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, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita 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. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers.

Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice.

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 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, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.

Mining nutri-dense accessions from rice landraces of Assam, India.

The Indian subcontinent is the primary center of origin of rice where huge diversity is found in the Indian rice gene pool, including landraces. North Eastern States of India are home to thousands of rice landraces which are highly diverse and good sources of nutritional traits, but most of them remain nutritionally uncharacterized. Hence, nutritional profiling of 395 Assam landraces was done for total starch, amylose content (AC), total dietary fiber (TDF), total protein content (TPC), oil, phenol, and total phytic acid (TPA) using official AOAC and standard methods, where the mean content for the estimated traits were found to be 75.2 g/100g, 22.2 g/100g, 4.67 g/100g, 9.8 g/100g, 5.26%, 0.40 GAE g/100g, and 0.34 g/100g for respectively. The glycaemic index (GI) was estimated in 24 selected accessions, out of which 17 accessions were found to have low GI (<55). Among different traits, significant correlations were found that can facilitate the direct and indirect selection such as estimated glycemic index (EGI) and amylose content (-0.803). Multivariate analyses, including principal component analysis (PCA) and hierarchical clustering analysis (HCA), revealed the similarities/differences in the nutritional attributes. Four principal components (PC) i.e., PC1, PC2, PC3, and PC4 were identified through principal component analysis (PCA) which, contributed 81.6% of the variance, where maximum loadings were from protein, oil, starch, and phytic acid. Sixteen clusters were identified through hierarchical clustering analysis (HCA) from which the trait-specific and biochemically most distant accessions could be identified for use in cultivar development in breeding programs.

Rootstock-mediated carbohydrate metabolism, nutrient contents, and physiological modifications in regular and alternate mango (Mangifera indica L.) scion varieties.

Most of the popular scion varieties of mango possess alternate/irregular bearing. There are many external and internal factors assigned, among them carbohydrate reserves, and nutrient content plays important roles in the floral induction process in many crop species. In addition to that rootstock can alter the carbohydrate reserve and nutrient acquisition of scion varieties in fruit crops. The present investigation was carried out to understand the effect of rootstocks on the physiochemical traits of leaf, and bud and nutrient content in regular and alternate bearing varieties of mango. The rootstock "Kurukkan" promoted starch content in leaves of both alternate bearing varieties 'Dashehari' (5.62 mg/g) and regular 'Amrapali' (5.49 mg/g) and encouraged higher protein content (6.71 mg/g) and C/N ratio (37.94) in buds of alternate bearing 'Dashehari'. While Olour rootstock upregulated the reducing sugar in leaves of 'Amrapali' (43.56 mg/g) and promoted K (1.34%) and B (78.58 ppm) content in reproductive buds of 'Dashehari'. Stomatal density in 'Dashehari' scion variety was found higher on Olour rootstock (700.40/mm 2), while the rootstock fails to modify stomatal density in the scion variety regular bearer 'Amrapali'. Further, a total of 30 carbohydrate metabolism-specific primers were designed and validated in 15 scion/rootstock combinations. A total of 33 alleles were amplified among carbohydrate metabolism-specific markers, which varied from 2 to 3 alleles with a mean of 2.53 per locus. Maximum and minimum PIC value was found for NMSPS10, and NMTPS9 primers (0.58). Cluster analysis revealed that scion grafted on Kurukkan rootstock clustered together except 'Pusa Arunima' on Olour rootstock. Our analysis revealed that Fe is the key component that is commonly expressed in both leaf and bud. Although Stomatal density (SD) and Intercellular CO2 Concentration (Ci) are more specific to leaf and Fe, B, and total sugar (TS) are abundant in buds. Based on the results it can be inferred that the physiochemical and nutrient responses of mango scion varieties are manipulated by the rootstock, hence, the scion-rootstock combination can be an important consideration in mango for selecting suitable rootstock for alternate/irregular bearer varieties.

