Rice Improvement Research Articles

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.).

The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.

Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2.

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion–deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.

CRISPR-Based Genome Editing: Advancements and Opportunities for Rice Improvement.

To increase the potentiality of crop production for future food security, new technologies for plant breeding are required, including genome editing technology—being one of the most promising. Genome editing with the CRISPR/Cas system has attracted researchers in the last decade as a safer and easier tool for genome editing in a variety of living organisms including rice. Genome editing has transformed agriculture by reducing biotic and abiotic stresses and increasing yield. Recently, genome editing technologies have been developed quickly in order to avoid the challenges that genetically modified crops face. Developing transgenic-free edited plants without introducing foreign DNA has received regulatory approval in a number of countries. Several ongoing efforts from various countries are rapidly expanding to adopt the innovations. This review covers the mechanisms of CRISPR/Cas9, comparisons of CRISPR/Cas9 with other gene-editing technologies—including newly emerged Cas variants—and focuses on CRISPR/Cas9-targeted genes for rice crop improvement. We have further highlighted CRISPR/Cas9 vector construction model design and different bioinformatics tools for target site selection.

Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.

Can the grains offer each other helping hands? Convergent molecular mechanisms associated with domestication and crop improvement in rice and maize

The grasses, Poaceae, are an extraordinarily ecologically successful clade, with more than 10 000 described extant species. The grasses include more than 30 domesticated grain crops, ranging from maize (Zea mays), rice (Oryza sativa), and wheat (Triticum aestivum), which are collectively responsible for 50% of all calories consumed by humans around the world, to minor and orphan crops such as teff (Eragrostis tef), pearl millet (Pennisetum glaucum), proso millet (Panicum milaceum), and Job’s tears (Coix lacryma-jobi) (Glémin and Bataillon, 2009).

Genetic analysis of yield and yield contributing traits in rice (Oryza sativa L.) BC2F3 population derived from MR264 × PS2

High yield potential in rice is indirectly determined by yield-related traits. These traits are complex and regulated by several genes whose expression is affected by environmental conditions. It is of great importance to disclose the genetic relationships between yield and its yield components for multi-trait improvement in rice. Therefore, the present study aimed to investigate the genetic variability and inheritance patterns of yield and yield attributed traits in BC2F3 rice lines to identify the ideal lines from the selection. A total of 36 improved versions of blast resistant plants in the BC2F3 population used in this study were developed from a single cross between a high yielding mutant rice variety but susceptible to blast, MR264, and Malaysian local variety donor for Pi-7(t) and Pikh blast resistant genes. Analysis of variance showed that all traits were significantly different for lines except grain length and grain width. High heritability and genetic advance were recorded for plant height, number of tillers, filled grain, 1000-grain weight and seed setting rate. A significant and positive correlation was recorded with most evaluated traits, except for grain length and grain width. Thirty-six BC2F3 lines were clustered into four major groups and the first three principal components (PC3) contributed 71.13% of the total variation, with 1000-seed weight, yield/hill and filled grain being the main discriminatory characters. There was an adequate genetic variability in the lines, and 1000-grain weight, yield/hill and filled grain traits could be considered for indirect selection in breeding programs in next generations.

Performance of Doubled Haploid Elite Rice (Oryza sativa L.) Germplasm for Grain Yield and Associated Traits in Harare, Zimbabwe

