Indica Genotypes Research Articles

Phenotypic, Physiological, and Gene Expression Analysis for Nitrogen and Phosphorus Use Efficienies in Three Popular Genotypes of Rice (Oryza sativa Indica).

Crop nitrogen (N) and phosphorus (P) use efficiencies (NUE/PUE) are important to minimize wastage and nutrient pollution, but no improved crop for both is currently available. We addressed them together in rice, in the view of its high consumption of NPK fertilizers. We analyzed 46 morphophysiological parameters for the N/P response in three popular indica genotypes, namely, BPT 5204, Panvel 1, and CR Dhan 301 at low, medium, and normal N/P doses. They include 18 vegetative, 15 physiological, and 13 reproductive parameters. The segregation of significantly N/P-responsive parameters correlating with NUE/PUE revealed 21 NUE, 22 PUE, and 12 common parameters. Feature selection analyses revealed the common high-ranking parameters including the photosynthetic rate at the reproductive stage, tiller number, root-shoot ratio, culm thickness, and flag leaf width. The venn selection using the reported NUE/PUE-related candidate genes in rice revealed five genes in common for both, namely OsIAA3, OsEXPA10, OsCYP75B4, OsSultr3;4, and OsFER2, which were associated with three of the common traits for NUE/PUE. Their expression studies using qRT-PCR revealed the opposite regulation in contrasting genotypes for OsSultr3;4 and OsEXPA10 in N-response and for OsFER2 in P-response, indicating their role in contrasting N/P use efficiencies. Overall, CR Dhan 301 has the highest NUE and PUE followed by Panvel 1 and BPT5204 among the studied genotypes.

Turbidity reduction efficacies of seed kernels of Mango (Mangifera indica) genotypes in Uganda

Alum and ferric salts as traditional chemical coagulants for turbidity removal in water and wastewater are expensive, and have known harmful effects. Thus, attempts to replace the chemical coagulants with safe and effective natural solutions are increasingly being made in terms of research studies to investigate the coagulation efficacies of various plants one of which is Mango (Mangifera indica). It is worth noting that M. indica has various genotypes of different origins across the world. In this study, eight (8) common M. indica genotypes in Uganda were identified, protein contents of their seed kernels determined, and coagulating efficacies investigated. Coagulation solution of each selected genotype was obtained by dissolving 5 g powder of the selected Mango seed kernel sample in 100 mL of distilled water. Next, 5 mL of this coagulant (or stock) solution was used to treat 200 mL of turbid water with turbidity ranging from 15 to 120 NTU. Using 0.01 M hydrochloric acid as an extraction solvent, protein contents of selected genotypes including Apple mango, Kate, Kent, Bire, Doodo red, Takataka, Kagoogwa, and Tommy Atkins were 38.02 %, 30.66 %, 15.94 %, 22.11 %, 21.50 %, 16.98 %, 16.36 %, and 17.87 %, respectively. Efficacies of coagulant from Apple mango, Kate, Kent, Bire, Doodo red, Takataka, Kagoogwa, and Tommy Atkins seed kernel samples were 92.2, 89.3, 66.0, 78.7, 76.9, 71.1, 68.9, and 73.1 %, respectively. Apple mango was the best performing genotype as a coagulant and this was followed by Kate. Coagulation efficacy was generally found to increase with increasing turbidity and/or coagulant's concentration. For instance, Apple Mango coagulant removed 16.7 %, 50.3 %, and 92.2 % of initial turbidity 15, 65 and 120 NTU, respectively. Kent removed 57.5, 66, and 69 % of initial turbidity 120 NTU using 5, 20, and 30 mL of stock solution, respectively. This study demonstrated the influence of the choice of a plant genotype on coagulation efficacy.

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice.

Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hapL are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hapH are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.

Transcriptional regulation of OsWRKY genes in response to individual and overlapped challenges of Magnaporthe oryzae and drought in indica genotypes of rice

