Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study.

The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.

Multi-environment evaluation of rice genotypes: impact of weather and culm biochemical parameters against sheath blight infection.

Introduction: Sheath blight caused by Rhizoctonia solani is one of the major diseases of rice, causing widespread crop losses. The use of semi-dwarf rice varieties in the ongoing nutrient-intensive rice cultivation system has further accentuated the incidence of the disease. An ideal solution to this problem would be identifying a stable sheath blight-tolerant genotype. Material and methods: A multi-environment evaluation of 32 rice genotypes against sheath blight infection was conducted over six seasons across two locations (Agricultural Research Farm, Institute of Agricultural Sciences, Banaras Hindu University (28.18° N, 38.03° E, and 75.5 masl), for four years during the wet seasons (kharif) from 2015 to 2018 and two seasons at the National Rice Research Institute (20°27'09" N, 85°55'57" E, 26 masl), Cuttack, Odisha, during the dry season (rabi) of 2019 and the kharif of 2019, including susceptible and resistant check. Percent disease index data were collected over 4 weeks (on the 7th, 14th, 21st, and 28th day after infection), along with data on other morphological and physiological traits. Result and discussion: The resistant genotypes across seasons were the ones with a higher hemicellulose content (13.93-14.64) and lower nitrogen content (1.10- 1.31) compared with the susceptible check Tapaswini (G32) (hemicellulose 12.96, nitrogen 1.38), which might explain the resistant reaction. Three different stability models-additive main effect and multiplicative interaction (AMMI), genotype + genotype x environment (GGE) biplot, and multi-trait stability index (MTSI)-were then used to identify the stable resistant genotypes across six seasons. The results obtained with all three models had common genotypes highlighted as stable and having a low area under the disease progress curve (AUDPC) values. The ideal stable genotypes with low disease incidence were IC 283139 (G19), Tetep (G28), IC 260917 (G4), and IC 277274 (G10), with AUDPC values of 658.91, 607.46, 479.69, and 547.94, respectively. Weather parameters such as temperature, rainfall, sunshine hours, and relative humidity were also noted daily. Relative humidity was positively correlated with the percent disease index.

Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation.

Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.

Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency.

Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.

Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping.

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

Unlocking the Nexus between Leaf-Level Water Use Efficiency and Root Traits Together with Gas Exchange Measurements in Rice (Oryza sativa L.).

Drought stress severely affects plant growth and development, causing significant yield loss in rice. This study demonstrates the relevance of water use efficiency with deeper rooting along with other root traits and gas exchange parameters. Forty-nine rice genotypes were evaluated in the basket method to examine leaf-level water use efficiency (WUEi) variation and its relation to root traits. Significant variation in WUEi was observed (from 2.29 to 7.39 µmol CO2 mmol−1 H2O) under drought stress. Regression analysis revealed that high WUEi was associated with higher biomass accumulation, low transpiration rate, and deep rooting ratio. The ratio of deep rooting was also associated with low internal CO2 concentration. The association of deep rooting with lower root number and root dry weight suggests that an ideal drought-tolerant genotype with higher water use efficiency should have deeper rooting (>30% RDR) with moderate root number and root dry weight to be sustained under drought for a longer period. The study also revealed that, under drought stress conditions, landraces are more water-use efficient with superior root traits than improved genotypes.

Comparative Proteomic Analysis of Rhizoctonia solani Isolates Identifies the Differentially Expressed Proteins with Roles in Virulence.

Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the isolates varied in their pathogenicity. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The PCR amplification confirmed that the RS15 and RS22 belonged to the Rhizoctonia subgroup of AG1-IA with a specific primer. The proteomic information generated has been deposited in the PRIDE database with PXD023430. The virulent isolate consisted of 48 differentially abundant proteins, out of which 27 proteins had higher abundance, while 21 proteins had lower abundance. The analyzed proteins acquired functionality in fungal development, sporulation, morphology, pathogenicity, detoxification, antifungal activity, essential metabolism and transcriptional activities, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi. A Quantitative Real-Time PCR (qRT-PCR) was used to validate changes in differentially expressed proteins at the mRNA level for selected genes. The abundances of proteins and transcripts were positively correlated. This study provides the role of the proteome in the pathogenicity of R. solani AG1-IA in rice and underpins the mechanism behind the pathogen's virulence in causing sheath blight disease.

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives.