A field experiment was conducted in 2018/2019 growing season at the Scientific Industrial Research and Development Center under irrigated conditions using the simple alpha lattice (7 ∗ 7) design, with three replications. The objective of the study was to determine the performance of 44 elite rice lines that were selected and shared from elite doubled haploid germplasm and five cultivars were used as checks. All evaluated genotypes exhibited significant variation in the traits measured except for number of grains/panicle, total tillers/plant, and effective tillers/plant. Elite line 70462 was found to be the highest yielding, with yield advantage of 66% over the high yielding local check (Nerica 7). High values for broad sense heritability were recorded for days to 50% heading, panicle length, culm length, number of filled grains/panicle, 1000-grain weight, grain length, grain shape, and grain yield and indicated lesser influence of environment in expression of these traits, hence amenable to simple selection. Correlation analysis revealed that grain yield manifested significantly positive correlation with filled grains/panicle contributing the highest correlation (r = 0.784), followed by culm length (r = 0.605), spikelet fertility/panicle (r = 0.677), grain length (r = 0.551), 1000-grain weight (r = 0.518), panicle length (r = 0.449), and number of grains/panicle (r = 0.328). Based on grain yield, number of filled grains/panicle and spikelet fertility/panicle, panicle length, and earliness, lines 70462, 60143, 70383, Arica 3, Sahel 177, 6040, 70537, 60409, and 70476 had the best performance. Selection of these traits would be more effective for yield improvement in rice and these promising lines could be used in the varietal development and can be tested in multilocational trials and on-farm trials in Zimbabwe with the possibility of release and commercialization.

Character Association of Yield and Yield Components of Various Varieties of Rice (Oryza sativa L.)

Yield and yield attributing parameters are the most widely targeted traits in rice improvement programmes. The relationship between yield and yield attributing traits are important for direct and indirect selection of traits which contribute to yield. Information on the extent of association between yield and yield components is important in the simultaneous improvement of correlated traits. This study was carried out to determine the direct and indirect contributions of yield components to yield of rice and the level of association. Path Coefficient Analysis was used to evaluate the character association of yield and yield components of twenty-five rice varieties at the Rivers State University Teaching and Research Farm, Port Harcourt, during the 2019 planting season under rainfed condition and complimented by irrigation in two different planting dates. The experiments were laid out in a randomized complete block design. Data were collected on yield and yield components. Leaf area, plant height, panicle length, panicle number, panicle weight, 100-grain weight and spikelet fertility correlated positively and significantly with grain yield per stand. The path coefficient analysis indicated that panicle number (0.265) and spikelet fertility (0.219) had the highest positive direct effect on grain yield per stand. Conversely, number of grains per panicle (-0.128), days to 50% flowering (-0.114), tiller number (-0.095) and panicle length (-0.056) exerted negative direct effect on grain yield per stand with 0.674 residual effects. Therefore, direct selection for leaf area, plant height, panicle number, panicle weight, 100 grain weight, and spikelet fertility will effectively improve yield in rice. Key words : Grain yield, Character Association, Oryza sativa, variation, yield components DOI: 10.7176/JNSR/13-8-02 Publication date: April 30 th 2022

Fine Mapping of Two Interacting Loci for Transmission Ratio Distortion in Rice (Oryza sativa L.)

Transmission ratio distortion (TRD) denotes the observed allelic or genotypic frequency deviation from the expected Mendelian segregation ratios in the offspring of a heterozygote. TRD can severely hamper gene flow between and within rice species. Here, we report the fine mapping and characterization of two loci (TRD4.1 and TRD4.2) for TRD using large F2 segregating populations, which are derived from rice chromosome segment substitution lines, each containing a particular genomic segment introduced from the japonica cultivar Nipponbare (NIP) into the indica cultivar Zhenshan (ZS97). The two loci exhibited a preferential transmission of ZS97 alleles in the derived progeny. Reciprocal crossing experiments using near-isogenic lines harboring three different alleles at TRD4.1 suggest that the gene causes male gametic selection. Moreover, the transmission bias of TRD4.2 was diminished in heterozygotes when they carried homozygous TRD4.1ZS97. This indicates an epistatic interaction between these two loci. TRD4.2 was mapped into a 35-kb region encompassing one candidate gene that is specifically expressed in the reproductive organs in rice. These findings broaden the understanding of the genetic mechanisms of TRD and offer an approach to overcome the barrier of gene flow between the subspecies in rice, thus facilitating rice improvement by introgression breeding.

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.

A Genetic Resource for Rice Improvement: Introgression Library of Agronomic Traits for All AA Genome Oryza Species.