In rainfed rice cultivation, severe blast (Magnaporthe oryzae) infection is frequently observed following intermittent drought. We simulated the natural rainfed rice field and explored the complex transcriptional regulations behind enhanced susceptibility of rice towards blast disease. We identified eight new OsWRKY genes in the indica subspecies of rice using the updated v5.0 PlantTFDB and GRAMENE making it altogether 109 OsWRKY genes. Distribution of the OsWRKY genes in the 12 chromosomes of indica rice was uneven. Where, chromosome 1 houses maximum number of genes but chromosome 5 has the highest gene density. Motif analysis depicted presence of a new motif i.e., an autophagy protein 16 (ATG16) associated to group IIa of the OsWRKY genes. We selected twenty biotic stress-responsive OsWRKY genes to check their transcript accumulation pattern in individual and overlapping challenges of blast and drought in three indica rice cultivars viz., blast susceptible HR-12, and blast resistant Tetep (Pi54) and C101A51 (Pi2). Transcripts of most OsWRKY genes in the resistant cultivars accumulated early (6 h) and at higher levels compared to the susceptible check. Interestingly, a significant decrease in transcript accumulation of most of the blast responsive OsWRKY genes was observed in all the three cultivars when exposed to the overlapping challenges. Additionally, a significant reduction in biosynthesis of both the defense enzymes PAL and PO in blast and drought overlapped condition in the resistant cultivars indicated partial breakdown of resistance due to intermittent drought. To conclude, the present study has contributed to understanding of the relationship between the expression pattern of 20 biotic stress responsive OsWRKY genes in indica rice grown in rainfed condition coupled with intermittent drought and blast susceptibility.

Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes.

With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited. In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation. The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.

Salinity Tolerance Characteristics of Marginally Located Rice Varieties in the Northernmost Rice-Growing Area in Europe

Detailed experiments were performed to investigate the effects of the marginal cultivation of temperate japonica rice on salinity tolerance in different developmental stages and to detect new genetic resources for further research and breeding projects. Eight rice varieties were screened for salinity tolerance in a greenhouse at two developmental stages. During seedling-stage screening, stress was induced with a 12 dS m−1 NaCl solution. For reproductive-stage analysis, we applied continuous salinity stress (8.39 dS m−1 of soil extract at 25 °C (EC25)). We compared the marginal rice genotypes (japonica_1) to widely grown controls (those being Mediterranean japonica genotypes, referred as the japonica_2 group, which also included one indica genotype). Without stress, marginally cultivated genotypes had significantly higher potassium storage capacity (406 µmol g−1) in flag leaves than did japonica_2 (347) or indica (267). Moreover, the seeds contained twice as much sodium (5.27) as did the others (2.19 and 2.00). Based on root-to-grain allocation, we identified two sodium excluders (‘Dular’ and ‘Dáma’) and six includers under constant salinity stress. Among the includers, we found that ‘M488’ had extremely high sodium concentration in both the flag leaves (250.54 µmol g−1) and the grains (13.57 µmol g−1). Rice varieties bred for the edge of their habitat show special physiological patterns. The differences are mainly manifested as lower levels of antioxidant pigments, higher amounts of potassium in flag leaves, and higher sodium levels in grains under normal conditions. With the onset of stress, higher tillering ability, enhanced antioxidant pigment synthesis, and rapid potassium translocation from the root are the key mechanisms which help the plants to avoid serious damage caused by salinity.

Callus induction and regeneration in selected indica genotypes of rice (Oryza sativa L.)

Plumule of four rice varieties viz., TRY 2, TRY 3, ADT 53 and CO 52 were studied for callus induction and regeneration using different concentrations and combinations of plant growth regulators in MS medium. The combination of MS medium with 2,4-D (2.0 mg/l) + Kn (0.5 mg/l) showed maximum callus induction frequency in all four varieties ranged from 93.33 to 76.67 compared to other growth regulator combinations. Upon subculture of the callus, MS medium with NAA (0.5 mg/l) + BAP (2.0 mg/l) was found to be superior for greening of calli and regeneration of shoots, followed by MS + NAA (0.5 mg/l) + BAP (1.5 mg/l). Among the four varieties TRY 2 and TRY 3 showed positive responses for regeneration. Key words: Rice, In vitro culture, Plumule culture, Callus induction and regeneration.

Yield-enhancing SPIKE allele from the aus-subtype indica rice and its allele specific codominant marker

Improving spikelet number without limiting panicle number is an important strategy to increase rice productivity. In this study, a spikelet number enhancing SPIKE-allele was identified from the aus subtype indica rice, cv. Bhutmuri, which has an identical japonica like corresponding sequence including a retrotransposon sequence, usually absent in indica genotypes, like IR64. An allele-specific singletube PCR-based codominant marker targeting an A/G single-nucleotide polymorphism (SNP) at the 3'UTR was identified for easier genotyping. The yield enhancing ability of the Bhutmuri-SPIKE allele carrying RILs and NILs over IR64-SPIKE allele carrying alleles was due to increased number of filled grains/panicle. More than three times higher abundance of SPIKE transcripts was observed in Bhutmuri and NILs carrying this allele compared with IR64 and its allele carrying NILs. Higher rate of photosynthesis at more than 900 μmolm-2s-1 light intensity and more than six small vascular bundles between the two large vascular bundles in the flag leaves of Bhutmuri and its allele carrying NILs were also observed. The identified SPIKE allele and the marker associated with it will be useful for increasing the productivity of rice by marker-assisted breeding.

