Identification of a Promising Novel Genetic Source for Rice Root-Knot Nematode Resistance through Markers Associated with Trait-Specific Quantitative Trait Loci.

Direct-seeded rice (DSR) is gaining popularity among farmers due to its environmentally safe and resource-efficient production system. However, managing the rice root-knot nematode (RRKN), , remains a major challenge in DSR cultivation. Developing genetic resistance is a pragmatic and effective approach compared to using hazardous pesticides.

Fine mapping of , a major QTL governing resistance to bakanae disease in rice.

Bakanae disease caused by is an emerging disease of rice causing losses in all rice-growing regions around the world. A BCF population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, . MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of helped in fine mapping the QTL to a region of 130 kb between the SNP markers and using 24 recombinants.

Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding.

Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, + and , and fungal blast resistance genes + and were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively.

Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement.

Background: Basmati is a speciality segment in the rice genepool characterised by explicit grain quality. For the want of suitable populations, genome-wide association study (GWAS) in Basmati rice has not been attempted.

Materials: To address this gap, we have performed a GWAS on a panel of 172 elite Basmati multiparent population comprising of potential restorers and maintainers.

From farm to plate: Spatio-temporal characterization revealed compositional changes and reduced retention of γ-oryzanol upon processing in rice.

Background: Antioxidants detain the development and proliferation of various non-communicable diseases (NCDs). γ-oryzanol, a group of steryl ferulates and caffeates, is a major antioxidant present in rice grain with proven health benefits. The present study evaluated the distribution and dynamics of γ-oryzanol and its components in spatial and temporal scales and also delineated the effect of processing and cooking on its retention.

Cross-talk between the cytokinin, auxin, and gibberellin regulatory networks in determining parthenocarpy in cucumber.

Cucumber is a model plant for studying parthenocarpy with abundant slicing- and pickling-type germplasm. This study was undertaken to understand the role of the important cytokines (CKs), auxin (AUX) and gibberellin (GA) biosynthesis and degradation genes for the induction of parthenocarpy in slicing and pickling germplasm. Two genotypes of gynoecious parthenocarpic cucumber, PPC-6 and DG-8, along with an MABC-derived gynoecious non-parthenocarpic line, IMPU-1, were evaluated in this study.

Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by - Hybridization in Rice.

The exploitation of heterosis through intersubspecific hybridisation between and has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the locus on chromosome 6 that ensures the specificity of hybridisation within and between and The allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes.

Kühn Pathophysiology: Status and Prospects of Sheath Blight Disease Management in Rice.

Sheath blight caused by necrotrophic fungus Kühn is one of the most serious diseases of rice. Use of high yielding semi dwarf cultivars with dense planting and high dose of nitrogenous fertilizers accentuates the incidence of sheath blight in rice. Its diverse host range and ability to remain dormant under unfavorable conditions make the pathogen more difficult to manage.

Population Structure of a Worldwide Collection of Tropical Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type.

Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical lines collected worldwide for population genetic structure and variability in yield-associated traits.

Drought Tolerant Near Isogenic Lines of Pusa 44 Pyramided With and , Show Accelerated Recovery Response in a High Throughput Phenomics Based Phenotyping.

Reproductive stage drought stress (RSDS) is a major challenge in rice production worldwide. Cultivar development with drought tolerance has been slow due to the lack of precise high throughput phenotyping tools to quantify drought stress-induced effects. Most of the available techniques are based on destructive sampling and do not assess the progress of the plant's response to drought.

Molecular Breeding for Improving Productivity of L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, .

Increasing rice production is quintessential to the task of sustaining global food security, as a majority of the global population is dependent on rice as its staple dietary cereal. Among the various constraints affecting rice production, reproductive stage drought stress (RSDS) is a major challenge, due to its direct impact on grain yield. Several quantitative trait loci (QTLs) conferring RSDS tolerance have been identified in rice, and is one of the major QTLs reported.

Genetic Analysis and Molecular Mapping of the Quantitative Trait Loci Governing Low Phytic Acid Content in a Novel LPA Rice Mutant, PLM11.

Breeding rice varieties with a low phytic acid (LPA) content is an effective strategy to overcome micronutrient deficiency in a population which consume rice as a staple food. An LPA mutant, Pusa LPA Mutant 11 (PLM11), was identified from an ethyl methane sulfonate (EMS)-induced population of Nagina 22. The present study was carried out to map the loci governing the LPA trait in PLM11 using an F population derived from a cross between a high phytic acid rice variety, Pusa Basmati 6, with PLM11.

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Landraces.

Aromatic rice of Manipur popularly known as is a speciality glutinous rice, for which protection under geographical indication in India has been granted recently. The agronomic and nutraceutical variability of the rice germplasm is yet to be genetically characterized. To address this gap, characterization of ninety-three landraces for agro-morphological traits, grain pigmentation, antioxidant properties, and molecular genetic variation was carried out to unravel their population genetic structure.

Discovery of a Novel Induced Polymorphism in 1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

The semi-dwarfing allele, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), , derived from a spontaneous mutation, has a 383-bp deletion in the gene. To date, as many as seven alleles of the gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion-deletions (InDels), or both.

Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, "Pusa Basmati 1121".

Background: Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties.

Marker aided introgression of 'Saltol', a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety 'Pusa Basmati 1509'.

Marker assisted backcross breeding was used to transfer Saltol, a major QTL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection.

Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain.

Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR).

Genetic and genomic approaches to address rapid rancidity of rice bran.

Rice bran is an invaluable by-product of paddy processing industry. It is rich in minerals, protein, lipids, and crude fiber. In addition, it also possesses compounds with anti-oxidant, anti-allergic, anti-diabetic, and anti-cancer properties.

WA-CMS-based iso-cytoplasmic restorers derived from commercial rice hybrids reveal distinct population structure and genetic divergence towards restorer diversification.

One hundred diverse iso-cytoplasmic restorer (ICR) lines carrying WA cytoplasm indicated significant but moderate variability for agro-morphological traits as well as for the microsatellite-based allele patterns. There were two major groups of ICRs based on agro-morphological clustering. Simple sequence repeat (SSR) markers identified allelic variants with an average of 2.

Marker-Assisted Introgression of QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety "Pusa Basmati 1".

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, .

Marker-assisted identification of restorer gene(s) in iso-cytoplasmic restorer lines of WA cytoplasm in rice and assessment of their fertility restoration potential across environments.

Iso-cytoplasmic restorers possess the same male sterile cytoplasm as the cytoplasmic male sterile (CMS) lines, thereby minimizing the potential cyto-nuclear conflict in the hybrids. Restoration of fertility of the wild abortive CMS is governed by two major genes namely, and . Therefore, assessing the allelic status of these restorer genes in the iso-cytoplasmic restorers using molecular markers will not only help in estimating the efficiency of these genes either alone or in combination, in fertility restoration in the hybrids in different environments, but will also be useful in determining the efficacy of these markers.

Marker Aided Incorporation of , a Major QTL Associated with Seedling Stage Salt Tolerance, into 'Pusa Basmati 1121'.

Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a quantitative trait locus (QTL), , using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to was used for foreground selection.

Mapping quantitative trait loci responsible for resistance to Bakanae disease in rice.

Background: Bakanae or foot rot disease caused by Fusarium fujikuroi [teleomorph: Gibberella fujikuroi (Sawada) Ito] is emerging as a serious disease in rice. The disease causes both quantitative and qualitative losses to the grains under the field conditions. Breeding for resistance to Bakanae disease is a promising strategy to manage this emerging disease.