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. Methods: Six rice varieties (four Basmati and two non-Basmati) belonging to indica group were analyzed at spatial scale in four different tissues (leaf blades, leaf sheaths, peduncle and spikelets) and temporal scale at three developmental stages (booting, milky and dough). Additionally, the matured grains were fractioned into husk, embryo, bran, and endosperm to assess differential accumulation in these tissues. Further, milling and cooking of the samples was done to assess the retention upon processing. After extraction of γ-oryzanol by solvent extraction method, individual components were identified by UPLC-QToF-ESI-MS and quantified by RP-HPLC. Results: The non-seed tissues were significantly different from the seed tissues for composition and quantitative variation of γ-oryzanol. Cycloartenyl caffeate was predominant in all the non-seed tissues during the three developmental stages while it showed significant reduction during the growth progression toward maturity and was totally absent in the matured grains. In contrary, the 24-methylenecycloartanyl ferulate, campesteryl ferulate and ß-sitosteryl ferulate showed significant increment toward the growth progression to maturity. Milling caused significant reduction, retaining only an average of 58.77% γ-oryzanol. Cooking of brown rice in excess water showed relatively lower average retention (43.31%) to samples cooked in minimal water (54.42%). Cooked milled rice showed least mean retention of 21.66%. Conclusion: The results demonstrate prominent compositional variation of γ-oryzanol during different growth stages. For the first time, the study demonstrated that ferulate esters of γ-oryzanol were predominant in the seed tissues while caffeate esters were dominant in non-seed tissues. Basmati cultivars show differential expression of γ-oryzanol and its components compared to non-Basmati cultivars. Cooking in excess water causes maximum degradation of γ-oryzanol. Post-harvest losses due to milling and cooking indicate the necessity of biofortification for γ-oryzanol content in rice grain.

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. Phenotypic data was generated for various agronomic and grain quality traits across seven different environments during two consecutive crop seasons. Based on the observed phenotypic variation, three agronomic traits namely, days to fifty per cent flowering, plant height and panicle length, and three grain quality traits namely, kernel length before cooking, length breadth ratio and kernel length after cooking were subjected to GWAS. Genotyped with 80K SNP array, the population was subjected to principal component analysis to stratify the underlying substructure and subjected to the association analysis using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Results: We identified 32 unique MTAs including 11 robust MTAs for the agronomic traits and 25 unique MTAs including two robust MTAs for the grain quality traits. Six out of 13 robust MTAs were novel. By genome annotation, six candidate genes associated with the robust MTAs were identified. Further analysis of the allelic combinations of the robust MTAs enabled the identification of superior allelic combinations in the population. This information was utilized in selecting 77 elite Basmati rice genotypes from the panel. Conclusion: This is the first ever GWAS study in Basmati rice which could generate valuable information usable for further breeding through marker assisted selection, including enhancing of heterosis.

Molecular mapping of QTLs for grain dimension traits in Basmati rice.

Basmati rice is known for its extra-long slender grains, exceptional kernel dimensions after cooking, high volume expansion, and strong aroma. Developing high yielding Basmati rice varieties with good cooking quality is a gigantic task. Therefore, identifying the genomic regions governing the grain and cooked kernel dimension traits is of utmost importance for its use in marker-assisted breeding. Although several QTLs governing grain dimension traits have been reported, limited attempts have been made to map QTLs for grain and cooked kernel dimension traits of Basmati rice. In the current study, a population of recombinant inbred lines (RIL) was generated from a cross of Sonasal and Pusa Basmati 1121 (PB1121). In the RIL population, there was a significant positive correlation among the length (RRL: rough rice length, MRL: milled rice length, CKL: cooked kernel length) and breadth (RRB: rough rice breadth, MRB: milled rice breadth and CKB: cooked kernel breadth) of the related traits, while there was significant negative correlation between them. QTL mapping has led to the identification of four major genomic regions governing MRL and CKL. Two QTLs co-localize with the earlier reported major gene GS3 and a QTL qGRL7.1, while the remaining two QTLs viz., qCKL3.2 (qMRL3.2) and qCKL4.1 (qMRL4.1) were novel. The QTL qCKL3.2 has been bracketed to a genomic region of 0.78 Mb between the markers RM15247 and RM15281. Annotation of this region identified 18 gene models, of which the genes predicted to encode pentatricopeptides and brassinosteroid insensitive 1-associated receptor kinase 1 precursor may be the putative candidate genes. Furthermore, we identified a novel QTL qKER2.1 governing kernel elongation ratio (KER) in Basmati rice.

Germplasm variability-assisted near infrared reflectance spectroscopy chemometrics to develop multi-trait robust prediction models in rice.