Decreased night temperature affects development and grain yield only in cold-susceptible rice (

It is largely known that low temperature stress can affect rice (Oryza sativa L.) development and yield. However, most studies have focussed on unique and uninterrupted cold treatment, which is not representative of cold conditions for early sowing in temperate and subtropical areas where cold nights are followed by warm days during early vegetative stages. In order to elucidate whether rice plants could recover from the damages caused by repetitive cold nights, we submitted a cold-tolerant (CT) and a cold-sensitive (CS) indica genotype to 28 cold nights (10°C) followed by warm days (26°C) and analysed the developmental and productivity traits of plants cultivated in greenhouse and field conditions. While CT plants were able to recover from cold damage without significant development and seed production penalties, CS plants were affected, presenting lower results in plant height, tiller number, number of seeds per plant, % of full seeds per plant, grain length and area, weight of 1000 full grains, and grain weight per plant, with a grain yield reduction of 82% and 30% when cultivated in greenhouse and field conditions, respectively. Such data on sowing period, night temperatures and the cold response of the rice cultivar used are important for the producer to consider.

Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw

BackgroundThe conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw.ResultsWe assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L.ConclusionsDespite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.

Bridging old and new: diversity and evaluation of high iron-associated stress response of rice cultivated in West Africa.

Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l-1 FeSO4·7H2O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O. sativa-japonica (7%), O. sativa-indica Group 1 (45%), and O. sativa-indica Group 2 (25%). Severe versus mild stress in the field was associated with a reduced SPAD value (12%), biomass (56%), and grain yield (57%), with leaf bronzing explaining 30% and 21% of the variation for biomass and grain yield, respectively. Association mapping using 175 indica genotypes identified 23 significant single nucleotide polymorphism (SNP) markers that mapped to 14 genomic regions. Genome-wide association study (GWAS) signals associated with leaf bronzing, a routinely used indicator of HIA stress, differed in hydroponic compared with field conditions. Contrastingly, six significant SNPs on chromosomes 8 and 9 were associated with the SPAD value under HIA stress in both field and hydroponic experiments, and a candidate potassium transporter gene mapped under the peak on chromosome 8. This study helps define criteria for assessing rice performance under HIA environments.

Identification of differentially expressed genes under heat stress conditions in rice (Oryza sativa L.).

Rice production in recent years is highly affected by rapidly increasing temperatures in the tropical and sub-tropical countries, which threatens the sustainable production in near future. Hence, understanding the heat tolerance mechanism and evolving tolerant varieties is an immense need in the staple crop rice. An experiment has been conducted to identify differentially expressed genes in rice under heat stress conditions by employing a diverse set of 32 rice genotypes that includes reported heat tolerant genotypes Nagina 22 (N22) and Dular. Screening of the genotypes at field conditions during Summer-2018 for reproductive stage heat tolerance (wherein the mean minimum (29.8°C) and maximum (38.4°C) temperatures surpassed optimum temperatures (25°C night/30°Cday) required for rice flowering and grain filling stages) and lab conditions employing thermal induction response (TIR) technique to know the genotype's acquired thermal tolerance revealed that the genotype FR13A (indica landrace) showed highest overall performance for multitude of traits viz., 95.29% of spikelet fertility (SF-%) at field level and 100% seedling survival percentage (SSP) at sub-lethal temperatures under laboratory conditions. The relative performance (under TIR) across all the three traits viz., relative shoot length (RSL) (4.91), relative root length (RRL) (equal to the control) and relative seedling dry weight (RSDW) (6.94) over control is high when compared to the other genotypes under study. However, the highly susceptible genotype PUSA1121 performed with 43.59 of SF%, 73.33% SSP, -43.59 of RSL, -36.02 of RRL over control. Hence, these contrasting genotypes were used for molecular analysis for identification of differentially expressed genes by employing 29 heat related gene specific primers. Five genes viz., OsGSK1, TT1, HSP70-OsEnS-45, OsHSP74.8 and OsHSP70 have shown differential expression between the two genotypes. Hence, the genotype FR13A, an 'indica' genotype, can be utilized in heat tolerance breeding programmes as donor parent in addition to the reported 'aus' genotypes, N22 and Dular. To our knowledge this is the first indica genotype identified for heat tolerance. The HSP70s, TT1 and OsGSK1 that proved with differential expression might be used for identification of gene specific InDels and thereby to develop functional markers that help in the marker assisted introgression breeding to develop heat tolerant varieties that can sustain production under dramatically changing climatic conditions.

