Identification of multiple abiotic stress tolerant donors for climate-resilient rice (Oryza sativa) development

The increasing occurrence of adverse weather events is continuously challenging agricultural production globally. The wide genetic base of rice (Oryza sativa L.) and the availability of a diverse set of germplasm can be explored to identify multiple abiotic stress-tolerant donors for rice improvement. Therefore, an experiment was conducted during 2018–21 at ICAR-National Rice Research Institute, Cuttack, Odisha to evaluate diverse rice germplasm (68 accessions) for vegetative stage drought and submergence stress and for their anaerobic germination potential. Under drought stress, 49 accessions showed a drought score (DS) of 1 indicating a tolerance response. The early vegetative score indicated that 58 accessions were highly vigorous, while the drought recovery score indicates that >90% of the genotypes showed good recovery after the drought cycle. The same genotypes showed a average survival rate (SR) of 48% under two weeks of complete submergence. Among them, 11 were found highly tolerant with >70% SR and 26 genotypes scored positive SUB1A locus by SNP-based functional marker AEX1. Nearly 50% of the genotypes scored positive for SUB1A, based on both AEX1 and Sub1A203 markers, which nearly matched the phenotyping result. Out of 68, only 4 accessions showed more than 50% germination under anaerobic conditions. A multivariate analysis showed that 11 genotypes had both drought and submergence tolerance, while 6 genotypes were having tolerance to drought and anaerobic germination. We found only 1 accession (IC516149) tolerant to all these 3 stresses which can be identified as a potential donor for multiple abiotic stresses

Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1–2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22)

Analysis of EMS induced <i style="">in vitro</i> mutants of <i style="">Asteracantha longifolia</i> (L.) Nees using RAPD markers

39-47Ethyl methyl sulfonate (EMS) treated leaf explants were grown in vitro on MS medium fortified with BA (8.88 µM) and NAA (2.69 µM). A total of 24 mutants including 4 dwarf mutants, 7 leaf mutants and 13 flower mutants, selected in IM1 culture generation, were analyzed at morphological, phytochemical and molecular level. Morphological analysis of mutants revealed significant variation in plant height (18.6 to 42.3 cm), internode length (2.2 to 5.82), leaf size and morphology, number of inflorescence (4 to 10), flower colour (white to violet) and phytosterol content (0.033 to 0.0467 mg/g). RAPD analysis involving 30 primers generated 185 amplified products; of which, 86 (46.73%) were polymorphic in nature. Jaccards similarity coefficient matrix between mutant lines inter se and with control plant ranges from 0.636 to 0.881. UPGMA based unrooted tree grouped all 24 mutant lines and control plant into two major clusters, which were sub-clustered into four, and the pattern well corresponded to the flower colour as well as phytosterol content data baring two mutant lines ALM-12 and ALM-13

<i style="mso-bidi-font-style:normal"><span style="font-size:11.0pt;mso-bidi-font-size:10.0pt;font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";mso-ansi-language:EN-GB;mso-fareast-language: EN-US;mso-bidi-language:AR-SA" lang="EN-GB">In vitro</span></i><span style="font-size:11.0pt;mso-bidi-font-size:10.0pt;font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";mso-ansi-language:EN-GB;mso-fareast-language: EN-US;mso-bidi-language:AR-SA" lang="EN-GB"> regeneration from node and leaf explants of <i style="mso-bidi-font-style:normal">Jatropha curcas</i> L. and evaluation of genetic fidelity through RAPD markers</span>

280-287Plantlet regeneration in Jatropha curcas L. (Family: Euphorbiaceae), an energy shrub, has been studied from nodal and leaf explants on basal MS medium. The nodal explants were found superior to leaf explants. Higher shoot bud differentiation was observed on MS media supplemented with 8 µ<i style="mso-bidi-font-style: normal">M N6-benzyladenine (BA; 6.2±0.83) from nodal explants in comparison to both 10 µM kinetin (Kn; 2.8±0.45) from leaf explants and a combination of 6.0 µM BA with 4.0 µ<i style="mso-bidi-font-style: normal">M Kn (5.0±0.71) from nodal explants. MS medium fortified with 8 µM BA and 2 µ<i style="mso-bidi-font-style: normal">M IBA (indole butyric acid) was found most suitable for both callus mediated organogenesis and elongation of shoots. Addition of 45 µM adenine sulphate, 15 µM glutamine and 10 µ<i style="mso-bidi-font-style: normal">M proline to this optimized MS medium enhanced the number of multiple shoot proliferation (9.8±0.84) per explant and elongation at the end of 2nd wk. The elongated shoots were successfully rooted on half-strength MS medium with a prior incubation on MS medium with NAA (a-napthalene acetic acid) or IBA or a combination of both; 2 µM IBA provided better response for rhizogenesis among them. Regenerated plantlets were successfully established in soil where 80±4% of them developed into morphologically normal and fertile plants. Forty RAPD decamer primers were used to assess genetic fidelity of regenerated plantlets along with the donor plant. Fourteen primers responded for amplification, generating 75 amplified products (160 to 2690 bp). The amplification pattern confirmed the genetic uniformity of the regenerated plantlets and substantiated the efficacy and suitability of this protocol for in vitro propagation of J. curcas, thereby favouring the economics of the cost of plant material and time factor. </span

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Not AvailableRice sheath blight (ShB) disease, caused by the fungal pathogen Rhizoctonia solani AG1-IA, is one of the devastating diseases and causes severe yield losses all over the world. No completely resistant germplasm is known till now, and as a result, the progress in resistance breeding is unsatisfactory. Basic studies to identify candidate genes, QTLs, and to better understand the host–pathogen interaction are also scanty. In this study, we report the identification of a new ShB-tolerant rice germplasm, CR 1014. Further, we investigated the basis of tolerance by exploring the disease responsive differentially expressed transcriptome and comparing them with that of a susceptible variety, Swarna-Sub1. A total of 815 and 551 genes were found to be differentially regulated in CR 1014 and Swarna-Sub1, respectively, at two different time points. The result shows that the ability to upregulate genes for glycosyl hydrolase, secondary metabolite biosynthesis, cytoskeleton and membrane integrity, the glycolytic pathway, and maintaining photosynthesis make CR 1014 a superior performer in resisting the ShB pathogen. We discuss several putative candidate genes for ShB resistance. The present study, for the first time, revealed the basis of ShB tolerance in the germplasm CR1014 and should prove to be particularly valuable in understanding molecular response to ShB infection. The knowledge could be utilized to devise strategies to manage the disease better.Not Availabl

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Not AvailableSheath blight disease of rice causes substantial crop losses and resistance sources are rare. A moderately resistant genotype CR 1014 was identified and hybridized with highly susceptible genotype Swarna-Sub1. In the F2 and F2:3 generations, three QTLs (qShB-1.1, qShB-1.2 and qShB-1.3) were mapped in chromosome-1. In F5 generation of the same cross and F4 generation of an alternative mapping population (Tapaswini/CR 1014), only the major QTL qShB-1.1 was recorded consistently with high LOD score (> 5.0). This stable QTL was co-localized with qShB1 reported earlier from Oryza nivara. A typical leucine rich repeat (LRR) motif containing gene (LOC_Os01g65650) and a chitin-inducible gibberellin-responsive protein coding non-LRR gene (LOC_Os01g65900) located within qShB-1.1 with high expression levels in leaf and shoot were predicted as putative candidate genes among others. Nearly 27.8% reduction in relative lesion height was recorded among several near isogenic lines of Swarna-Sub1 carrying the QTL region from CR 1014.ICA

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Not AvailableThe Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1–2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).Department of Biotechnolog