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Background: Indigenous traditional coloured rices are rich in dietary fibre, resistant starch, minerals, bioactive compounds and antioxidants like anthocyanins, luteins and phenols. Kavuni is one such brownish black medical landrace of rice considered as nutrition supplement since 400BC as it cures gastritis, peptic ulcer and also enhances blood circulation and known for its anti diabetic and anti-inflammatory properties. Lutein is the only dietary oxycarotenoid found in both the macula and lens of the human eye, and acts as blocker of blue light damage, quench reactive oxygen species, prevent age related macular degeneration, cataracts, cardiovascular disease and lung cancer. Aim: The objective of the present investigation was to characterize the lutein content and antioxidant potential of Kavuni and released mega varieties of rice (ASD 16, Swarna Sub1) and its derivatives obtained from crosses ASD 16 and Kavuni; Swarna Sub1 and Kavuni. Methodology & Results: It was found that lutein (quantified by HPLC) was much higher in Kavuni (225 µg/100 g) compared with white rice varieties (ASD 16-15 µg/100g and Swarna Sub1-21 µg/100 g) and the DPPH (2, 2-diphenyl-1-picrylhydrazyl) scavenging ability (for quantification of antioxidant potential) were in the order (Kavuni >>ASD16, Swarna Sub1. Pigmented grain genotypes having higher lutein content had higher percentage of free radical scavenging activity of DPPH and lower IC50 values compared to non pigmented genotypes. Conclusion: It is conceivable that the medicinal landraces of rice could be exploited as one of the potential sources for plant - based pharmaceutical products.

Twenty six genotypes and four check varieties were studied for drought tolerance in rice. The experiment was conducted under both irrigated and stress regimes. Ten different drought tolerant contributing traits were evaluated under stress regime and five yield contributing traits were evaluated under irrigated regime. Among the studied genotypes, IR 87651-26-1-1-3 possessed desirable mean performance under stress for grain yield with other studied traits except number of panicles per plant. Under irrigated regime, the genotypes IR 87753-13-1-1-3, IR 87638-10-1-1-3, IR 87759-5-2-1-3 and IR 83381-B-B-137-3 were advantageous for grain yield and other studied traits except number of panicles per plant. From the variability studies under stress, the traits viz., leaf rolling, leaf senescence, leaf drying, panicle exsertion and grain yield exhibited high genetic advance indicated additive gene action and selection is desirable for these traits. High heritability with advantageous genetic advance was recorded for plant height and grain yield under non-stress regime. From the association analysis, grain yield had positive correlation with plant height, number of panicles per plant and panicle length and negative correlation with days to fifty per cent flowering, leaf rolling, leaf senescence, leaf drying and panicle exsertion under stress. Grain yield was positively correlated with days to fifty per cent flowering, plant height and panicle length under non stress. The desirable genotypes recognized from this study may be utilized as donors and the desirable traits identified may be exploited for drought tolerance rice breeding programs.

BPH is the most destructive pest of rice. Host plant resistance is the most desirable way to control the BPH damage. The single gene resistance is easily broken by the evolution of new BPH biotypes, it can be addressed by the gene pyramiding. In order to improve CO43Sub1 with BPH resistance, the foreground selection was carried out in BC2F2 lines derived from the cross CO43Sub1 and donor IR71033-121-15. In this, 44 plants were homozygous and 13 plants were heterozygous for Bph20. Seven plants were homozygous and 31 plants were found heterozygous for Bph21. Only four plants were found to be homozygous for both the genes. Fifteen lines were selected for the phenotypic screening of BPH resistance. The lines 32-4- 34 and 32-4-35 were resistance to BPH and six lines were observed with moderate resistance.

