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.
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. The slicing and pickling cucumber genotypes PPC-6 and DG-8 were strongly parthenocarpic in nature and set fruit normally without pollination. Endogenous auxin and gibberellin were significantly higher in parthenocarpic than non-parthenocarpic genotypes, whereas the concentration of cytokinins varied among the genotypes at different developmental stages. However, the exogenous application of Zeatin and IAA + Zeatin was effective in inducing parthenocarpic fruit in IMPU-1. Expression analysis with important CK, AUX, and GA biosynthesis-related genes was conducted in IMPU-1, PPC-6, and DG-8. The expression of the CK synthase, IPT, IPT3, PaO, LOG1, LOG2, CYP735A1, and CYP735A2 was up-regulated in the parthenocarpic genotypes. Among the transcription factor response regulators (RRs), positive regulation of CSRR8/9b, CSRR8/9d, CSRR8/9e, and CSRR16/17 and negative feedback of the CK signalling genes, such as CsRR3/4a, CsRR3/4b, CsRR8/9a, and CsRR8/9c, were recorded in the parthenocarpic lines. Homeostasis between cytokinin biosynthesis and degradation genes such as CK oxidases (CKXs) and CK dehydrogenase resulted in a non-significant difference in the endogenous CK concentration in the parthenocarpic and non-parthenocarpic genotypes. In addition, up-regulation of the key auxin-inducing proteins and GA biosynthesis genes indicated their crucial role in the parthenocarpic fruit set of cucumber. This study establishes the critical role of the CKs, AUX, and GA regulatory networks and their cross-talk in determining parthenocarpy in slicing and pickling cucumber genotypes.
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), Meloidogyne graminicola, remains a major challenge in DSR cultivation. Developing genetic resistance is a pragmatic and effective approach compared to using hazardous pesticides. Pusa Basmati 1121 (PB1121) is the most popular Basmati rice variety, but it is highly susceptible to RRKN. In contrast, Phule Radha (PR) has shown highly resistant reaction to RRKN, as reported in our earlier study. We generated an F2:3 population from the cross of PB1121/PR and evaluated it for RRKN resistance-related traits under artificial inoculation conditions. The distribution pattern of traits in the F2:3 population indicated that resistance may be governed by a few major-effect genes and many minor-effect genes. The molecular markers reported to be associated with QTLs governing RRKN resistance traits were used to test in the current population. Although the simple linear regression identified significant associations between the markers and RRKN resistance-associated traits, these associations were spurious as the LOD score was below the threshold limit. This indicates that PR possesses novel genomic regions for resistance to RRKN as it does not possess any of the earlier reported QTLs.
Uppermost internode length (UIL) and panicle exsertion are two important traits that contribute significantly to increased yield in rice. The present study was conducted using recombinant inbred lines (RILs) comprising 201 lines derived from RTN10B and IRG213. These RILs were evaluated at three different locations— Delhi, Karnal, and Aduthurai. We report the mapping of quantitative trait loci (QTLs) for uppermost internode length and the panicle exsertion ratio (PER), as well as QTLs for plant height (PH), tiller number, length of the second internode, length of the third internode, length from the flag leaf to the panicle tip (PFL), and panicle length (PL). Mapping was performed using a custom microsatellite linkage map constructed for the population, having a total span of 2077.1 cM with 104 markers. A total of 22 QTLs were identified for various traits, among which 19 were found distributed in four hotspots. A total of 11 major effect QTLs and 11 minor effect QTLs were identified for various internode length-related traits. Among the four QTLs identified for PFL, three QTLs— qPFL1.1 , qPFL1.2, and qPFL2.1 —co-localized with previously reported QTLs, while qPFL8.1 was a novel QTL. A major QTL hotspot was identified on chromosome 1, located at the marker interval of RM12055-RM320. The size of the major QTL hotspot on chromosome 1 was 1.4 Mb and contained a total of seven HEs for PER, PFL, PH, PL, UIL, SIL, and TIL. Based on the in-silico analysis of the major QTL hotspot on chromosome 1, we identified 15 putative candidate genes associated with internode length- and panicle-related traits. Furthermore, narrowing the genomic region through the fine mapping of the marker intervals facilitated the identification of candidate genes to enable more precise marker-assisted selection for uppermost internode length and panicle exsertion.