We studied variation in adaptive traits and genetic association to understand the low P responses, including the symbiotic association of arbuscular mycorrhizal (AM) fungal colonization in Oryza species (O. sativa, O. nivara, and O. rufipogon). In the present experiment, we performed the phenotypic variability of the morphometric and geometric traits for P deficiency tolerance and conducted the association studies in GLM and MLM methods. A positive association between the geometric trait of the top-view area and root traits suggested the possibility of exploring a non-destructive approach in screening genotypes under low P. The AMOVA revealed a higher proportion of variation among the individuals as they belonged to different species of Oryza and the NM value was 2.0, indicating possible gene flow between populations. A sub-cluster with superior-performing accessions had a higher proportion of landraces (42.85%), and O. rufipogon (33.3%) was differentiated by four Pup1-specific markers. Association mapping identified seven notable markers (RM259, RM297, RM30, RM6966, RM242, RM184, and PAP1) and six potential genotypes (IC459373, Chakhao Aumbi, AC100219, AC100062, Sekri, and Kumbhi Phou), which will be helpful in the marker-assisted breeding to improve rice for P-deprived condition. In addition, total root surface area becomes a single major trait that helps in P uptake under deficit P up to 33% than mycorrhizal colonization. Further, the phenotypic analysis of the morphometric and geometric trait variations and their interactions provides excellent potential for selecting donors for improving P-use efficiency. The identified potential candidate genes and markers offered new insights into our understanding of the molecular and physiological mechanisms driving PUE and improving grain yield under low-P conditions.

Improvement of Phosphorus Use Efficiency in Rice by Adopting Image-Based Phenotyping and Tolerant Indices.

Phosphorus is one of the second most important nutrients for plant growth and development, and its importance has been realised from its role in various chains of reactions leading to better crop dynamics accompanied by optimum yield. However, the injudicious use of phosphorus (P) and non-renewability across the globe severely limit the agricultural production of crops, such as rice. The development of P-efficient cultivar can be achieved by screening genotypes either by destructive or non-destructive approaches. Exploring image-based phenotyping (shoot and root) and tolerant indices in conjunction under low P conditions was the first report, the epicentre of this study. Eighteen genotypes were selected for hydroponic study from the soil-based screening of 68 genotypes to identify the traits through non-destructive (geometric traits by imaging) and destructive (morphology and physiology) techniques. Geometric traits such as minimum enclosing circle, convex hull, and calliper length show promising responses, in addition to morphological and physiological traits. In 28-day-old seedlings, leaves positioned from third to fifth played a crucial role in P mobilisation to different plant parts and maintained plant architecture under P deficient conditions. Besides, a reduction in leaf angle adjustment due to a decline in leaf biomass was observed. Concomitantly, these geometric traits facilitate the evaluation of low P-tolerant rice cultivars at an earlier stage, accompanying several stress indices. Out of which, Mean Productivity Index, Mean Relative Performance, and Relative Efficiency index utilising image-based traits displayed better responses in identifying tolerant genotypes under low P conditions. This study signifies the importance of image-based phenotyping techniques to identify potential donors and improve P use efficiency in modern rice breeding programs.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Trait variations and expression profiling of OsPHT1 gene family at the early growth-stages under phosphorus-limited conditions.

To better understand the early response of genotypes to limited-phosphorus (P) conditions and the role of the phosphate transporter OsPHT1 gene family in the presence of PSTOL1, it is essential to characterize the level of tolerance in rice under limited-P conditions. In the present experiment, six rice genotypes were studied in three-way interactions [genotype (G) × phosphorus (P) × duration (D)] by comparing them at two instances (14 d and 28 d) under seven different concentrations of P (0.5‒10.0 ppm) in a hydroponic system. Trait differences and interactions of these traits were clearly distinguished among the various P rates. However, aboveground trait expression registered increased growth from 6.0 to 10.0 ppm of P. The major root-attributed traits in 0.5 ppm of P are significantly increased vis-à-vis 10 ppm of P. Analysis of variance displayed a significant difference between the genotypes for PSTOL1 and PHT1 expression. In low P, maximum root length with a shoot and root dry weight was observed in a new indigenous accession, IC459373, with higher expression of PSTOL1 than in Dular and IR64-Pup1 in 0.5 ppm of P at 14 d. Among the 13 PHT1 genes, OsPT1, OsPT2, OsPT6, and OsPT13 showed significant upregulation in IC459373, Dular, and IR64-Pup1. These results indicated that studying the expression levels of the PSTOL1 and PHT1 gene family at the early growth stages would be helpful in identifying superior donors to improve low-P tolerance and P-use efficiency in rice breeding programs.

Non-destructive phenotyping for early seedling vigor in direct-seeded rice.

BACKGROUND: Early seedling vigor is an essential trait of direct-seeded rice. It helps the seedlings to compete with weeds for water and nutrient availability, and contributes to better seedling establishment during the initial phase of crop growth. Seedling vigor is a complex trait, and phenotyping by a destructive method limits the improvement of this trait through traditional breeding. Hence, a non-invasive, rapid, and precise image-based phenotyping technique is developed to increase the possibility to improve early seedling vigor through breeding in rice and other field crops. RESULTS: To establish and assess the methodology using free-source software, early seedling vigor was estimated from images captured with a digital SLR camera in a non-destructive way. Here, the legitimacy and strength of the method have been proved through screening seven diverse rice cultivars varying for early seedling vigor. In the regression analysis, whole-plant area (WPA) estimated by destructive-flatbed scanner (WPAs) and non-destructive imaging (WPAi) approaches was strongly related (R2 > 83%) and suggested that WPAi can be adapted in place of destructive methods to estimate seedling vigor. In addition, this study has identified a set of new geometric traits (convex hull and top view area) for screening breeding lines for early seedling vigor in rice, which decreased the time by 80% and halved the cost of labor in data observation. CONCLUSIONS: The method demonstrated here is affordable and easy to establish as a phenotypic platform. It is suitable for most glasshouses/net houses for characterizing genotypes to understand the plasticity of shoots under a given environment at the seedling stage. The methodology explained in this experiment has been proven to be practical and suggested as a technique for researchers involved in direct-seeded rice. Consequently, it will help in the simultaneous screening of genotypes in large numbers, the identification of donors, and in gaining information on the genetic basis of the trait to design a breeding program for direct-seeded rice.