Early duration rice culture CB 06 535, a derivative of the cross ADT 43 / RR 272 -1745 was released as TNAU Rice CO 51 during the year 2013 as an alternate variety to ADT 43 with 105 -110 days duration with additional desirable features like high yield, physiological efficiency and better adaptability. This culture with semi dwarf stature has efficient tillering capacity, long droopy panicles with highly acceptable plant characters and is a good replacement for the rice variety ADT 43 due to its high grain yield and pest and disease resistance. In the overall performance, the culture, CB 06 535 recorded a mean productivity of 6623 kg/ha in seven years of trials with 10.72 per cent increase over ADT 43. At Nallampalli, Dharmapuri district, the culture has recorded the highest yield of 11,377 kg/ha among the trials conducted, demonstrating the highest yield potential of this variety. The culture CB 06 535 is moderately resistant to blast, BPH and GLH under artificial condition. It produces medium slender white rice with intermediate amylose, soft gel consistency and moderate gelatinization temperature. It produces good quality cooked rice besides high milling and head rice recovery. CB 06 535 with higher yield, better pest and disease resistance and good cooking quality in comparison to the check ADT 43 is suitable for cultivation during Kar/ Kuruvai /Sornavari /Navarai and the seasons / tracts wherever early maturing rice varieties are cultivated throughout Tamil Nadu.

Rice crops in South and Southeast Asian countries suffer critical yield losses due to rice tungro disease caused by joint infection with rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV). Previously, for generating RNA interference-based transgenic resistance against tungro viruses, RTBV ORF IV was used as a transgene to develop RTBV resistance in a popular high-yielding scented rice variety. The transgene from this line was then introgressed into five popular high-yielding but tungro-susceptible rice varieties by marker-assisted backcross breeding with a view to combine the resistant trait with the agronomic traits. The present work includes a resistance assay of the BC3F5 lines of these varieties under glasshouse conditions. Out of a total of 28 lines tested, each consisting of 12 individual plants, eight lines showed significant amelioration in height reduction and 100- to 1000-fold reduction in RTBV titers. The RNAi-mediated resistance was clearly manifested by the presence of virus-derived small RNA (vsRNA) specific for RTBV ORF IV in the transgenic backcrossed lines.

Highlights • Genetic gain for rice grain yield for International Rice Research Institute drought breeding program was estimated. • Positive trend of 0.68 %, 0.87 %, 1.9 % under irrigated control, moderate and severe drought achieved. • Superiority of new rice varieties over currently grown demonstrated on farmers’ fields. • International Rice Research Institute developed rice varieties can protect farmers from crop losses under drought conditions., The complexity of genotype × environment interactions under drought reduces heritability, which determines the effectiveness of selection for drought tolerance and development of drought tolerant varieties. Genetic progress measured through changes in yield performance over time is important in determining the efficiency of breeding programmes in which test cultivars are replaced each year on the assumption that the new cultivars will surpass the older cultivars. The goal of our study was to determine the annual rate of genetic gain for rice grain yield in a drought-prone rainfed system in a series of multi-environment trials conducted from 2005 to 2014 under the Drought Breeding Network of Indian sites in collaboration with the International Rice Research Institute (IRRI). Our results show a positive trend in grain yield with an annual genetic yield increase of about 0.68 % under irrigated control, 0.87 % under moderate reproductive stage drought stress and 1.9 % under severe reproductive stage drought stress due to breeding efforts. The study also demonstrates the effectiveness of direct selection for grain yield under both irrigated control as well as managed drought stress screening to improve yield in typical rainfed systems. IRRI's drought breeding programme has exhibited a significant positive trend in genetic gain for grain yield over the years under both drought stress as well as favorable irrigated control conditions. Several drought tolerant varieties released from the programme have outperformed the currently grown varieties under varied conditions in the rainfed environments on farmers’ fields.

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the major diseases causing a severe yield reduction in rice-growing regions. One dominant (Xa21) and two recessive genes (xa13 and xa5) were introgressed into CB 174 R through marker-assisted breeding. The present study found three (Xa21 + xa13 + xa5) and two (Xa21 + xa13 or Xa21 + xa5 or xa5 + xa13) gene-introgressed combinations in the early segregated materials through foreground selection. The identified homozygous/heterozygous individuals were forwarded to the next cycles of breeding to fix homozygous conditions for all three genes with an improved agronomic performance background and, thus, could be used as a donor source for a future rice breeding program.

