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Parvathy S.T.,Indian Agricultural Research Institute | Parvathy S.T.,ICAR Indian Institute of Oilseeds Research | Srinivasan R.,Indian Agricultural Research Institute
Plant Biotechnology Reports | Year: 2016

Cryptic promoter elements play a significant role in evolution of plant gene expression patterns and are prospective tools for creating gene expression systems in plants. In a previous report, a 452 bp promoter fragment designated as cryptic root-specific promoter (AY601849) was identified immediately upstream to T-DNA insertion, in the intergenic region between divergent genes SAHH1 and SHMT4, in T-DNA tagged mutant M57 of Arabidopsis thaliana. In silico analysis of 452 bp promoter revealed typical eukaryotic promoter architecture, presence of root-specific motifs and other cis-regulatory motifs responsible for the spatial and temporal expression. GUS expression driven by 452 bp in M57 was developmentally as well as light-regulated. The AT-rich 452 bp promoter does not show homology to any known sequences. The 452 bp promoter was further proved cryptic and detailed molecular characterization of the promoter carried out through serial 5′ and 3′ deletion analysis, by cloning the promoter fragments upstream to promoter-less GUS vector. A 279 bp fragment obtained by deleting 173 bp from 5′ end of 452 bp was capable of driving root-specific expression, similar to that of full-length promoter. Further, root tip-specific, root-specific and core-regulatory motifs for root-specific expression were identified at positions 173–227, 251–323 and 408–452 bp, respectively, from the 5′ end of 452 bp. The 452 bp promoter was equally functional in inverse orientation, hence bidirectional and symmetric. In heterologous systems, such as Brassica juncea and Oryza sativa, the promoter activity was not significant since GUS was not visually detected in transient assays. © 2016, Korean Society for Plant Biotechnology and Springer Japan. Source

Rao E.S.,Indian Institute of Horticultural Research | Rao E.S.,Genetic Resources and Seed Unit | Kadirvel P.,ICAR Indian Institute of Oilseeds Research | Kadirvel P.,Genetic Resources and Seed Unit | And 6 more authors.
PLoS ONE | Year: 2015

Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0%to 25.8%phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A-297-6 and SpDREB1A-297-12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten markerassisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato. © 2015 Rao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

Mulpuri S.,ICAR Indian Institute of Oilseeds Research | Muddanuru T.,ICAR Indian Institute of Oilseeds Research
Australasian Plant Disease Notes | Year: 2016

Symptoms of phyllody on sunflower in India have previously been reported however, lately, the frequency of phyllody observed has increased. Transmission electron microscope (TEM) examination and PCR including nested PCR analyses using universal primers (P1/P7 and R16F2n/R2) specific to phytoplasma confirmed that the floral abnormalities are due to phytoplasma infection. Nucleotide BLAST analysis of the PCR sequences showed highest identity with sequences of phytoplasma members of the 16SrII group (‘Candidatus Phytoplasma aurantifolia’). Further, phylogenetic analysis of the 16S rRNA sequences clustered the sequences of both sunflower (HAP1) and sesame (SIP1) with other members of 16SrII. ‘Candidatus Phytoplasma’ species assignment and 16Sr group/subgroup classification using iPhyClassifier confirmed that the phytoplasma causing sunflower phyllody is a ‘Candidatus Phytoplasma aurantifolia’ related strain and belongs to the 16SrII-D group. The molecular characters of sunflower phytoplasma were compared with that of the phytoplasma associated with sesame phyllody (used as reference) which showed that the R16F2n/R2 sequences of both the phytoplasmas are identical indicating that the 16SrII-D phytoplasma that is associated with sesame phyllody can infect sunflower as well. © 2016, Australasian Plant Pathology Society Inc. Source

Jacob J.,ICAR Indian Institute of Millets Research | Sujatha M.,ICAR Indian Institute of Oilseeds Research | Varaprasad S.K.,ICAR Indian Institute of Oilseeds Research
Plant Genetic Resources: Characterisation and Utilisation | Year: 2016

Acetohydroxyacid synthase (AHAS) inhibiting herbicides have played a significant role in effective weed control in the cultivation of sunflower since their discovery. The development of sunflower lines and hybrids resistant to these herbicides made their post-emergence application possible. In this study, wild Helianthus species were screened phenotypically for imidazolinone (IMI) and sulfonylurea (SU) resistance by herbicide spray and for allelic variations at Ahasl1 (Ahas1 large subunit) locus using simple sequence repeat and single nucleotide polymorphism markers. Helianthus praecox accession 1823 plants showed promising resistance to three classes of SU-based herbicides and Helianthus nuttallii accession NUT05 plants remained green for a longer time after imazethapyr spray. A total of 50 accessions belonging to 21 wild Helianthus species of different ploidy levels were analysed for allelic variation along with some parents of commercial sunflower hybrids. None of the wild species showed the resistant allele (Ahasl1-1) similar to SCG101 (IMI-resistant line), although it is present in some of the parental lines of hybrids. However, the parental lines having Ahasl1-1-type allele failed to survive the field dose of imazethapyr spray. Inter-species and inter-accessional allelic variation could be observed among the species. PRA1823 and NUT05 showed repeat length variations at Ahasl1 locus. Sequencing of full length Ahasl1 gene from both these accessions did not reveal any resistance mutations in the protein sequences. The molecular basis of the phenotypes identified in this study could be explored further and utilized in breeding programmes for imparting herbicide resistance in cultivated hybrids across sunflower growing regions of the world. Copyright © NIAB 2016 Source

Kadirvel P.,ICAR Indian Institute of Oilseeds Research | Ravi D.,ICAR Indian Institute of Oilseeds Research | Ravi D.,Telangana University | Mukta N.,ICAR Indian Institute of Oilseeds Research | And 8 more authors.
Plant Genetic Resources: Characterisation and Utilisation | Year: 2016

Safflower is a traditional oilseed crop in the world. Its seed oil is a healthy edible oil containing high amount of unsaturated fatty acids. Genetically diverse exotic cultivars are valuable germplasm for introducing new diversity in safflower improvement programmes. In this study, we characterized safflower cultivars of India (30) and Mexico (23) comprising varieties, hybrids and advanced lines developed over 50 years for genetic distinctiveness using 38 simple sequence repeat (SSR) loci. Genetic diversity estimates across cultivar groups (total, India and Mexico) were as follows: mean number of alleles (3.2, 3.1, 2.6), expected heterozygosity (0.42, 0.37, 0.37) and polymorphism information content (0.36, 0.33, 0.32) respectively, which suggested narrow SSR allelic diversity within and between cultivar groups. However, distance-based cluster analysis (neighbour-joining tree) and model-based STRUCTURE analysis revealed that safflower cultivars of India and Mexico, with the exception of a few, form two genetically distinct groups. High level of genetic variation explained between the populations (40%) and Fst estimate (0.4) suggested that the cultivar groups were highly differentiated with limited gene flow supporting a strong genetic structuring. High oil (~38%) and high oleic (73–79%) contents of a subset of Mexican safflower varieties and advanced lines were confirmed in field trials in India. These exotic sources from Mexico are valuable for safflower breeding programmes in India to develop new cultivars with high oil yielding potential and high oleic acid content, which is the current market demand. Copyright © NIAB 2016 Source

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