Identification of QTLS for NH4+ and NO3- use efficiency under water stress and non-stress conditions and expression analysis of glutamine synthetase and nitrate reductase in rice (Oryza Sativa L.)

Nitrogen (N) is one of the most critical inputs and the current average nitrogen use efficiency (NUE) in the rice field is approximately 33%, poorest among cereals. Predominant form of N in aerobic soils is nitrate (NO3-) while ammonium (NH4+) exists in anaerobic soils. Development of cultivars with improved NH4+ or NO3- use efficiency by harnessing inherent significant variability for NUE can be an important approach. Considering these facts, the present study was established with one hundred twenty two and selected thirty two recombinant inbred lines (RILs) of two indica genotypes, Danteshwari × Dagad deshi under three nitrogen forms and three environments. The trend analysis of NH4+-N and NO3--N dynamics revealed that NH4+-N concentration persisted more under anaerobic condition and NO3--N concentration under aerobic conditions. Three way-ANOVA showed high level of significance for variance components (G, N, E) and their interactions effects (GXN, GXE, NXE, EXNXG) for yield and NUE and their component traits. Mean performance of genotypes depicted higher values for agronomically important traits i.e. yield and NUE under NH4+ as compared to NO3--N and N0. The phenotypic and genotypic data was statistically analyzed for QTLs identification for yield and NUE traits. A total of 58 QTLs conferring the corresponding five traits were detected under three N forms and two environments. We also investigated the different members of AMT (Ammonium transporters), NRT (Nitrate transporters), GS (Glutamine Synthetase) and GOGAT (Glutamate Synthase) genes, involved in NUE and analyzed the expression pattern of each gene using gene-specific primer in young rice seedlings. Collectively, OsGln1;1, OsGln1;2, OsGln1;3, OsGln2, OsGlt1 and OsGlt2 manifested different and reciprocal responses to nitrate and ammonium supply. The activity of enzymes NR, NiR, GS and GOGAT was significantly affected by NH4+and NO3- treatment. These results assist us to identify NH4+ and NO3- responsive cultivars which could be used for cultivation and/or used as parent’s in future breeding program to produce better nitrogen use efficiency varieties under water stress and non-stress conditions.

Genetic potential of rice under alternate-wetting-and-drying irrigation management for barnyardgrass (Echinochloa crus-galli) suppression and grain yield production

AbstractBarnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] is one of the most troublesome and competitive weed species in rice (Oryza sativa L.) grown under conventional flood (FLD) irrigation and is expected to be similarly damaging under alternate-wetting-and-drying (AWD) irrigation. Several indica rice genotypes have been shown to suppress E. crus-galli under FLD management, but very little is known about the nature and potential of weed suppression using AWD irrigation. In this 3-yr field study, we evaluated seven diverse rice genotypes for their weed suppression and grain yield potential under FLD and AWD irrigation. The E. crus-galli dry biomass at midseason was 11% less under AWD compared with FLD. Overall, plots of an indica variety and a hybrid resulted in less E. crus-galli dry biomass under AWD compared with FLD. Grain yield in weed-free AWD plots averaged 12% less than in weed-free FLD plots. Grain yield of the tropical japonica (TRJ) type, ‘Bengal’, was 32% lower under AWD than FLD, whereas grain yields of the two indica genotypes, PI 312777 and ‘Rondo’, and a hybrid were similar in both irrigation systems. Grain yield reduction in E. crus-galli–infested AWD plots averaged greater than 90%. Thus, E. crus-galli greatly reduced the grain yield of all rice genotypes tested in both FLD and AWD systems in this study. Grain yield of the indica and hybrid genotypes was relatively less affected by the AWD treatments compared with the TRJ genotypes, particularly with Bengal, suggesting that the weed-suppressive genotypes, PI 312777 and Rondo, would be better suited to AWD irrigation systems and for inclusion in weed-suppression rice-breeding programs in the southern United States.