Plant selections with desirable root characters have been a major objective in breeding drought resistant variety of rice. Present study was therefore conducted to study the performance of rice varieties for yield, yield contributing characters, root characters and their association with drought tolerance. Drought resistant entries had recorded higher root thickness, root volume and deep root system than the susceptible genotypes. Correlation studies revealed that, all the characters showed positive and significant correlation with single plant yield. Drought score on the other hand exhibited significant negative correlation with yield. Spikelet fertility positively correlated with 1000 grain weight and yield but negatively correlated with drought score. Root depth was found positively correlated with root volume, root thickness, fresh weight of shoot and root and dry weight of shoot and root and exhibited significant negative correlation with drought score. This means that deep rooted varieties tend to be drought tolerant and have thick roots. Strong association between drought score and root thickness suggested that this character to be an important trait in identifying varieties for use in upland rice improvement for drought tolerance. Hence the characters to be given importance in selection are panicle/m2, spikelet fertility and 1000 grain weight as they exhibited highly positive correlation with grain yield and also a positive inter-correlation among themselves. Selection based on root thickness and root depth is highly suitable for identifying varieties for use in upland rice improvement for drought tolerance.

Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae is one of the most important widespread disease around the globe and can cause severe yield reductions of up to 30% of the total yield. Genetic variability was studied in 54 families of CB 174 R × IRBB 60 rice with bacterial blight resistance genes introgressed at the Department of Rice, Tamil Nadu Agricultural University, Coimbatore, India. Traits such as plant height and the number of productive tillers per plant were found to have negative skewness in this study, indicating the duplication of gene effects. Panicle length and the number of grains per panicle were found to have positive kurtosis, indicating gene interactions. The phenotypic coefficient of variation was slightly higher than the genotypic coefficient of variation for all traits, indicating that the observed variation was not only due to genotypic but also due to the environmental effect on the expression of these traits. High heritability coupled with high genetic advance as a percent of the mean was observed for plant height. Moreover, moderate heritability coupled with high genetic advance as a percent of the mean was observed for the single plant yield of rice. Cluster and principal component analyses revealed that the 54 F2:3 families were grouped into three clusters based on six agro-morphological traits. Clusters III and II had higher mean values for most of the studied traits than cluster I. Intercrossing lines from distinct clusters can be identified and crossed to generate larger variability to produce desirable recombinants for higher yield with a wide genetic base.

An exploratory research work was conducted to study the character association and their direct and indirect effects on grain yield in three bacterial blight resistance genes introgressed segregating populations (F2) in rice. Data for yield and five other traits which were component of yield were recorded in 449 F2 individuals in all three crosses. Thousand grain weight was highly correlated with single plant yield in (r=0.95**, p (r=0.48**, p (r=0.44**, p

The present investigation was undertaken to study the effect of different yield QTL (DTY2.2, DTY3.1 and DTY8.1) under drought and their physiological response to drought stress. Backcross Inbred Lines (BILs) of IR64 (CB-193 and CB-229) along with IR64, APO and the traditional rice variety Norungan were raised in green house condition under water stress and control to evaluate the effect of the QTL on grain yield. The BIL CB-193 recorded higher photosynthetic rate (22.051), transpiration rate (7.152) and Ci/Ca ratio (0.597) whereas the BIL CB-229 recorded high relative water content (80.76%). It was found that the combination of three QTL (CB-229) performed better than the susceptible parent and the line with two QTL (CB-193 Fine-mapping of two QTLs viz., qDTY2.2 and qDTY8.1, for grain yield (GY) were conducted using backcross derived lines. Composite interval mapping analyses resolved the originally identified qDTY2.2 region of 6.7 cM into a segment of 2.1 cM and two sub QTLs at region between RM23132 and RM1578 (75.75 cM- 77.66 cM), RM515 and RM1578 (75.11 cM-77.66 cM) were identified in qDTY8.1 region. However this study provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.

Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.

