Genetic enhancement of reproductive stage drought tolerance in RPHR-1005R and derivative rice hybrids through marker-assisted backcross breeding in rice (Oryza sativa L.).

BACKGROUND: Drought stress is considered as one of the major production constraints in rice. RPHR-1005R is a restorer line (R-Line) with a popular, medium-slender grain type, and is the male parent of the popular Indian rice hybrid, DRR-H3. However, both the hybrid and its restorer are highly vulnerable to the drought stress, which limits the adoption of the hybrid. Therefore, the selection of the restorer line RPHR-1005R has been made with the objective of enhancing drought tolerance. METHODS AND RESULTS: In this study, we have introgressed a major QTL for grain yield under drought (qDTY 1.1) from Nagina22 through a marker-assisted backcross breeding (MABB) strategy. PCR based SSR markers linked to grain yield under drought (qDTY1.1 - RM431, RM11943), fertility restorer genes (Rf3-DRRM-Rf3-10, Rf4-RM6100) and wide compatibility (S5n allele) were deployed for foreground selection. At BC2F1, a single plant (RPHR6339-4-16-14) with target QTL in heterozygous condition and with the highest recurrent parent genome recovery (85.41%) and phenotypically like RPHR-1005R was identified and selfed to generate BC2F2. Fifty-eight homozygous lines were advanced to BC2F4 and six promising restorer lines and a hybrid combination (APMS6A/RPHR6339-4-16-14-3) were identified. CONCLUSIONS: In summary, the six improved restorer lines could be employed for developing heterotic hybrids possessing reproductive stage drought tolerance. The hybrid combination (APMS6A/RPHR6339-4-16-14-3) was estimated to ensure stable yields in drought-prone irrigated lowlands as well as in directly seeded aerobic and upland areas of India.

Dynamics of starch formation and gene expression during grain filling and its possible influence on grain quality.

In rice, grain filling is a crucial stage where asynchronous filling of the pollinated spikelet's of the panicle occurs. It can influence both grain quality and yield. In rice grain, starch is the dominant component and contains amylose and amylopectin. Amylose content is the chief cooking quality parameter, however, rice varieties having similar amylose content varied in other parameters. Hence, in this study, a set of varieties varying in yield (04) and another set (12) of varieties that are similar in amylose content with variation in gel consistency and alkali spreading value were used. Panicles were collected at various intervals and analysed for individual grain weight and quantities of amylose and amylopectin. Gas exchange parameters were measured in varieties varying in yield. Upper branches of the panicles were collected from rice varieties having similar amylose content and were subjected to gene expression analysis with fourteen gene specific primers of starch synthesis. Results indicate that grain filling was initiated simultaneously in multiple branches. Amylose and amylopectin quantities increased with the increase in individual grain weight. However, the pattern of regression lines of amylose and amylopectin percentages with increase in individual grain weight varied among the varieties. Gas exchange parameters like photosynthetic rate, stomatal conductance, intercellular CO2 and transpiration rate decreased with the increase in grain filling period in both good and poor yielding varieties. However, they decreased more in poor yielders. Expression of fourteen genes varied among the varieties and absence of SBE2b can be responsible for medium or soft gel consistency.

Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants.

Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.

Improvement of bacterial blight resistance of the high yielding, fine-grain, rice variety, Gangavati sona through marker-assisted backcross breeding.

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB.

Native bio-control agents from the rice fields of Telangana, India: characterization and unveiling the potential against stem rot and false smut diseases of rice.

The stem rot caused by Sclerotium hydrophilum and false smut caused by Ustilaginoidea virens are two of the major production constraints in rice cultivation in India and other countries. Stem rot and false smut can be effectively controlled with synthetic fungicides. However, the indiscriminate use of chemical fungicides may cause development of resistance among the pathogens. In addition to this, synthetic fungicides also exhibit harmful impacts on the environment. Exploiting microbe-based alternatives for managing plant diseases diminishes public concerns about the ill effects of pesticide usage in crops. In this regard, the present study was designed to investigate the potential of native microbial biocontrol agents (BCAs) from rice rhizosphere for the sustainable management of stem rot and false smut diseases in rice. Potential BCAs and pathogens were identified and characterized through morphological, biochemical, and sanger sequencing techniques. Bio-efficacy tests of potential BCAs against stem rot and false smut diseases on rice under glasshouse conditions indicated higher seed vigour index of the treated seeds, significant improvement in the growth of the seedling, increased dry weight, reduction in percentage disease index viz., 70.03% (stem rot) and 69.24% (false smut) over the control plants. Phytohormones indole acetic acid (IAA), abscisic acid (ABA), gibberellic acid (GA), salicylic acid (SA), and zeatin (tZ) were detected and quantified in the four potential BCAs using liquid chromatography- tandem mass spectrometry (LC-MS/MS). Scanning electron microscopy (SEM) studies revealed the endophytic nature of the strains in rice. The study indicated a positive correlation between the diversity and concentration of phytohormones released by the bioagents and enhanced plant growth promotion and disease suppression in rice.

Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice.

Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01412-1.

Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations.

BACKGROUND: Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. RESULTS: We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. CONCLUSIONS: Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.

Improving blast resistance of maintainer line DRR 9B by transferring broad spectrum resistance gene Pi2 by marker assisted selection in rice.

Hybrid rice technology offers great promise to further enhance rice production and productivity for global food security. Improving hybrid rice parental lines is the first step in developing heterotic rice hybrids. To improve resistance against blast disease, a maintainer line DRR 9B was fortified with a major broad-spectrum blast resistance gene Pi2 through marker-assisted selection. The rice blast caused by Magnaporthe oryzae is a major disease and can cause severe yield losses upto 100%. The NILs of Samba Mahsuri namely BA-23-11-89-12-168 possessing Pi2 was utilized as a donor parent. The PCR-based molecular marker tightly linked to Pi2 gene was used for the foreground selection at BC1F1 generation. The molecular marker tightly linked to the major fertility restorer gene Rf4 was used for negative selection (i.e., selection of plants possessing non fertility restoring alleles) at BC1F1 generation to identify maintainer lines. The positive plants with Rf4 gene were added to the restorer pool for restorer line development. At each stage, MAS for Pi2 coupled with stringent phenotypic selection for agro-morphological and grain quality traits were exercised. At BC1F3 generation, one hundred families were screened against blast disease at uniform blast nursery (UBN) and selected resistant lines were advanced to next generations. In the BC1F5 generation plants were subjected to agro-morphological evaluation for yield and yield-contributing traits. The selected plants at BC1F5 generation were crossed with DRR 9A to assess the maintainer ability of blast resistance lines and for further CMS line conversion for hybrid rice breeding for developing blast resistance rice hybrids.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials.

BACKGROUND: Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29). RESULTS: Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+ Concentration 1). CONCLUSION: DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Whole genome sequencing data of native isolates of Bacillus and Trichoderma having potential biocontrol and plant growth promotion activities in rice.

Six native isolates of Trichoderma and Bacillus having potential for biocontrol and plant growth-promoting activities in rice were isolated from different rice growing regions of India. These isolates were screened for their efficiency in both in vitro and in vivo conditions for three years. The identity of the isolates was confirmed both by morphological and molecular characterization. Three Bacillus spp. viz., Bacillus velenzensis strain BIK2, Bacillus cabrialesii strain BIK3 and Bacillus paralicheniformis strain BIK4 and Trichoderma spp. viz., Trichoderma asperellum strain TAIK1, and T. asperellum strain TAIK5, native to the Telangana state, in Southern India except for strain TAIK4 (Rewa district in the state of Madhya Pradesh in Central India). These promising isolates were subjected for whole genome sequencing using the Illumina platform and data was presented. The data was emanated for Trichoderma asperellum (TAIK1), Trichoderma asperellum (TAIK4), Trichoderma asperellum (TAIK5), Bacillus velezensis (BIK2), Bacillus cabrialesii (BIK3) and Bacillus paralicheniformis (BIK4) isolates had an average 100X coverage of 109X, 150X and 116X; 1447X, 905X and 585X respectively. Further studies on the annotation of the data obtained in correlation with the lab and field performance of these microbes would enable them to be used in metagenomics studies to compare their performance under natural conditions with different microbiota and popular rice varieties. Bioformulation of these strains would be more appropriate with the availability of this genomic data.

Revealing the effect of seed phosphorus concentration on seedling vigour and growth of rice using mutagenesis approach.

The harvested plant products, specifically, the grains of cereals are major drivers of soil phosphorus (P) depletion. However, the breeding or biotechnology efforts to develop low P seeds have not been attempted because of possible adverse effects on seedling vigour and crop establishment. Several studies have contradictory observations on influence of seed P on seedling vigour. Lack of appropriate genetic material has been the major bottleneck in reaching the consensus. In this study, we used 30 EMS induced mutants of rice cultivar Nagina22 to understand the role of seed P on seedling vigour and associated physiological processes. Seedling vigour, morpho-physiological characteristics, acid phosphatases, alpha-amylase, and expression of P transporter genes were analyzed in seedlings obtained from seeds of high and low grain P mutants. The study suggests that seed P has a significant role on seedling vigour, chlorophyll content and photosynthesis process of young seedlings, and P transport from roots. Notably, we identified few mutants such as NH4791, NH4785, NH4714, NH4663, NH4614, and NH4618 which showed least influence of low seed P on seedling vigour and other metabolic processes. Therefore, these mutants can be used in breeding programs aiming for development of low P grains. Also, these and other identified mutants can be used to decipher the genetic and molecular mechanisms regulating the differential response of seed P on germination, seedling vigour and several other physiological processes influencing the crop growth and establishment.