Incorporating genome-wide association into eco-physiological simulation to identify markers for improving rice yields.

We explored the use of the eco-physiological crop model GECROS to identify markers for improved rice yield under well-watered (control) and water deficit conditions. Eight model parameters were measured from the control in one season for 267 indica genotypes. The model accounted for 58% of yield variation among genotypes under control and 40% under water deficit conditions. Using 213 randomly selected genotypes as the training set, 90 single nucleotide polymorphism (SNP) loci were identified using a genome-wide association study (GWAS), explaining 42-77% of crop model parameter variation. SNP-based parameter values estimated from the additive loci effects were fed into the model. For the training set, the SNP-based model accounted for 37% (control) and 29% (water deficit) of yield variation, less than the 78% explained by a statistical genomic prediction (GP) model for the control treatment. Both models failed in predicting yields of the 54 testing genotypes. However, compared with the GP model, the SNP-based crop model was advantageous when simulating yields under either control or water stress conditions in an independent season. Crop model sensitivity analysis ranked the SNP loci for their relative importance in accounting for yield variation, and the rank differed greatly between control and water deficit environments. Crop models have the potential to use single-environment information for predicting phenotypes under different environments.

Phenotyping for Nitrogen Use Efficiency: Rice Genotypes Differ in N-Responsive Germination, Oxygen Consumption, Seed Urease Activities, Root Growth, Crop Duration, and Yield at Low N

The biological improvement of fertilizer nitrogen use efficiency (NUE) is hampered by the poor characterization of the phenotype and genotype for crop N response and NUE. In an attempt to identify phenotypic traits for N-response and NUE in the earliest stages of plant growth, we analyzed the N-responsive germination, respiration, urease activities, and root/shoot growth of 21 Indica genotypes of rice (Oryza sativa var. indica). We found that N delays germination from 0 to 12 h in a genotype-dependent and source-dependent manner, especially with urea and nitrate. We identified contrasting groups of fast germinating genotypes such as Aditya, Nidhi, and Swarnadhan, which were also least delayed by N and slow germinating genotypes such as Panvel 1, Triguna, and Vikramarya, which were also most delayed by N. Oxygen uptake measurements in the seeds of contrasting genotypes revealed that they were affected by N source in accordance with germination rates, especially with urea. Germinating seeds were found to have endogenous urease activity, indicating the need to explore genotypic differences in the effective urea uptake and metabolism, which remain unexplored so far. Urea was found to significantly inhibit early root growth in all genotypes but not shoot growth. Field evaluation of 15 of the above genotypes clearly showed that germination rates, crop duration, and yield are linked to NUE. Slow germinating genotypes had longer crop duration and higher yield even at lower N, indicating their higher NUE, relative to fast germinating or short duration genotypes. Moreover, longer duration genotypes suffered lesser yield losses at reduced N levels as compared to short duration genotypes, which is also a measure of their NUE. Together, these results indicate the potential of germination rates, crop duration, urea utilization and its effect on root growth in the development of novel phenotypic traits for screening genotypes and crop improvement for NUE, at least in rice.

Identification of splice variant of OsGBF1 in Oryza sativa ssp. indica genotypes under salinity stress

G-box-binding factors are plant transcription factors, involved in a wide range of biological processes including abiotic stress responses. In this study, we analyzed the expression of OsGBF1 during salt stress in two contrasting Oryza sativa spp. indica genotypes, Rasi and Tellahamsa. Two-day-old seedlings were exposed to NaCl stress under two different conditions. One set was exposed to 100mM NaCl before transferring to 250mM (induction stress), while another set was transferred directly to 250mM (shock stress). During early induction stress, OsGBF1 was up-regulated in Rasi when compared to Tellahamsa. We cloned full-length OsGBF1 from these two genotypes, and analyzed the sequences. Our analysis indicated the presence of transcript variants, which are designated as OsGBF1a and 1b. OsGBF1b variant retained introns, which lead to the generation of premature termination codon. OsGBF1b transcript levels were not significantly different at 12-h of induction stress in Tellahamsa and Rasi. At 24-h of shock stress, OsGBF1b was up-regulated in both genotypes and the transcript was more in Rasi. Since, OsGBF1a and 1b are predicted to be splice variants, we examined expression pattern of OsSKIP, a splicing factor and component of the spliceosome. In induction stress, OsSKIP was up-regulated at 12- and 24-h in Rasi when compared to Tellahamsa. On the contrary, at 24-h shock stress, OsSKIP was down-regulated in Rasi when compared to Tellahamsa. It is possible that OsSKIP expression was increased in Rasi during induction stress for accurate splicing that could aid in tolerance. This is the first report on OsGBF1 splice variant and the variant could have specific functions linked to stress tolerance in rice.