Rice is a major staple food across the world in which wide variations in nutrient composition are reported. Rice improvement programs need germplasm accessions with extreme values for any nutritional trait. Near infrared reflectance spectroscopy (NIRS) uses electromagnetic radiations in the NIR region to rapidly measure the biochemical composition of food and agricultural products. NIRS prediction models provide a rapid assessment tool but their applicability is limited by the sample diversity, used for developing them. NIRS spectral variability was used to select a diverse sample set of 180 accessions, and reference data were generated using association of analytical chemists and standard methods. Different spectral pre-processing (up to fourth-order derivatization), scatter corrections (SNV-DT, MSC), and regression methods (partial least square, modified partial least square, and principle component regression) were employed for each trait. Best-fit models for total protein, starch, amylose, dietary fiber, and oil content were selected based on high RSQ, RPD with low SEP(C) in external validation. All the prediction models had ratio of prediction to deviation (RPD) > 2 amongst which the best models were obtained for dietary fiber and protein with R 2 = 0.945 and 0.917, SEP(C) = 0.069 and 0.329, and RPD = 3.62 and 3.46. A paired sample t-test at a 95% confidence interval was performed to ensure that the difference in predicted and laboratory values was non-significant.

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

The exploitation of heterosis through intersubspecific hybridisation between indica and japonica 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 S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n 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. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.

Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm.

Allelic variability of the aroma gene, betaine aldehyde dehydrogenase 2 (BADH2) was studied in a random subset of indigenous aromatic rice germplasm along with a few exotic aromatic accessions. Use of functional markers of four badh2 alleles identified that the test panel possessed only two alleles, badh2-E7 and badh2-p-5'UTR. Two other alleles, badh2.2 and badh2-E4-5.2 were absent. Based on the alleles present, four functional polymorphisms (FP) were detected, namely FP1 to FP4. 188 genotypes possessed FP1 having both the badh2-p-5'UTR and badh2-E7 (71.8%) alleles. The badh2 allele with FP1 is named badh2-E7-p. 39 genotypes (14.9%) possessed only the badh2-p-5'UTR allele (FP3), while three genotypes were found to carry only the badh2-E7 allele (FP2). We also found that 32 genotypes (12.2%) did not have any of the target aroma alleles tested in this study (FP4). Interestingly, for badh2-p-5'UTR marker, the expected 198 bp amplicon for the non-aromatic allele could not be detected among any of the genotypes tested. Instead, an amplicon of 456 bp length appeared with 100% presence in the non-aromatic checks. Notwithstanding, the 456 bp allele also showed a 16% presence among the aromatic lines. This article forms the first report of this allele, named badh2-p1, among aromatic rice. Quantification of 2-Acetyl-1-Pyrroline (2AP) content and sensory evaluation among the test genotypes showed that those with FP1 are highly aromatic than the genotypes carrying other types of FPs. But, a few strongly aromatic lines showed lower 2AP content. The BADH2 characterization carried out in this study is suggestive of identifying the additional gene(s)/ allele(s) governing aroma among the Indian fragrant rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01181-9.

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

Sheath blight caused by necrotrophic fungus Rhizoctonia solani 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. As there are no sources of complete resistance, management through chemical control has been the most adopted method for sheath blight management. In this review, we provide an up-to-date comprehensive description of host-pathogen interactions, various control measures such as cultural, chemical, and biological as well as utilizing host plant resistance. The section on utilizing host plant resistance includes identification of resistant sources, mapping QTLs and their validation, identification of candidate gene(s) and their introgression through marker-assisted selection. Advances and prospects of sheath blight management through biotechnological approaches such as overexpression of genes and gene silencing for transgenic development against R. solani are also discussed.

Population Structure of a Worldwide Collection of Tropical Japonica 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 indica 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 japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.

A novel LOX3-null allele (lox3-b) originated in the aromatic Basmati rice cultivars imparts storage stability to rice bran.

Rapid deterioration of rice bran due to the LOX3 enzyme catalysed oxidation of PUFA is the major bottleneck for its utilization in various downstream applications. In the present study, we have identified a set of nine novel LOX3-null rice accessions carrying a deletion of C residue in the exon2 causing a frameshift mutation resulting in a truncated non-functional LOX3 protein. Our study, further manifested the predominance of C deletion based LOX3-null allele, named lox3-b, in the aromatic rice germplasm particularly in the Indian Basmati rice group. The LOX3-null genotypes exhibited significantly reduced rancidity, after six months of storage. They also showed significantly lower percentage reduction of linoleic acid (LA), higher γ-oryzanol content and lower hexanal content. A functional dCAPS marker designed based on the deletion polymorphism clearly differentiated LOX3 and lox3-b alleles, and has the potential application in marker assisted rice breeding programmes to develop cultivars with better bran storability.