Phosphorus (P), an essential macronutrient, is a prerequisite for various plant-growth mechanisms including root establishment/development, early/late vegetative stage development and reproductive stage development. Rice (Oryza sativa) is very sensitive to P starvation. Most cultivated genotypes have poor tolerance levels to P deficiency and consequently the grain yield is severely affected by P starvation. Since P deficiency of soils is a major concern of rice production areas, it is necessary to develop new cultivars with enhanced P tolerance. This is also an expectation of farmers and the Agriculture ministry of southern states of India where rice cultivation is intensive. Our objective was to introgress the phosphorus starvation tolerance (OsPSTOL1) gene through marker-assisted backcross breeding (MABB) in to two intermediate genetic stocks of popular local-varieties namely, ASD 16 and ADT 43 which harbour bacterial blight and blast resistance (R) genes. To delve into the P starvation phenotypic effect, we have generated a set of four backcross inbred lines (BILs) with enhanced P starvation tolerance. The developed BILs showed altered root architecture pattern and greater root surface area with increased P uptake, confirming their adaptability to P deficient soil conditions. Further, a correlation between root traits and low/high P conditions indicates the function of introgressed OsPSTOL1 in BILs. The enhanced root characteristics, therefore, enabled the plants to access and effectively absorb available nutrients from soil. In summary, the unique features of the OsPSTOL1 BILs with bacterial blight and blast resistance can aid varietal development suitable for cultivation in P deficient soils.

An investigation was carried out with three newly developed temperature sensitive genic male sterile (TGMS) lines for their floral traits, seed production potential and outcrossing ability in ten cross combinations. In the TGMS lines, fertile pollens had an average diameter of 0.89 mm while the sterile pollens was with 0.02 mm diameter.TS-29-150GY produced the biggest fertile pollens with 0.92 mm and other two lines produced relatively smaller pollens with 0.91 and 0.85 mm. Pollen fertility during the fertility reversion period was an average of 60.7%. TS-29-150GY had the maximum of 66.9% spikelet fertility whereas other two lines (TNAU18S and TNAU60S) had relatively lower spikelet fertility of 27.8% and 26.7%, respectively. Average of 17.00 g of seed yield was obtained in the TGMS lines during the fertility reversion period. TS-29-150GY had the highest value of 21.20 g of seed yield while TNAU18S and TNAU60S produced 16.6 g and 13.2 g of seed yield, respectively. The low seed production ability of these three TGMS lines was attributed only to the environmental conditions prevailing during the period. All three TGMS lines had considerable outcrossing potential of 41.2%, 24.6% and 25.0%, respectively. The cross combinations viz. TNAU18S/IET21508 (36 g/plant), TNAU18S/IET21044 (13 g/plant), TNAU18S/IET21009 (26.5 g/plant), TNAU60S/CB-09-106 (26.2 g/plant), TNAU60S/IET21009 (14 g/plant) and TS29-150-GY/DRR 3306 (39.2 g/plant) showed perfect synchronization with acceptable hybrid seed yield, indicating suitability of TGMS system under Indian condition. Based on the outcrossing related traits viz. panicle exertion, angle of glume opening, stigma length and pollen size, TNAU18S was identified as the best, followed by TS-29-150GY.

Thermosensitive genic male sterility (TGMS) is a most comfortable type of male sterility for the production of two-line hybrids in rice. In TGMS system, genes responsible for male sterility and its reversibility is of great importance to create a new pathway for development of new male sterile lines in rice. In this study, genetic analysis based on F2 population derived from a cross between TNAU 60S and IET 21009 revealed that a single recessive gene controls male sterility in TNAU 60S. Marker analysis combined with bulked segregant analysis (BSA) was used and located the target gene on chromosome 2. Fine mapping with 86 SSR markers on chromosome 2 between 20.0 cM and 27.0 cM revealed that tms gene is located at 24.3 cM between two SSR markers RM12713 and RM12722. Among the six genes, two genes LOC_Os02g12420 and LOC_Os02g12680 which encodes receptor like kinase and cytochrome P450 respectively were considered as candidate genes for thermosensitive gene male sterility in TNAU 60S because of very high differential expression between sterile and fertile samples.

Gene wise list of sequence variants discovered through EcoTILLING by sequencing. (DOC 107 kb)

Water deficit is the major limiting factor in crop production which has a significant influence by changing climate. With increasing occurrence of water-deficit stress in warming globe, it becomes inevitable to comprehend and dissect the role of oxidation-induced metabolic alterations. Reactive oxygen species (ROS), such as singlet oxygen, hydrogen peroxide, superoxide anion, and hydroxyl radicals which are produced in low level at intercellular sites especially in chloroplasts and peroxisomes, has had shown enhanced concentrations during water-deficit condition. Higher amount of ROS acts as toxic substance which can damage cellular components such as lipids, proteins, and DNA. Plants have evolved its antioxidant systems to restrict ROS accumulation as general stress signaling process. This oxidative stress plays a major role in plant water-deficit responses in terms of oxidative damage and related redox signaling.