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs.

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.

Resistance to Multiple Temperate and Tropical Stem and Sheath Diseases of Rice

Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH. Two populations of advanced breeding germplasm, one with 316 tropical japonica and the other with 325 indica genotypes, were evaluated in field and greenhouse trials for resistance to the diseases. Phenotypic means for field and greenhouse disease resistance, adjusted by FT and PH, were analyzed for associations with 29,000 single nucleotide polymorphisms (SNPs) in tropical japonica and 50,000 SNPs in indica. A total of 29 QTL were found for resistance that were not associated with FT or PH. Multilocus models with selected resistance-associated SNPs were fitted for each disease to estimate their effects on the other diseases. A QTL on chromosome 9 accounted for more than 15% of the phenotypic variance for the three diseases. When resistance-associated SNPs at this locus from both the tropical japonica and indica populations were incorporated into the model, resistance was improved for all three diseases with little impact on FT and PH.

Identification of QTLs for nitrate and ammonium use efficiency under direct seeded condition and differential expression of genes involved in their absorption and metabolic pathway

Considering water and labor crises, area under direct seeded rice cultivation has increased. With the direct seeding during the early seedling stage the rice crop is very sensitive to water stress and nutrient deficiencies. The availability of nutrients is highly influenced by water status. Over the years, we have critically observed that under direct seeded condition at seedling stage if drought occurs the plants suffer more because of nutrient deficiency rather than water deficiency. The continued plant growth and development under changed rhizosphere depends heavily on availability of nitrogen and other nutrients (P, Fe and S) and the ability of the root system to absorb these nutrients efficiently and use in metabolism under their changed forms. Rice has evolved and adopted for efficient utilization of ammonical form of nitrogen, while nitrate from is less efficiently used at least during seedling and early vegetative phases. Most of the genotypes (except a few) we evaluated exhibited extremely low level of Nitrate transporter and Nitrate Reductase activities which are key factor and enzyme in absorption and utilization of nitrate form of nitrogen. Therefore, the identification of lines with greater nitrate use efficiency, mainly because of more efficient High Affinity Transporters, increased expression of nitrate reductase and nitrite reductase along with ammonium transporters and GS and GOGAT will certainly have key role in N efficiency of rice genotypes particularly under water stress conditions. In study 1, one hundred twenty two and selected thirty two recombinant inbred lines (RILs) of two indica genotypes, Danteshwari × Dagaddeshi were evaluated under three nitrogen forms and three environments (Irrigated, Rainfed and Terminal stage drought) along with root studies under soil filled glass rhizotrons at IGKV, Raipur, for generation of phenotypic data. The genotypic data of 162 SSR and HvSSR based markers were developed and used for identifying QTLs for agronomically complex trait i.e. NUE. The phenotypic and genotypic data was statistically analyzed for QTLs identification for yield & NUE traits using QTL Cartalographer. QTLs for nitrate and ammonical use efficiency varied significantly. A presence of QTL clusters between HvSSR 1–87(38.9cM) to HvSSR 1–89 (40.6cM) on chromosome 6, RM 449 (81.9cM) to RM5 (9.4cM) on chromosome 5, HvSSR 9–25 (14.6cM) to HvSSR 9–27 (15.5cM) on chromosome 9 and RM 434 (57.7cM) to RM 410 (64.4cM) on chromosome 5 signifies important genomic regions associated with evaluated traits under different conditions and will be useful in marker assisted breeding for NUE in rice. In study 2, we investigated the different members AMT (Ammonium transporters), NRT (Nitrate transporters), GS (Glutamine Synthetase) & GOGAT (Glutamate Synthase) genes, involved in NUE and analyzed the expression pattern of each gene using gene-specific primer in young rice seedlings by quantitative real time PCR, revealing a distinct expression pattern of these genes. Collectively, OsGln1;1, OsGln1;2, OsGln1;3, OsGln2, OsGlt1 and OsGlt2 manifested different and reciprocal responses to nitrate and ammonium supply. The relationship of these genes/enzymes and its interaction with water stress will be presented during the conference.