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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.

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.

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.

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.

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.

‘Kavuni’ a traditional brownish black rice variety is known for its anti-diabetic properties and is grown under limited areas of Tamil Nadu, India. The present study was aimed at profiling the nutritional and therapeutic values of Kavuni grains in comparison with three other popularly eaten white rice varieties of Tamil Nadu viz., CO 50, IR64 and White Ponni. Biochemical analysis revealed the significant differences in the nutritional composition of Kavuni grains when compared to other three white rice genotypes viz., 29–35 % reduced level of total soluble sugars, low fat content (8–35 %), 21–52 % increased dietary fibre and 7–24 % increased total protein content. Kavuni grains had significantly higher amount of iron (20–30 %), calcium (33–45 %), copper (9.5–14.7 %), sodium (21–38 %), potassium (7–15 %) and magnesium (8.9–26 %). GC-MS analysis showed that phenolic acids and flavonoids were predominant in the Kavuni grains whereas sugars and fatty acids were predominant in the grains of a white rice variety CO 50. Further, Kavuni was found to possess significantly higher levels of different carotenoids (β-carotene—46.2 μg/100 g; lutein—221.6 μg/100 g), total phenolics (28.8 μg/100 g) and higher anti-oxidant activity. Methanol and ethyl acetate extracts of Kavuni grains were found to exhibit significantly higher level of inhibitory activity against α-amylase and α-glucosidase than the extracts of CO 50 (α-amylase IC50—0.1, 1.0 μg/ml and α-glucosidase IC50 0.04, 0.05 μg/ml).

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.

Blast disease is considered as a major limiting factor in the global rice production because of its wide distribution and destructiveness. Near Isogenic Lines (NILs) harboring different blast resistant Pi genes were surveyed for blast resistance along with resistant and susceptible varieties. These genotypes were randomly crossed to transfer disease resistance to agronomically superior varieties ADT 43, Improved White Ponni and BPT5204. Disease reaction was recorded in both artificial as well as natural epiphytotic conditions and differential response to blast disease incidence was observed. The minimum blast incidence was observed in F1s of ADT 43/CT13432-3R, ADT 43/C101A51 and ADT 43/C101LAC across the environments. Advanced back cross inbred lines developed from the cross combination ADT 43/CT13432-3R were also screened against blast disease. Gene pyramided back cross lines exhibited higher resistance than susceptible genotypes. Among the genotypes tested under epiphytotic conditions at different environments, lines with gene combinations Pi1 + Pi2 + Pi33 + Pi54 and Pi1 + Pi2 + Pi33 were highly resistant to blast disease than those with single genes indicating that these non-allelic genes have a complementary effect. Variation in resistance reaction was observed for the same gene when it acts alone or in combinations and also when the same genes were present in different genetic backgrounds. The gene pyramided lines developed in this study can serve as excellent donors for blast resistance in rice improvement and also for basic studies on gene-race interactions.

Generation, screening and isolating mutants for any developmental and adaptive traits plays a major role in plant functional genomics research. Identification and exploitation of mutants possessing contrasting root growth behavior and salinity tolerance in rice will help us to identify key genes controlling these traits and in turn will be useful for manipulating abiotic stress tolerance through tilling and genetic engineering in rice. In this study, we have screened about 1500 mutants (M 2 generation) generated by treating an upland drought tolerant genotype Nagina 22 with Ethyl Methane Sulfonate (EMS), for their root growth behavior and salinity tolerance under hydroponic conditions. Six independent mutant lines possessing significantly shorter roots and three mutant lines exhibiting greater degree of salinity tolerance than the wild type plants were identified. The identified mutant lines were advanced to M 5 generation to allow the mutants to reach homozygosity, and the fixed mutants were confirmed for their phenotype. One mutant namely N22-C-241-5-6 was found to possess significantly shorter roots than wild type N22, and it was also noticed that the mutant was devoid of root cap. Among the three salinity tolerant mutant lines identified, N22-C-334-3 was found to possess a greater degree of tolerance upto 250 mM Nacl stress at germination stage. These identified mutant lines can be used for further physiological, biochemical and molecular biology experiments to identify candidate gene(s) controlling root growth behavior and salinity tolerance in rice. Keywords : Rice, mutation, EMS, altered rood growth and salinity tolerant mutant African Journal of Biotechnology Vol. 12(40), pp. 5852-5859