Rice improvement depends on the availability of genetic variation, and AA genome Oryza species are the natural reservoir of favorable alleles that are useful for rice breeding. To systematically evaluate and utilize potentially valuable traits of new QTLs or genes for the Asian cultivated rice improvement from all AA genome Oryza species, 6,372 agronomic trait introgression lines (ILs) from BC2 to BC6 were screened and raised based on the variations in agronomic traits by crossing 170 accessions of 7 AA genome species and 160 upland rice accessions of O. sativa as the donor parents, with three elite cultivars of O. sativa, Dianjingyou 1 (a japonica variety), Yundao 1 (a japonica variety), and RD23 (an indica variety) as the recurrent parents, respectively. The agronomic traits, such as spreading panicle, erect panicle, dense panicle, lax panicle, awn, prostrate growth, plant height, pericarp color, kernel color, glabrous hull, grain size, 1,000-grain weight, drought resistance and aerobic adaption, and blast resistance, were derived from more than one species. Further, 1,401 agronomic trait ILs in the Dianjingyou 1 background were genotyped using 168 SSR markers distributed on the whole genome. A total of twenty-two novel allelic variations were identified to be highly related to the traits of grain length (GL) and grain width (GW), respectively. In addition, allelic variations for the same locus were detected from the different donor species, which suggest that these QTLs or genes were conserved and the different haplotypes of a QTL (gene) were valuable resources for broadening the genetic basis in Asian cultivated rice. Thus, this agronomic trait introgression library from multiple species and accessions provided a powerful resource for future rice improvement and genetic dissection of agronomic traits.

Studies on Soil Physico-chemical Properties in Rice Based Cropping Systems of Long Term Fertilizer Experiments

Soil samples collected from All India Coordinated Rice Improvement Programme from three different locations initiated in 1989-90 viz. Maruter(Andhra Pradesh-Rice Rice cropping system), Titabar (Assam-Rice Rice cropping system) and Mandya-(Karnataka- Rice Cowpea cropping system); with 8 treatments involving combinations of organic and inorganic sources of nutrients and three replications laid under Randomized Block Design, were collected, processed and analyzed for different soil physicochemical properties viz. pH, EC, OC and CEC properties to study the effect of varied fertilization practices in the long run which help in assessing the soil health status. Results showed that over 30 years of continuous experimentation the soils physico-chemical properties did not vary significantly among different treatments except organic carbon content. It ranged from 0.52-0.63%, 0.22-0.31% and 0.26-0.40% in Maruteru, Titabar and Mandya respectively. The results clearly brought out that monocropping over 30 years without any manures and fertilizers completely resulted in the depletion of nutrients. Inclusion of the pulse crop (cowpea) improved the soil fertility status especially in organic carbon

Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design

Breeding rice (Oryza sativa L.) with high yield, superior quality, desired grain shape and high resistance is the goal of breeding to meet the needs of current consumers. It is usually hard to combine multiple complex traits based on traditional breeding methods because they are frequently antagonistic to each other. However, molecular design breeding, as a novel breeding method, is an optional alternative to this challenge. To demonstrate molecular design breeding, 15 favorable genes from five parent lines were pyramided together to develop elite rice with high-yield, superior-quality, desired grain shape and high resistance to brown planthopper (BPH). The parental lines were 9311, the recurrent parent, carrying APO1, Ghd7, Ghd8 and Gn1a for high yield, GS3 and qSW5 for grain shape, and Wx and ALK for eating and cooking quality; 1880 with Gn8.1 for large panicles; Luo-Yu-Xiang carrying GW7 for grain shape and SBE3, SSIV2 and SSIII for eating and cooking quality; Luoyang6 with Bph6 and Luoyang9 with Bph9 for BPH resistance. After careful screening for the 15 targeted genes, desired phenotype and maximum genetic background from 9311, three molecular design lines with desired phenotypes, named as MD1 (Molecular design 1), MD2 and MD3 were developed. MD3 carried all 15 targeted genes, and MD1 and MD2 had 14 of the 15 targeted genes. Only SBE3 was not introgressed into MD1 and MD2 but this had minimal impact on the gel consistency and alkali spreading value. These newly bred lines exhibited higher yield potential, better grain quality with slender grains, low amylose content, high gel consistency and alkali spreading value, and higher BPH resistance compared to the parent 9311. In this study, we successfully created three novel rice lines with high yield, superior quality and improved BPH resistance by rational molecular design. Our results demonstrate molecular design is a powerful strategy to improve multiple complex traits and will provide a reference for the future commercial rice improvement.