Challenges and opportunities in productivity and sustainability of rice cultivation system: a critical review in Indian perspective.

Abstract: Rice-wheat cropping system, intensively followed in Indo-Gangetic plains (IGP), played a prominent role in fulfilling the food grains demand of the increasing population of South Asia. In northern Indian plains, some practices such as intensive rice cultivation with traditional method for long-term have been associated with severe deterioration of natural resources, declining factor productivity, multiple nutrients deficiencies, depleting groundwater, labour scarcity and higher cost of cultivation, putting the agricultural sustainability in question. Varietal development, soil and water management, and adoption of resource conservation technologies in rice cultivation are the key interventions areas to address these challenges. The cultivation of lesser water requiring crops, replacing rice in light-textured soil and rainfed condition, should be encouraged through policy interventions. Direct seeding of short duration, high-yielding and stress tolerant rice varieties with water conservation technologies can be a successful approach to improve the input use efficiency in rice cultivation under medium-heavy-textured soils. Moreover, integrated approach of suitable cultivars for conservation agriculture, mechanized transplanting on zero-tilled/unpuddled field and need-based application of water, fertilizer and chemicals might be a successful approach for sustainable rice production system in the current scenario. In this review study, various challenges in productivity and sustainability of rice cultivation system and possible alternatives and solutions to overcome such challenges are discussed in details.

Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population.

A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03045-7.

Evaluation of genotype by environment interaction and adaptability in lowland irrigated rice hybrids for grain yield under high temperature.

Recent predictions on climate change indicate that high temperature episodes are expected to impact rice production and productivity worldwide. The present investigation was undertaken to assess the yield stability of 72 rice hybrids and their parental lines across three temperature regimes over two consecutive dry seasons using the additive main effect and multiplicative interaction (AMMI), genotype and genotype × environment interaction (GGE) stability model analysis. The combined ANOVA revealed that genotype × environment interaction (GEI) were significant due to the linear component for most of the traits studied. The AMMI and GGE biplot explained 57.2% and 69% of the observed genotypic variation for grain yield, respectively. Spikelet fertility was the most affected yield contributing trait and in contrast, plant height and tiller numbers were the least affected traits. In case of spikelet fertility, grain yield and other yield contributing traits, male parent contributed towards heat tolerance of the hybrids compared to the female parent. The parental lines G74 (IR58025B), G83 (IR40750R), G85 (C20R) and hybrids [G21 (IR58025A × KMR3); G3 (APMS6A × KMR3); G57 (IR68897A × KMR3) and G41 (IR79156A × RPHR1005)] were the most stable across the environments for grain yield. They can be considered as potential genotypes for cultivation under high temperature stress after evaluating under multi location trials.

Novel major QTLs associated with low soil phosphorus tolerance identified from the Indian rice landrace, Wazuhophek.

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.

PAP90, a novel rice protein plays a critical role in regulation of D1 protein stability of PSII.

Introduction: Photosystem II (PSII) protein complex plays an essential role in the entire photosynthesis process. Various known and unknown protein factors are involved in the dynamics of the PSII complex that need to be characterized in crop plants for enhancing photosynthesis efficiency and productivity. Objectives: The experiments were conducted to decipher the regulatory proteins involved in PSII dynamics of rice crop. Methods: A novel rice regulatory protein PAP90 (PSII auxiliary protein ~90 kDa) was characterized by generating a loss-of-function mutant pap90. The mutation was characterized at molecular level followed by various experiments to analyze the morphological, physiological and biochemical processes of mutant under control and abiotic stresses. Results: The pap90 mutant showed reduced photosynthesis due to D1 protein instability that subsequently causes inadequate accumulation of thylakoid membrane complexes, especially PSII and decreases PSII functional efficiency. Expression of OsFtsH family genes and proteins were induced in the mutant, which are known to play a key role in D1 protein degradation and turnover. The reduced D1 protein accumulation in the mutant increased the production of reactive oxygen species (ROS). The accumulation of ROS along with the increased activity of antioxidant enzymes and induced expression of stress-associated genes and proteins in pap90 mutant contributed to its water-limited stress tolerance ability. Conclusion: We propose that PAP90 is a key auxiliary protein that interacts with D1 protein and maintains its stability, thereby promoting subsequent assembly of the PSII and associated membrane complexes.