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)

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

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)

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

Super pool wise sequencing statistics. (DOCX 15 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.,)isone ofthemostimportant cerealcropsworldwide.Inthisstudy,phytoplasmashavebeen detected in symptomatic leaves of four varieties of rice using nested-PCR with primer pairs P1/P7 and R16F2n/R16R2, which amplified a 1.2 kb fragment of the 16S rRNA gene. The nucleotide sequence analysis of the fragment had 100 % identity among the sequences from the four varieties (GenBank Accession numbers: JX290545, JX290546, JX290547 and JX290548) and 99 % nucleotide sequence identity with 16S rRNA gene sequences of the Rice orange leaf disease phytoplasmas from the Philippines and Thailand, Maize bushy stunt phytoplasma and Wheat blue dwarf phytoplasma belonging to the 'Candidatus Phytoplasma asteris' (16SrI) group. This is the first report of 16SrI group phytoplasmas infecting rice in India.

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.

A study was undertaken for screening the EMS induced mutants of N22 for identifying high biomass mutants. In a population of 10000 mutants, 280 mutants were selected phenotypically and forwarded in which dry matter production along with 18 other traits including days to fifty per cent flowering, plant height, number of tillers per plant, number of productive tillers per plant, efficient tillering percentage, flag leaf length, flag leaf width, panicle length, number of filled grains per panicle, number of chaffy grains per panicle, spikelet fertility, hundred grain weight, grain length, grain breadth, wet biomass, grain yield , harvest index and vein density were characterized, Physiological traits namely SPAD reading, photosynthetic rate, transpiration rate, stomatal conductance and Ci/Ca ratio were also recorded. A total of 58 per cent had higher grain yield than N22 while a total of 214 mutants recorded with high dry matter production than N22. In terms of physiological efficiency, genotypes with high vein density are associated with high biomass as in the case of any C4 plants. Wild type N22 has 50 minor veins and 8 major veins while 56 mutants possessed more than 50 minor veins and 10 major veins. Two mutants namely PL.No.36 and Pl.No.183 were found to be promising, which recorded high dry matter production with more number of minor veins, had high chlorophyll content and high photosynthetic rate.

Background Drought is the most severe abiotic stress reducing rice yield in rainfed drought prone ecosystems. Variation in intensity and severity of drought from season to season and place to place requires cultivation of rice varieties with different level of drought tolerance in different areas. Multi environment evaluation of breeding lines helps breeder to identify appropriate genotypes for areas prone to similar level of drought stress. From a set of 129 advanced rice (Oryza sativa L.) breeding lines evaluated under rainfed drought-prone situations at three locations in eastern India from 2005 to 2007, a subset of 39 genotypes that were tested for two or more years was selected to develop a drought yield index (DYI) and mean yield index (MYI) based on yield under irrigated, moderate and severe reproductive-stage drought stress to help breeders select appropriate genotypes for different environments. Results ARB 8 and IR55419-04 recorded the highest drought yield index (DYI) and are identified as the best drought-tolerant lines. The proposed DYI provides a more effective assessment as it is calculated after accounting for a significant genotype x stress-level interaction across environments. For rainfed areas with variable frequency of drought occurrence, Mean yield index (MYI) along with deviation in performance of genotypes from currently cultivated popular varieties in all situations helps to select genotypes with a superior performance across irrigated, moderate and severe reproductive-stage drought situations. IR74371-70-1-1 and DGI 75 are the two genotypes identified to have shown a superior performance over IR64 and MTU1010 under all situations. Conclusion For highly drought-prone areas, a combination of DYI with deviation in performance of genotypes under irrigated situations can enable breeders to select genotypes with no reduction in yield under favorable environments compared with currently cultivated varieties. For rainfed areas with variable frequency of drought stress, use of MYI together with deviation in performance of genotypes under different situations as compared to presently cultivated varieties will help breeders to select genotypes with superior performance under all situations.