Imaging Systems and Applications: introduction to the feature issue.

Imaging systems have numerous applications in industrial, military, consumer, and medical settings. Assembling a complete imaging system requires the integration of optics, sensing, image processing, and display rendering. This issue features original research covering several aspects of imaging systems ranging from microscopic to radar imaging scale. Various applications include pulsed thermographic imaging for underdrawing visualization in paintings, image spectral classification using a single pixel camera, and an improved algorithm for millimeter-wave near-field one-side stationary bistatic synthetic aperture radar. Other applications include a cost-effective device capable of quantitative measurement of the embryo and endosperm areas of brown rice and resolution improvement of a microsphere-assisted microscope with arrays of plasmonic structures.

Molecular Characterization of Different Varieties of rice (Oryza sativa L.) using SSR Markers

The present study was performed to analyze molecular diversity among different varieties of rice using SSR markers, which are effective and reliable tools for this type of analysis. A total of 34 different alleles were generated using 17 SSR primers. Out of these 33 alleles were found to be polymorphic and only one was monomorphic. On average, 2 alleles per primer and 1.94 polymorphic alleles per primer was calculated. In the cluster analysis three varieties KATKIRICE, SONUMRICE and 1010 were found to be diverse from other varieties of rice. These varieties may be used as diverse parents for the future breeding programs for rice improvement. According to Jaccard’s similarity coefficient, the highest genetic diversity was observed between KATKIRICE and CHANDRAHASNI. Both varieties were grouped distantly. Out of 17 primers, the best 10 primers were selected based on polymorphic banding patterns for genetic diversity analysis. These selected 10 primers are sufficient to discriminate the group of rice varieties. These findings not only highlight the capacity of the SSR technique but also help in the selection of diverse rice varieties for conservation and crop improvement.

A new gain-of-function OsGS2/GRF4 allele generated by CRISPR/Cas9 genome editing increases rice grain size and yield

Grain size is one of the most important factors affecting rice grain quality and yield, and attracts great attention from molecular biologists and breeders. In this study, we engineered a CRISPR/Cas9 system targeting the miR396 recognition site of the rice GS2 gene, which encodes growth-regulating factor 4 (OsGRF4) and regulates multiple agronomic traits including grain size, grain quality, nitrogen use efficiency, abiotic stress response, and seed shattering. In contrast to most previous genome editing efforts in which indel mutations were chosen to obtain null mutants, a mutant named GS2E carrying an in-frame 6-bp deletion and 1-bp substitution within the miR396-targeted sequence was identified. GS2E plants showed increased expression of GS2 in consistent with impaired repression by miR396. As expected, the gain-of-function GS2E mutant exhibited multiple beneficial traits including increased grain size and yield and bigger grain length/width ratio. Thousand grain weight and grain yield per plant of GS2E plants were increased by 23.5% and 10.4%, respectively. These improved traits were passed to hybrids in a semi-dominant way, suggesting that the new GS2E allele has great potential in rice improvement. Taken together, we report new GS2 germplasm and describe a novel gene-editing strategy that can be widely employed to improve grain size and yield in rice. This trait-improvement strategy could be applied to other genes containing miRNA target sites, in particular the conserved miR396-GRF/GIF module that governs plant growth, development and environmental response.

Precision Genome Editing Toolbox: Applications and Approaches for Improving Rice’s Genetic Resistance to Pathogens