Super pool wise sequencing statistics. (DOCX 15 kb)

PCR compositions followed for the amplification of EcoTILLING fragments. (DOCX 14 kb)

Details of gene specific primers designed to amplify EcoTILLING fragments. (DOCX 14 kb)

PCR cycle condition and composition standardized for the amplification of different EcoTILLING fragments in candidate genes. (DOCX 14 kb)

PCR reaction conditions followed for the amplification of EcoTILLING fragments. (DOCX 14 kb)

Details of rice accessions selected for EcoTILLING by sequencing. (DOCX 46 kb)

The present investigation mainly focused to study the physiological and molecular characterization of 101 Backcross Inbred Lines (BILs) of rice (BC1F5) for drought tolerance derived from the cross combination of Norungan // TKM9/ Norungan. The traits like photosynthetic rate, transpiration rate and stomatal conductance were observed using infrared gas analyzer (IRGA) and the population was phenotyped for other traits. Estimation of genetic parameters revealed that, among the physiological traits observed, the trait transpiration rate recorded higher value of heritability (0.28) and genetic advance (17.49). Association analysis recorded that, all the physiological traits studied under severe water deficit condition had high and significant positive correlation with plot yield. The trait photosynthetic rate had exhibited significant positive correlation with transpiration rate and stomatal conductance but recorded negative correlation with relative water content (RWC). Single marker analysis was performed with the genetic data and the trait mean values observed under stress condition. Among 167 SSR (microsatellite) markers surveyed, around 15 markers were identified and found to be linked to at least one of the investigated trait and many markers were reported to be linked with more than one trait. Characterization of Quantitative trait loci (QTLs) for drought tolerance in this study provides insight into an understanding of the mode of drought tolerance in rice and to perform MAS (Marker aided selection) aimed at the efficient pyramiding of favorable QTL alleles to improve drought tolerance in elite background of popular rice varieties.

In Department of Rice, Tamil Nadu Agricultural University, Coimbatore, a medium duration fine grain rice variety CO52 was released for cultivation in transplanted situation for late samba / thaladi season . CO52 rice variety recorded a mean grain yield of 6191 kg/ha and possessess quality grain traits comparable to the predominantly cultivated fine grain types. It is a derivative of the cross between BPT 5204 and CO(R) 50 which matures in 130-135 days. The variety was tested in the station trial for three (2009-2011)years, Multi Location Trial for two (2011-12 and 2012-13) years, Adaptive Research Trial for two (2013-14 and 2014-15) years, OFT for three (2013-14, 2014-15 and 2015-16) years and in AICRIP trial for two (2011 and 2015) years. CO52 variety is moderately resistant to insect pests viz., plant hoppers and leaf hoppers and diseases viz., blast, sheath rot, brown spot and sheath blight. It produces medium slender white rice with high milling percentage, high head rice recovery, high linear elongation ratio, intermediate amylose content, soft gel consistency and moderate gelatinization temperature indicating its suitability for cooking with a remunerative market price and consumer preference similar to Improved White Ponni and BPT 5204.

A total of 67 aromatic rice germplasm lines were evaluated for nine traits by PCA and cluster analysis for determining the pattern of variation, relationship among individuals and their characteristics. Out of nine PCs, four exhibited more than 1.0 eigen values and showed 70.14 per cent total variability among the characters. PC1 showed high proportion of total variation 25.9 per cent and PC2, PC3 and PC4 contributed 16.96 per cent, 15.06 per cent and 12.22 per cent of the total variance, respectively. Highest positive eigen vector was observed in grain width (0.46) followed by plant height (0.34) in PC1 indicated the large effect in the overall variation of the genotypes. From the cluster analysis, clusters I, II and III had desirable mean values for days to 50 per cent flowering, plant height, number of productive tillers/plant, grain length, grain width, 100 grain weight, panicle length and single plant yield. The genotypes in these clusters would be utilized for aromatic rice improvement breeding.