Grain Fe and Zn content, heterosis, combining ability and its association with grain yield in irrigated and aerobic rice.

Genetic improvement of rice for grain micronutrients, viz., iron (Fe) and zinc (Zn) content is one of the important breeding objectives, in addition to yield improvement under the irrigated and aerobic ecosystems. In view of developing genetic resources for aerobic conditions, line (L) × tester (T) analysis was conducted with four restorers, four CMS lines and 16 hybrids. Both hybrids and parental lines were evaluated in irrigated and aerobic field conditions for grain yield, grain Fe and Zn content. General Combining Ability (GCA) effects of parents and Specific Combining Ability (SCA) effects of hybrids were observed to be contrasting for the micronutrient content in both the growing environments. The grain Fe and Zn content for parental lines were negatively correlated with grain yield in both the contrasting growing conditions. However, hybrids exhibited positive correlation for grain Fe and Zn with grain yield under limited water conditions. The magnitude of SCA mean squares was much higher than GCA mean squares implying preponderance of dominance gene action and also role of complementary non-allelic gene(s) interaction of parents and suitability of hybrids to the aerobic system. The testers HHZ12-SAL8-Y1-SAL1 (T1) and HHZ17-Y16-Y3-Y2 (T2) were identified as good combiners for grain Zn content under irrigated and aerobic conditions respectively.

Marker assisted improvement of low soil phosphorus tolerance in the bacterial blight resistant, fine-grain type rice variety, Improved Samba Mahsuri.

Improved-Samba-Mahsuri (ISM), a high-yielding, popular bacterial blight resistant (possessing Xa21, xa13, and xa5), fine-grain type, low glycemic index rice variety is highly sensitive to low soil phosphorus (P). We have deployed marker-assisted backcross breeding (MABB) approach for targeted transfer of Pup1, a major QTL associated with low soil P tolerance, using Swarna as a donor. A new co-dominant marker, K20-1-1, which is specific for Pup1 was designed and used for foreground selection along with functional markers specific for the bacterial blight resistance genes, Xa21, xa13, and xa5. A set of 66 polymorphic SSR marker were used for the background selection along with a pair of flanking markers for the recombination selection in backcross derived progenies and in BC2F2 generation, 12 plants, which are homozygous for Pup1, all the three bacterial blight resistance genes and possessing agro-morphological traits equivalent to or better than ISM were selected and selfed to produce BC2F3s. They were evaluated in plots with low soil P and normal soil P at ICAR-IIRR, Hyderabad for their low soil P tolerance, and bacterial blight resistance and superior lines were advanced to BC2F6. One of the lines, when tested at multiple locations in India was found promising under both normal as well as low soil P conditions.

Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping.

The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23-22.76% of the phenotypic variance with LOD scores range of 6.5-10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.

Marker Assisted Gene Pyramiding (MAGP) for bacterial blight and blast resistance into mega rice variety "Tellahamsa".

Bacterial blight (BB) and fungal blast diseases are the major biotic constraints that limit rice productivity. To sustain yield improvement in rice, it is necessary to developed yield potential of the rice varieties by incorporation of biotic stress resistance genes. Tellahamsa is a well-adapted popular high yielding rice variety in Telangana state, India. However, the variety is highly susceptible to BB and blast. In this study, simultaneous stepwise transfer of genes through marker-assisted backcross breeding (MABB) strategy was used to introgress two major BB (Xa21 and xa13) and two major blast resistance genes (Pi54 and Pi1) into Tellahamsa. In each generation (from F1 to ICF3) foreground selection was done using gene-specific markers viz., pTA248 (Xa21), xa13prom (xa13), Pi54MAS (Pi54) and RM224 (Pi1). Two independent BC2F1 lines of Tellahamsa/ISM (Cross-I) and Tellahamsa/NLR145 (Cross-II) possessing 92% and 94% recurrent parent genome (RPG) respectively were intercrossed to develop ICF1-ICF3 generations. These gene pyramided lines were evaluated for key agro-morphological traits, quality, and resistance against blast at three different hotspot locations as well as BB at two locations. Two ICF3 gene pyramided lines viz., TH-625-159 and TH-625-491 possessing four genes exhibited a high level of resistance to BB and blast. In the future, these improved Tellahamsa lines could be developed as mega varieties for different agro-climatic zones and also as potential donors for different pre-breeding rice research.