In the present scenario of a looming food crisis, improving per hectare rice productivity at a greater pace is among the topmost priorities of scientists and breeders. In the past decades, conventional, mutational, and marker-assisted breeding techniques have played a significant role in developing multiple desired rice varieties. However, due to certain limitations, these techniques cannot furnish the projected food security of the 2050 population’s aching stomachs. One of the possible options would be precise crop genome editing using various tools, viz., TALENs and CRISPR/Cas9 to resolve this multifaceted crisis. Initially, the potentiality of these technologies was tested only in the rice protoplasts. Later, the techniques were employed to edit calli with help of modified vectors, CRISPR variants, cassette cloning systems, and delivery methods. With the continuous technological advancements such as base editing, multiplexing, etc., the precision, rapidness, efficiency, reliability, potency, and range of applications of these platforms have increased and even been used for gene function studies. This leads to a revolution in the field of the rice improvement program, especially the stress tolerance against various pests and pathogens in which the susceptibility factors located within the rice genome are targeted through genome editing tools. Therefore, in this current article, we have summarized the advancements in the rice genome editing tools during the last decade concerning enhanced biotic stress tolerance. Additionally, we have focused on the regulatory aspects of genome editing with associated risks and limitations, and the prospects to reshape the rice genome for durable resistance to complex biotic stress.

Selectable Markers to Marker-Free Selection in Rice.

Inadequate rice production worldwide is largely attributed to abiotic and biotic stresses, along with high sensitivity of cultivable plant germplasm. In the field of cereal biotechnology, rice engineering plays an important role in achieving tolerance to such stresses. Plant transformation and selection play crucial role in rice engineering. This review summarized the antibiotic, herbicide and metabolic selection marker genes (SMG) employed in diverse rice engineering studies. These SMGs are no longer required after the transformation has been achieved, hence undesirable at the commercial level. This study also included several strategies employed in rice engineering to eliminate such foreign DNA elements. These include co-transformation, site-specific recombination, transposon and CRISPR base approaches. CRISPR/Cas9 being simple and efficient, is considered a crucial step toward clean gene technology. Further ease and applicability of CRISPR/Cas9 in the embryos directly can help us to modify target genes with efficient marker-free selection in minimum time. Overall, this review summarizes and analyse the recent advances that have enormous potential in rice improvement.

Functional, amino acid composition and protein profiling of protein isolates from different pigmented, nonpigmented and improved rice varieties and their effects on starch thermal and dynamic rheological behaviour

SummaryThe amino acids composition, protein profiling and functional properties of protein isolates from different pigmented rice (PR), nonpigmented rice (NPR) and improved rice (IR) varieties were determined and their effects of incorporation on starch thermal, and dynamic rheological were evaluated to know the possible interactions in food matrix. Protein isolates (PI) from PR and IR showed better foaming capacity and, foam stability than those from NPR. PI from both the PR and IR showed higher proportion of histidine, threonine, valine, methionine, phenylalanine and isoleucine. PI from IR showed higher accumulations of glutelins (31 and 33kDa, 21 and 22 kDa) and prolamins (15kDa, 16kDa, 17 kDa and 20kDa) than those from rice types. Starches from IR showed higher storage modulus (Gʹ) and loss modulus (Gʺ) than that from PR, and NPR, and decreased on addition of PI. PI from PB1121 IR was more suitable for protein enrichment due to more lightness value, and superior functionality (emulsification and foaming properties). Starch‐protein interaction affects the functionality, and behaviour of matrix and, developing hypoallergenic infant formulations or other food products.

Ex situ conservation and qualitative characterization of traditional cultivars of rice (Oryza sativa L.)

Genetic diversity of rice cultivars offers adequate opportunity for added advantage for rice improvement. Current study with 132 traditional rice cultivars had been collected from West Bengal, Manipur and Assam. Those cultivars are being preserved at repository of Uttar Banga Krishi Viswavidyalaya since 2009. Few of them had used in breeding programme to develop new desirable variety with unique characteristics. Those traditional cultivars were phenotypically characterized using PPV&FRA descriptor. In this piece of work, 44 traits were considered to record the morphological differences among the traditional cultivars. All the traditional cultivars showed one or few distinctive features that made different from each other. Finally the traditional cultivars were classified based few anticipated distinctive characters. Amylose content in endosperm was very low in ten, low in twelve, medium in 61 and high in 49 traditional cultivars. Amylose content of milled rice is a significant parameter in respect of consumer preference. Under Indian context, consumers prefer rice with medium amylose content (20-25%) in the endosperm. Strong aroma was emitted by 25, mild aroma by 23 and no aroma in 84 cultivars.