milled to obtain brown (unpolished) rice and milled (white or polished) rice, respectively and were stored in double-sealed re-closable low-density polyethylene (LDPE) zipper bags (62.5 µm) at ambient temperature (23-27°C) until analysis. As expected, brown rices had better nutritional profiles than their milled counterparts with significantly higher (p<0.05) crude fat (2.99± 0.10 − 3.99 ± 0.09%), crude fiber (0.12 ± 0.00 − 0.70 ± 0.02%), and total ash (1.53 ± 0.2 − 3.71 ± 0.30%) content. Among the brown rices, Anadi brown had better nutritional profile with the highest iron (1.56 ± 0.14 mg/ 100 g), calcium (86.4 ± 3.30 mg/100 g), total ash (3.71 ± 0.30%), crude fiber (0.70 ± 0.02%), and crude fat content (3.99 ± 0.09%). Bhotange and Kalo Nuniya had uniform distribution of iron and calcium, respectively, throughout the entire rice kernel.

Cardinal Temperatures and Thermal Time for Germination of Sarawak Traditional Rice

Germination of two rice landraces, namely Bario Sederhana and Biris, was determined from twelve temperatures (12.5 – 40 ºC) in a series of incubation experiments. The cardinal temperatures and thermal time for germination were estimated from a ‘broken-stick’ linear model. Both landraces had a Tb of 10 ºC, Topt between 32 – 33 ºC, and Tmax of 43 ºC. At the sub-optimal temperatures, the thermal time for germination was 62 ºCd for Bario Sederhana and 53 ºCd for Biris. Within the supra-optimal range (Topt to Tmax), both landraces required 27-29 ºCd for seed germination. The maximum final germination for Bario Sederhana was 93% at 30 ºC while Biris had 100% seeds population germinated at 27.5 ºC.

Identification of resistant donors from South Indian landraces for brown planthopper, Nilaparvata lugens (Stal.), Delphacidae, Hemiptera in rice

A total of 126 rice landraces along with resistant (PTB 33) and susceptible (TN 1) check were screened using the protray method. Out of which 13 genotypes having a score of 3.0 - 7.0 were shortlisted and re-evaluated under the modified seed-box screening method. Results of the two experiments showed variation in resistance level with damage score of 3.0 to 9.0. Only one landrace Mysore Malli and PTB 33 were found to be resistant with damage score of 3.0 and four landraces viz., Chetty Samba, Panamara Samba, Vellai Gundu Samba and Vellai Kombi Samba were found to be moderately resistant in both the screening method. In protray screening, 8 landraces were found to be moderately susceptible, 66 landraces were found as susceptible and 48 landraces were highly susceptible. In modified seed-box screening, 5 landraces were found as moderately susceptible, 3 landraces were susceptible and TN 1 in both the methods was found as highly susceptible with a score of 9.0. Cluster analysis performed for 126 landraces based on damage score, nymphal settlement, chlorophyll and Nitrogen content grouped them into six clusters. Among the six clusters, resistant and moderately resistant landraces are grouped in cluster 4 which had low damage score and nymphal settlement and moderate chlorophyll and Nitrogen content.

Antixenosis and antibiosis mechanisms of resistance to Asian rice gall midge, Orseolia oryzae (Wood‐Mason) in rice land races

AbstractAsian rice gall midge is one of the important pests of rice, which attacks the crop from nursery to the end of the tillering stage. Managing this pest through plant resistance is the most viable and economical. Two hundred‐two rice genotypes were phenotyped against Asian rice gall midge, Orseolia oryzae (Wood‐Mason) and the mechanism of resistance in terms of antixenosis and antibiosis was studied. Antixenosis mechanism for adult settlement and egg laying indicated that the susceptible genotypes were preferred more than the resistant genotypes in a free choice test. First instar maggots were found and did not continue their growth on resistant genotypes further. However, in susceptible genotypes, they molted successfully and emerged as adults. No choice tests revealed that the emergence of adults in susceptible genotypes took less time than in resistant genotypes. Higher adult sex ratio was found in susceptible genotypes. Estimation of biochemical components in rice shoot apices of selected genotypes revealed that higher levels of total phenols, wax content, total flavonoids and total free amino acids were present in the resistant genotypes. Still, the number of total sugars, reducing sugars and total protein contents were significantly higher in the susceptible genotypes. Hence, the resistance mechanism in rice gall midge was displayed as a combination of antixenosis and antibiosis mechanism. The output of the study would be helpful in breeding for rice varieties resistant to Asian rice gall midge.

Agronomic evaluation of rice (<i>Oryza sativa</i>) landraces for sustainable crop resilience in a changing climate

Water scarcity and the adverse effects of climate change have significant impact on rice cultivation, leading to declining yields worldwide. The study focuses on red lateritic zone of West Bengal, where irregular rainfall and low water retention pose formidable challenges for farmers. The study was carried out at Zonal Drought Resistance Paddy Research Station, Hathwara, Purulia, West Bengal during 2021 and 2022 to evaluate the agronomic performance of selected landraces, known for their tolerance to stress. Characters like plant height, days to maturity, total grain/ plant, filled grains/plant, and spikelet fertility showed positive correlations with seed yield. Proline content and chlorophyll levels were higher in landraces as compared to the existing varieties. Findings suggest that late-maturing varieties exhibit tolerance mechanism while early varieties demonstrate an escape mechanism in response to water stress. The research underscores that by harnessing the genetic diversity of landraces rice breeding can be enriched to enhance resilience against changing climatic conditions. Overall, this study provides valuable insights into mitigating the impact of climate change on rice cultivation by utilizing landraces in breeding programs, ensuring food security, and supporting the livelihoods of vulnerable farming communities.