Rice (Oryza sativa L.) belongs to Poaceae family and serves as food for more than half of the global population. Domesticated from O. preperennis about 10,000 years ago, it is cultivated in a wide range of ecosystems right from below the sea level to high mountain regions. Genetic improvement in India has helped in improving average productivity from 0.67 tons/ha in 1950–1951 to 2.74 t/ha during 2020–2021. Development of research infrastructure along with basic research helped in gaining understanding of the genetic nature of economically important traits. The major breakthrough in yield improvement was achieved through utilisation of sd1 in developing semi-dwarf high yielding varieties with sturdy stem, spurring the green revolution. Hybrid rice further enhanced rice productivity. Deciphering rice genome and advances in genomics helped in functional characterisation of ∼2800 economically important genes governing yield, resistance to major biotic and abiotic stresses, grain and nutritional quality, which enabled the integration of molecular markers in breeding. Thirty-six MAS-derived varieties with resistance to biotic and/or abiotic stress and 12 varieties with enhanced Zn and/or protein content have been released in India. Advances in genetics, breeding, genomics and phenomics, have enabled population improvement through genomic selection, while genome-editing has helped in creating novel alleles for useful genes. Aided by an evolving system for multi-location evaluation of elite genotypes under the All India Coordinated Rice Improvement Programme and a robust system of seed supply chain for dissemination of improved rice varieties, higher adoption by farmers has helped in improving and sustaining rice productivity. However, sustaining it in the face of climate change is a major challenge. Adoption of advanced tools and techniques can help rapid and precise breeding of improved rice varieties suited to changing human needs.
A novel zebra leaf mutant, Pusa Zebra 18 derived spontaneously from F2 intercross population of Pusa 44 near-isogenic lines (NILs) exhibits distinguishable yellowish cross bands across the green leaf blade, specifically expressed in the seedling stage from 6 DAT, which diffuses progressively, leading to the recovery of the normal green leaf by 30 DAT. We elucidated the genetics and nature of inheritance for zebra trait in F2 and BC1F2 populations by crossing Pusa 6B with Pusa Zebra 18. The leaves of the F1 were a normal green color, indicating that the seedling stage zebra leaf trait in Pusa Zebra 18 is recessive. Chi-square goodness of fit analysis of these segregating populations showed that the segregation ratio was fitting to the Mendelian segregation ratio of 3:1. The seedling stage zebra leaf mutation in Pusa Zebra 18 is monogenic recessive in nature. Further, mapping, fine mapping, cloning, and functional characterization need to be carried out, which will help gain insight into the mechanism involved in chlorophyll biosynthesis and regulation studies in rice.
Phytic acid (PA) acts as chelator of cationic mineral elements iron (Fe) and zinc (Zn) and obstructs their absorption in the human gut. We have evaluated a set of 162 traditional rice landraces for phytic acid phosphorus (PA-P), inorganic phosphorus (Pi) and total phosphorus (TP). Wide variability was observed for PA-P, Pi and TP ranging from 1.12 to 3 mg/g, 0.004 to 0.16 mg/g and 1.17 to 3.04 mg/g respectively. The mineral micronutrients, Fe and Zn were not in correlation with PA-P, Pi and TP implicating the possibility of their independent improvement while PAP showed a significant positive correlation with TP and significant negative correlation with Pi. Principal component analysis (PCA) identified two principal components PC1 and PC2, explaining 50.6 % and 32.1 % of the total variation, respectively. Cluster analysis grouped the accessions into four clusters. The study has also led to the identification of promising donors such as P1490 and Gowri with low PA content to be utilized in rice biofortification programmes.
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