Drought tolerant lines of Improved White Ponni (IWP) were developed by marker assisted back crossing of IWP with Apo. Three drought tolerant backcross inbred lines (BILs), developed by introgressing the drought tolerance QTLs from Apo were evaluated for drought tolerance along with their parents based on drought indices. Twenty drought indices were calculated based on grain yield under drought and irrigated conditions. Yield in drought and irrigated conditions were significantly and positively correlated with mean productivity index, harmonic mean, geometric mean of productivity and stress tolerance index. Ranking method and three dimensional plot discriminated IWP-4-2 as the most drought tolerant genotype, which was placed in group A (Genotypes, which performed good under drought and irrigated conditions), and outperformed the drought tolerant parent, Apo. IWP-4-2 possessed medium slender grains similar to the recurrent parent, IWP. Based on its drought tolerance and grain type IWP-4-2 can also be used as donor parent for developing climate resilient rice variety suitable to conditions obtaining in Tamil Nadu.

The present investigation was carried out to study the gas exchange parameters in backcross inbred lines of ‘Improved White Ponni’ (IWP) introgressed with different drought yield QTLs and their parents raised under control and stress conditions. Various gas exchange parameters and single plant yield were observed using portable photosynthetic system (infra red gas analyser -IRGA). Among the genotypes, three combination of QTL line IWP-4-2 recorded significantly higher photosynthetic rate (22.97 μ mol CO2 m−2 s−1), stomatal conductance (0.36 mol H2O m−2 s−1), transpiration rate (6.25 mmol H2O m−2 s−1), internal CO2 concentration (240.82) ratio between internal and atmospheric CO2 concentration (0.25) and single plant yield (15.11) which was on par with the tolerant parent Apo (an high yielding indica cultivar moderately tolerant to drought stress) under severe moisture stress regime. Overall study clearly revealed that, the performance of introgressed line with three drought QTLs (IWP-4-2) was better than two drought QTL introgressed lines of IWP-1-52 and IWP-1-57. Results from graphical genotyping using three foreground and 36 polymorphic background markers revealed that, the three QTL introgressed line IWP-4-2 had 72.20% genome recovery from Improved White Ponni, 13.89% from APO and 13.89% heterozygous region.

Mapping QTLs Related to Zinc Deficiency Tolerance under Aerobic Rice Ecosystem 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 (Zinc) bioavailability changes in addition to water deficit. Achieving high yields under aerobic conditions requires new varieties of “aerobic rice” combining both the water stress tolerance and nutrient (especially Zinc) deficiency tolerance traits. The present study was undertaken to know the genetic and molecular basis of zinc (Zn) deficiency tolerance using an indica/indica F4 RIL population of CO51 (A high yielding low land variety with low zinc efficiency) and CB-06-803-2 (An improved upland culture with high zinc efficiency) comprising of 246 RILs. These RILs were phenotyped under aerobic system in control (+Zn) and stress (-Zn) plots and genotyped using 80 SSR markers specific to zinc transporter genes (ZIP family) and root related traits. The parents for the mapping population were selected by screening 60 rice germplasm lines for ZE under aerobic condition. The reported map position of gramene database was used to estimate the QTLs and followed inclusive composite interval mapping of additive and dominant (ICIM-ADD) method. The QTL analysis resulted in the identification of three QTLs viz., zinc efficiency in shoot (ZES), days to 50 per cent flowering in control (DFFC) and shoot zinc content in stress (SZCS) condition..