Genome-wide association mapping of genes for anthocyanin and flavonoid contents in Vietnamese landraces of black rice

Pigmented rice is desirable in healthy human diets because of potential health benefits compared to white rice. Based on the high diversity of Vietnamese black rice landrace, mapping the loci and predicting putative candidate genes for anthocyanin and flavonoid contents in these landraces would be useful to support the improvement of pigmented rice. A panel of 94 black rice accessions from the National Plant Genebank of Vietnam was analyzed to determine the anthocyanin and flavonoid levels in the whole grain and genotyped using an improved 7 K SNP array. Phenotypic and genotypic data were integrated in a genome wide association study. This identified 32 SNPs significantly associated with total anthocyanin content and 16 SNPs associated with total flavonoid content located on Chromosomes (Chrs.) 1, 2, 3, 6, 7, 8, 11 and 12 and on Chrs. 1, 3, 4, 6, 7, 8, 10, 11 and 12, respectively. A total of 72 candidate genes were co-located with the significant SNPs, of which 44 were predicted to be related to the pathways of biosynthesis of anthocyanin and flavonoid. Twenty candidate genes first reported in this study including the structural genes, LOC_Os03g62300.1 coding for chalcone isomerase and LOC_Os06g41800.1 coding for dihydroflavonol reductase and the regulatory gene, LOC_Os06g43090.1 coding for a MYB transcription factor, were strongly associated with anthocyanin synthesis. These candidate genes and significant SNPs could be used to analyze the function of genes and factors involved in anthocyanin synthesis and to improve pigmented rice by marker-assisted selection.

Characterization of Traditional Rice Varieties for Leaf Blast Resistant Genes Pi5, Pi54, Pi9 and Pi2 using Gene Specific Markers

Magnaporthe oryzae poses a serious risk to rice growing regions worldwide. To combat this, future breeding efforts that aim to develop resistant varieties will need to identify and screen blast-resistant cultivars from existing germplasms. Thus, present study aimed to identify four major blast resistant genes (Pi54, Pi5, Pi2 and Pi9) in 20 traditional rice varieties using functional and linked markers. Results of the present study identified that fifteen traditional rice landraces were found to possess at least one resistant gene and three traditional landraces (Aanaikomban, Chenellu and Jai Sri Ram) had two resistant genes. These identified traditional rice landraces could be used as promising donor against rice blast disease for future rice breeding programmes to develop superior cultivars.

New variants of AvrPiz-t identified in Pyricularia oryzae from Malaysia

Rice blast disease (causal agent: Pyricularia oryzae) is an important rice disease worldwide as it can cause significant yield loss. Resistance genes in rice can recognise the corresponding avirulence genes (Avr-gene) of P. oryzae and suppress the attack of the pathogen as proposed in ‘gene-for-gene’ interaction. This interaction is highly specific. The resistance will be rapidly breakdown owing to the plasticity of Avr-gene. The breaking down of disease resistance can cause problem in managing the disease as well as sustaining a resistant rice variety. This paper aimed to study and analyse the sequence variation of AvrPiz-t gene from P. oryzae isolates in Malaysia (Sarawak) together with AvrPiz-t sequences available from National Centre for Biotechnology Information (NCBI). This study compared the AvrPiz-t haplotype found with previously reported haplotypes. A total of 20 Malaysian P. oryzae isolates were obtained from six divisions of Sarawak and were verified using internal transcribed spacer. Together with seven Malaysian P. oryzae isolates from a previous study, a total of 27 AvrPiz-t gene sequences from Malaysian isolates were successfully amplified and verified. The AvrPiz-t open reading frame (ORF) of 27 Malaysian isolates were aligned with 123 AvrPiz-t ORF from other countries that were available in NCBI database and 100 AvrPiz-t ORF from a previous study (Total = 250 sequences). Unique sequences were identified and translated into amino sequence. The amino acid sequences were aligned with haplotype sequences from previous studies. In total, there were 19 AvrPiz-t haplotypes, with eight newly identified haplotypes. The AvrPiz-t haplotypes were distributed across 14 countries with haplotype H9 as the dominant haplotype. Neutrality tests were performed for the 250 AvrPiz-t ORF sequences. The 250 isolates of P. oryzae were undergoing directional natural selection.. Detached leaf inoculation using filter paper method of selected Malaysia (Sarawak) P. oryzae isolates carrying one of the new AvrPiz-t haplotypes showed different level of pathogenicity towards Sarawak rice landraces. The data obtained serves as baseline information for disease management in Malaysia, especially for Sarawak state. Additionally, the information is also a reference for future rice breeding program in Sarawak.

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.