Identification, Characterization, and Evaluation of Nematophagous Fungal Species of Arthrobotrys and Tolypocladium for the Management of Meloidogyne incognita.

Root-knot nematodes belonging to the genus Meloidogyne are agriculturally important pests, and biocontrol strategies offer safer alternatives for their management. In the present study, two fungal species from Indian soils were identified as Arthrobotrys thaumasia and Tolypocladium cylindrosporum based on morphological characteristics and further confirmed using molecular markers. In vitro evaluation of A. thaumasia against M. incognita and Caenorhabditis elegans showed 82 and 73% parasitism, respectively, whereas T. cylindrosporum gave 65.2 and 57.7% parasitism, respectively. Similarly, culture filtrates of A. thaumasia caused 57.7 and 53.7% mortality of M. incognita and C. elegans, respectively, whereas T. cylindrosporum caused higher mortality of 87.3 and 64%, respectively. Besides, greenhouse evaluation of both fungi against M. incognita infecting tomato significantly reduced nematode disease burden reflecting parasitic success measured as the total number of galls, egg masses, eggs per egg mass, and derived nematode multiplication factor. Application of A. thaumasia and T. cylindrosporum reduced nematode multiplication factor by 80 and 95%, respectively, compared with control. General metabolite profiling of tested fungi using gas chromatography-mass spectrometry and ultra-performance liquid chromatography-quadrupole/time of flight mass spectrometry reported for the first time here showed presence of various volatile and non-volatile compounds with nematicidal activity, viz., trimethyl-heptadiene, methyl-hexadecanol, dodecadienal, decane, terpendole E, dodecane, acetamido-6-anthraquinone, and hexadecanol. Also, other compounds such as undecane, dibutyl-disulfide, octadecenal, paganin, talathermophilin, dactylarin, tolypyridone A, tolypyridone B, pyridoxatin, and destruxin were identified, reported in the literature to possess antibacterial, antifungal, and insecticidal properties. This is the first report of the occurrence of both fungi from India and pioneer demonstration of T. cylindrosporum for root-knot nematode management.

Profiling of 2-Acetyl-1-Pyrroline and Other Volatile Compounds in Raw and Cooked Rice of Traditional and Improved Varieties of India.

Herein, optimized headspace solid phase microextraction with gas chromatography-tandem mass spectrometry (HS-SPME-GC-MS/MS) was used to estimate the 2-acetyl-1-pyrroline (2-AP) in raw and cooked rice samples of ten different traditional and improved varieties. Furthermore, HS-SPME-GC-MS-based volatile profiling was subjected to untargeted analyses to identify major odorants in raw and cooked rice samples, and to understand chemical proximities among volatile profiles. Results showed that 2-AP content was remarkably increased in cooked rice compared to raw. Among the varieties studied, Pusa-1652 (Improved Kala Namak) and Kala Namak-2 were superior in the 2-AP content than Basmati varieties. Additionally, Govind Bhog, Kala Jeera and Jeera-32 had 2-AP content equivalent to or superior to Basmati rice varieties. Altogether, 18 and 22 volatiles were identified in the raw and cooked rice samples studied, respectively. Of these, ethyl butyrate, ethyl 3-methylbutanoate, 2-undecanone, ethyl benzoate, ethyl benzeneacetate, 2-methylnaphthalene, and 1-methylnaphthalene were characteristically detected in the cooked rice. The high amount of 2-ethyl-1-hexanol was uniquely found in raw rice samples, which can be a marker compound for freshly milled rice. Along with 2-AP, butanoic acid and benzoic acid derivatives, phenylethyl alcohol, ethyl 3-hydroxybutyrate, and indole may be responsible for the overall perceived characteristic Basmati-like aroma in cooked rice.

Molecular Breeding for Improving Productivity of Oryza sativa L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, qDTY12.1.