CR1009 Sub 1 a new version of long duration short bold grain rice variety CR1009 with submergence tolerance was released by Department of Rice, Tamil Nadu Agricultural University, Coimbatore, to overcome submergence during samba season for flood prone areas of Tamil Nadu. CR1009 Sub1 is a product of Marker Assisted Selection of the cross CR 1009 / FR 13 A and it was developed by IRRI in collaboration with NRRI, Cuttack. CR1009 Sub1 rice variety recorded a mean grain yield of 5759 kg/ha with 8.90 per cent increase over CR1009. The variety was tested over three years in station trial (2008-2010), one year in Multi location trial (2010-11), two years in Adaptive research trial (2011-12 and 2012-13), two years in OFT (2010-11, & 2011-12) and one year in AICRIP trial (2010-11). CR1009 Sub1 is moderately resistant to BPH, WBPH, Brown spot and Leaf Blast. CR1009 Sub1 has short bold grain type with good milling percentage (69.8%) and head rice recovery (62.5%), high amylose content (25.0) intermediate gelatinization temperature and soft gel consistency indicating its similarity to CR1009 and also suitable for idly making. This variety was released by TNAU during 2015 and notified during 2017.

Blast caused by Pyricularia oryzae is one of the major constraints limiting rice production globally. Study was undertaken at TNAU, India using a set of selected genotypes including cultivated varieties and (Near Isogenic Lines) NILs and they were screened for blast resistance both genotypically and phenotypically. Genetic diversity was studied among the genotypes and those which are diverse in blast resistance but had similar morphological and quality traits were selected as parents for breeding programme. Selected genotypes were crossed and advanced to further generations up to BC4F1 by marker assisted back crossing. Genetic variability and heritability parameters were assessed among these segregating generations for yield and resistance traits and their trend in each generation was analysed. The disease resistance traits showed high variability in segregating generations as the parents were selected based on the diversity in disease reaction and therefore gives scope for improvement through selection. High heritability coupled with low genetic advance was found in all characters in the segregating generations except single plant yield and panicle length.

We studied the genetics of fertility restoration by producing three-way test cross (TWTC) hybrids involved different combinations of restorers, maintainers and partial restorers of rice. Pollen and spikelet fertility of 16 TWTC hybrids were studied. Six TWTC involving restorer/restorer combinations as male parents produced progenies with fertility levels ranging from complete to zero. No specific ratio of segregation was observed. The crosses involving maintainer/maintainer combinations as male parents showed fully fertile and partial fertile/sterile plants in their progenies. These could be due to nonallelic gene interactions for fertility restoration between the two restorer or maintainer parents, or due to the influence of some modifying genes in the nuclear genome. TWTC involving partial restorer / restorer and partial restorer/partial restorer as the male parents also produced fully fertile and partial fertile/sterile plants suggesting the complex genetics of fertility restoration in rice. There were no previous results depicting the complementation effects of maintainers for fertility restoration.

Rice (Oryza sativa L.) is the “Global Grain” because of its use as prime staple food in about 100 countries of the world. Aerobic rice provides for effective use of water as the concept of flooding paddy fields is abandoned in this ecosystem. But due to the transition from flooding of paddy fields to aerobic system of rice cultivation many factors that determine nutrient (Zn) bioavailability changes in addition to water deficit. Achieving higher yields under aerobic conditions requires new varieties of “aerobic rice” combining both the water stress tolerance and nutrient (especially Zn) deficiency tolerance traits. Molecular marker technologies are the effective tools and they are used for the assessment of genetic variability because they are not influenced by the environment. Among the molecular markers, Simple Sequence Repeat (SSR) has proved to be the most powerful tool for variety identification in rice and has much potential in genetic and breeding studies. Among the 16 SSR markers specific to zinc deficiency tolerance used for assessing the genetic diversity, 13 primer pairs (81.25%) were polymorphic. The number of alleles per microsatellite locus ranged from 2 to 5, averaging 2.53 alleles per locus. Polymorphism information content (PIC) values ranged from 0.43 (RM242) to 0.69 (RM1089 and RM3331), with an average of 0.58. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram revealed two major groups with three clusters and the wide range of dissimilarity values (0.68–1.00) which showed a high degree of diversity among the germplasm lines. The results of the genetic diversity will be useful for the selection of the parents for developing zinc deficiency tolerant rice variety under aerobic condition through molecular breeding programme.