Project description:Basmati is considered a unique varietal group of rice (Oryza sativa L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the aromatic group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 (indica rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the aus group than with the japonica and indica groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, aromatic (22 varieties), aus (four varieties), and indica (four varieties), based on genome-wide SNPs. All 22 aromatic Basmati varieties harbored the fragrant-inducing Badh2 allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant (P < 0.05 and P < 0.01) differences between the aromatic and indica/aus groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will serve as an important resource for molecular breeding and genetic analysis of Basmati varieties.
Project description:Plant associated rhizobacteria prevailing in different agro-ecosystems exhibit multiple traits which could be utilized in various aspect of sustainable agriculture. Two hundred thirty four isolates were obtained from the roots of basmati-385 and basmati super rice varieties growing in clay loam and saline soil at different locations of Punjab (Pakistan). Out of 234 isolates, 27 were able to solubilize zinc (Zn) from different Zn ores like zinc phosphate [Zn3 (PO4)2], zinc carbonate (ZnCO3) and zinc oxide (ZnO). The strain SH-10 with maximum Zn solubilization zone of 24 mm on Zn3 (PO4)2ore and strain SH-17 with maximum Zn solubilization zone of 14-15 mm on ZnO and ZnCO3ores were selected for further studies. These two strains solubilized phosphorous (P) and potassium (K) in vitro with a solubilization zone of 38-46 mm and 47-55 mm respectively. The strains also suppressed economically important rice pathogens Pyricularia oryzae and Fusarium moniliforme by 22-29% and produced various biocontrol determinants in vitro. The strains enhanced Zn translocation toward grains and increased yield of basmati-385 and super basmati rice varieties by 22-49% and 18-47% respectively. The Zn solubilizing strains were identified as Bacillus sp. and Bacillus cereus by 16S rRNA gene analysis.
Project description: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), <i>Saltol</i>, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to <i>Saltol</i> was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP). A set of 51 BC<sub>3</sub>F<sub>2</sub> lines homozygous for <i>Saltol</i> were advanced to develop four improved near isogenic lines (NILs) of PB1121 with seedling stage salt tolerance. The background genome recovery in the NILs ranged from 93.3 to 99.4%. The improved NILs were either similar or better than the recurrent parent PB1121 for yield, grain and cooking quality and duration. Biochemical analyses revealed significant variation in shoot and root Na<sup>+</sup> and K<sup>+</sup> concentrations. Correlation between shoot and root Na<sup>+</sup> concentration was stronger than that between root and shoot K<sup>+</sup> concentration. The effect of QTL integration into the NILs was studied through expression profiling of <i>OsHKT1;5</i>, one of the genes present in the <i>Saltol</i> region. The NILs had significantly higher <i>OsHKT1;5</i> expression than the recurrent parent PB1121, but lower than FL478 on salt exposure validating the successful introgression of <i>Saltol</i> in the NILs. This was also confirmed under agronomic evaluation, wherein the NILs showed greater salt tolerance at seedling stage. One of the NILs, Pusa1734-8-3-3 (NIL3) showed comparable yield and cooking quality to the recurrent parent PB1121, with high field level seedling stage salinity tolerance and shorter duration. This is the first report of successful introgression of <i>Saltol</i> into a Basmati rice cultivar.
Project description:BACKGROUND:Rice plant growth is comprised of distinct phases, such as vegetative, reproductive, grain filling and maturity phases. In these phases synthesis and availability of primary and secondary metabolites including volatile organic compounds (VOC's) is highly variable. In scented rice, aroma volatiles are synthesized in aerial plant parts and deposited in mature grains. There are more than 100 VOCs reported to be responsible for flavor in basmati rice. It will be interesting to keep track of aroma volatiles across the developmental stages in scented rice. Therefore, the aroma volatiles contributing in aroma with special reference to the major compound 2 acetyl-1-pyrroline (2AP) were screened at seven developmental stages in scented rice cultivars Basmati-370 and Ambemohar-157 along with non-scented rice cultivar IR-64 as a control following HS-SPME-GC-MS method. In addition, the expression levels of key genes and precursor levels involved in 2AP biosynthesis were studied. RESULTS:The study indicated that volatilome of scented rice cultivars is more complex than non-scented rice cultivar. N-heterocyclic class was the major distinguishing class between scented from non-scented rice. A total of 14 compounds including, 2AP were detected specifically in scented rice cultivars. Maximum number of compounds were synthesized at seedling stage and decreased gradually at reproductive and maturity. The seedling stage is an active phase of development where maximum number green leaf volatiles were synthesized which are known to act as defense molecules for protection of young plant parts. Among the 14 odor active compounds (OACs), 10 OACs were accumulated at higher concentrations significantly in scented rice cultivars and contribute in the aroma. 2AP content was highest in mature grains followed by at booting stage. Gene expression analysis revealed that reduced expression of betaine aldehyde dehydrogenase 2 (badh2) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and elevated level of triose phosphate isomerase (TPI) and ?1-Pyrolline-5-carboxylic acid synthetase (P5CS) transcript enhances 2AP accumulation. CONCLUSIONS:Most diverse compounds were synthesized at seedling stage and OACs were accumulated more at flowering followed by seedling stage. Distinct accumulation pattern exists for 2AP and other aroma volatiles at various developmental stages. The study revealed the mechanism of 2AP accumulation such that 2AP in mature grains might be transported from leaves and stem sheath and accumulation takes place in grains.
Project description:BACKGROUND:The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group's evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties. RESULTS:We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32?Mb and 10.53?Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica-the rice group most closely related to circum-basmati-as well as the presence and absence variants of over 20?Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. CONCLUSION:The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.
Project description:One hundred forty one basmati rice genotypes collected from different geographic regions of North Western Himalayas were characterized using 40 traits linked microsatellite markers. Number of alleles detected by the abovementioned primers were 112 with a maximum and minimum frequency of 5 and 2 alleles, respectively. The maximum and minimum polymorphic information content values were found to be 0.63 and 0.17 for the primers RM206 and RM213, respectively. The genetic similarity coefficient for the most number of pairs ranged between of 0.2-0.9 with the average value of 0.60 for all possible combinations, indicating moderate genetic diversity among the chosen genotypes. Phylogenetic cluster analysis of the SSR data based on distance divided all genotypes into four groups (I, II, III and IV), whereas model based clustering method divided these genotypes into five groups (A, B, C, D and E). However, the result from both the analysis are in well agreement with each other for clustering on the basis of place of collection and geographic region, except the local basmati genotypes which clustered into three subpopulations in structure analysis comparison to two clusters in distance based clustering. The diverse genotypes and polymorphic trait linked microsatellites markers in the present study will be used for the identification of quantitative trait loci/genes for different economically important traits to be utilized in molecular breeding programme of rice in the future.
Project description:<h4>Background</h4>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.<h4>Results</h4>We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) "Robin" into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC<sub>4</sub>F<sub>4</sub> near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin.<h4>Conclusion</h4>Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.