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 qDTY12.1 is one of the major QTLs reported. We report the successful introgression of qDTY12.1 into Pusa 44, a drought sensitive mega rice variety of the northwestern Indian plains. Marker-assisted backcross breeding (MABB) was adopted to transfer qDTY12.1 into Pusa 44 in three backcrosses followed by four generations of pedigree selection, leading to development of improved near isogenic lines (NILs). Having a recurrent parent genome (RPG) recovery ranging from 94.7-98.7%, the improved NILs performed 6.5 times better than Pusa 44 under RSDS, coupled with high yield under normal irrigated conditions. The MABB program has been modified so as to defer background selection until BC3F4 to accelerate generational advancements. Deploying phenotypic selection alone in the early backcross generations could help in the successful recovery of RPG. In addition, the grain quality could be recovered in the improved NILs, leading to superior selections. Owing to their improved adaptation to drought, the release of improved NILs for regions prone to intermittent drought can help enhance rice productivity and production.

Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice.

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

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. It forms a basis for the extraction of rice bran oil and preparation of various functional foods with health benefits and potential to prevent chronic health issues. Nevertheless, the rapid deterioration of bran upon storage acts as a major limitation in exploiting the full potential of rice bran. In this review, we have discussed three strategies to address rapid rancidity of rice bran and enhance its shelf life and storability vis-a-vis emphasizing the importance of rice bran in terms of its nutritional composition. One strategy is through exploitation of the null mutations in the genes governing lipases and lipoxygenases leading to nonfunctional enzymes (enzyme deficient approach), another strategy is through reducing the PUFA content that is more prone to oxidation (substrate deficient approach) and a third strategy is through enhancing the antioxidant content that effectively terminate the lipid peroxidation by donating the hydrogen atom.

Drought Tolerant Near Isogenic Lines of Pusa 44 Pyramided With qDTY2.1 and qDTY3.1, 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. In this study, we have used state-of-the-art image-based phenotyping in a phenomics platform that offers a controlled environment, non-invasive phenotyping, high accuracy, speed, and continuity. In rice, several quantitative trait loci (QTLs) which govern grain yield under drought determine RSDS tolerance. Among these, qDTY2.1 and qDTY3.1 were used for marker-assisted breeding. A set of 35 near-isogenic lines (NILs), introgressed with these QTLs in the popular variety, Pusa 44 were used to assess the efficiency of image-based phenotyping for RSDS tolerance. NILs offered the most reliable contrast since they differed from Pusa 44 only for the QTLs. Four traits, namely, the projected shoot area (PSA), water use (WU), transpiration rate (TR), and red-green-blue (RGB) and near-infrared (NIR) values were used. Differential temporal responses could be seen under drought, but not under unstressed conditions. NILs showed significant level of RSDS tolerance as compared to Pusa 44. Among the traits, PSA showed strong association with yield (80%) as well as with two drought tolerances indices, stress susceptibility index (SSI) and tolerance index (TOL), establishing its ability in identifying the best drought tolerant NILs. The results revealed that the introgression of QTLs helped minimize the mean WU per unit of biomass per day, suggesting the potential role of these QTLs in improving WU-efficiency (WUE). We identified 11 NILs based on phenomics traits as well as performance under imposed drought in the field. The study emphasizes the use of phenomics traits as selection criteria for RSDS tolerance at an early stage, and is the first report of using phenomics parameters in RSDS selection in rice.

Role of nutraceutical starch and proanthocyanidins of pigmented rice in regulating hyperglycemia: Enzyme inhibition, enhanced glucose uptake and hepatic glucose homeostasis using in vitro model.

Dysregulation of glucose homeostasis result in hyperglycemia and pigmented rice, unique combination of high quality starch and phenolics has the potential in regulating it. In this study, pigmented rice was characterized in terms of nutraceutical starch (NS) and phenolic content. Further the effect of rice phenolics on carbolytic enzyme inhibition, glucose uptake, hepatic glucose homeostasis and anti-glycation ability was analyzed in vitro. The most relevant effect on enzyme inhibition (α-amylase: IC50-42.34 µg/mL; α-glucosidase: IC50:63.89 µg/mL), basal uptake of glucose (>39.5%) and anti-glycation ability (92%) was found in red rice (RR), than black rice (BR). The role of RR phenolics in regulating glucose homeostasis was deciphered using hepatic cell line system, which found up-regulation of glucose transporter 2 (GLUT2) and glycogen synthase 2 (GYS2); while expression of gluconeogenic genes were found down regulated. To our knowledge this study is the first report validating the role of starch-phenolic quality towards anti-hyperglycemic effect of RR.