Understanding interaction effect of arbuscular mycorrhizal fungi in rice under elevated carbon dioxide conditions.

Arbuscular mycorrhizal fungi (AMF), particularly the Glomerales group, play a paramount role in plant nutrient uptake, and abiotic and biotic stress management in rice, but recent evidence revealed that elevated CO2 concentration considerably reduces the Glomerales group in soil. In view of this, the present study was initiated to understand the interaction effect of native Glomerales species application in rice plants (cv. Naveen) under elevated CO2 concentrations (400 ± 10, 550 ± 20, and 700 ± 20 ppm) in open-top chambers. Three different modes of application of the AMF inoculum were evaluated, of which, combined application of AMF at the seedling production and transplanting stages showed increased AMF colonization, which significantly improved grain yield by 25.08% and also increased uptake of phosphorus by 18.2% and nitrogen by 49.5%, as observed at 700-ppm CO2 concentration. Organic acids secretion in rice root increased in AMF-inoculated plants exposed to 700-ppm CO2 concentration. To understand the overall effect of CO2 elevation on AMF interaction with the rice plant, principal component and partial least square regression analysis were performed, which found both positive and negative responses under elevated CO2 concentration.

Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice.

Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.

Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice.

In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.

Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches.

BACKGROUND: Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. RESULTS: Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation. CONCLUSION: Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers.

Early seedling vigor (ESV) is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS). It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA) and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR) markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC) value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM) and mixed linear model (MLM) approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

Incorporation of Bacterial Blight Resistance Genes Into Lowland Rice Cultivar Through Marker-Assisted Backcross Breeding.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in many rice growing countries. Pyramided lines carrying two BB resistance gene combinations (Xa21+xa13 and Xa21+xa5) were developed in a lowland cultivar Jalmagna background through backcross breeding by integrating molecular markers. In each backcross generation, markers closely linked to the disease resistance genes were used to select plants possessing the target genes. Background selection was continued in those plants carrying resistant genes until BC(3) generation. Plants having the maximum contribution from the recurrent parent genome were selected in each generation and hybridized with the recipient parent. The BB-pyramided line having the maximum recipient parent genome recovery of 95% was selected among BC3F1 plants and selfed to isolate homozygous BC(3)F(2) plants with different combinations of BB resistance genes. Twenty pyramided lines with two resistance gene combinations exhibited high levels of tolerance against the BB pathogen. In order to confirm the resistance, the pyramided lines were inoculated with different X. oryzae pv. oryzae strains of Odisha for bioassay. The genotypes with combination of two BB resistance genes conferred high levels of resistance to the predominant X. oryzae pv. oryzae isolates prevalent in the region. The pyramided lines showed similarity with the recipient parent with respect to major agro-morphologic traits.

Comparison of Sub1 markers and their combinations for submergence tolerance and analysis of adaptation strategies of rice in rainfed lowland ecology.

Ninety lowland rice cultivars of the eastern region of India were collected and screened for submergence and water logging tolerance and further used for validating the efficiency of molecular markers and their combinations for submergence tolerance. Submergence tolerance and elongation ability of the tested genotypes were measured in screening tanks along with tolerant and susceptible checks. The genotypes FR13A, Khoda, CR Dhan 300, Savitri Sub1, IR64 Sub1, IC-568009 and IC-568842 exhibited high submergence tolerance may be used as donor in the breeding program. Landrace 'Khoda' showed tolerance to submergence with moderate elongation ability for adaption. Boitalpakhia, Gayatri, Atiranga, Aghonibora, Chakaakhi, Moti, IC-567993 and IC-568921 possessed both characters of moderate elongation ability and moderate tolerance to submergence. Both of these traits are required for lowland varieties of eastern India to survive under flash flood and accumulated stagnant water conditions. RM8300, Sub1A203, AEX, Sub1BC2 and Sub1C173 were employed for molecular screening to identify the submergence-tolerant genotypes. Sub1A203 was capable of differentiating the tolerant and susceptible genotypes into groups. RM8300 and Sub1BC2 could also differentiate the genotypes with inclusion of some susceptible genotypes. The AEX and Sub1C173 marker could not show discrimination among the genotypes with respect to the traits. Using Sub1A203+Sub1BC2 was better amongst the combinations studied. The results of the study indicated a trend toward a negative association of Sub1BC2 with submergence tolerance while AEX and Sub1C marker did not show any significant association. The donors identified can be useful as parental lines while the molecular markers can be used for marker-assisted breeding work.