Biology subjects

Thiyagarajan, K.

Publications and source records attributed to Thiyagarajan, K..

5 recordsLinked to original sources

bioRxiv2026

Computational predictions and evolutionary analysis of LrK10 kinase-related putative PSTOL1 gene homeologs in wheat and orthologs of its wild relatives.

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesize that the putative wheat TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examine the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversions tracts between these two genes and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appears to have diverged from a common ancestor, acquiring distinct structural organizations and biological functions.

genomics↗

bioRxiv2023

Factors influencing Agrobacterium-mediated genetic transformation efficiency in wheat.

Assessment of the efficiency of Agrobacterium tumefaciens mediated transformation in four bread wheat varieties was focused and upon optimization of experiments done to obtain tangible results. The four varieties namely Fielder, Navojoa, Baj and Kachu/saul were transformed with optimized protocols, subsequently randomly selected from selection medium amalgamated with phosphinothricin (Glufosinate). Initially the variety Fielder was proceeded with 36 different concentrations of synthetic auxins 2,4-D and Picloram as 36 treatments. The treatment 30 (48 g of 2,4-D and 64 g of Picloram) has shown higher efficiency and is comparable in terms of the three traits studied. Additionally, antioxidants and growth regulators were adjusted to obtain better result towards reasonable transformation frequency. Based on the optimization for the variety Fielder, additional varieties were also tested and selected against the selectable marker PPT. Selected genotypes were subjected for gusA or Bar gene PCR amplification. The result revealed the frequency of transgenesis with the range of 60-70% with the varieties studied, however the whole experiment needs further repetitions for confirmatory result. Transgenic genotypes of the Fielder variety showed moderate to strong GUS expression in leaves, anthers, seeds, seed coats, roots compare to non-transgenic control plant tissues. PPT leaf painting assay showed the lack of necrosis on painted area of leaves in transgenic genotypes compared to the non-transgenic ones.

plant biology↗

bioRxiv2022

Allele mining, evolutionary genetic analysis of TaHKT1;5 gene and evaluation of salinity stress in selected lines of wheat.

This study reports the novel allelic diversity in HKT 1;5 gene (High Affinity Potassium Transporter) in bread wheat and its phylogenetic relationship among the paralogs/orthologs of in Triticum aestivum and its wild relatives. HKT 1;5 gene is a known and pivotal gene associated with the salinity tolerance in plants upon the discrimination of K+ over Na+ in leaves without change in Na+ concentration in root. This gene was sequenced in a diverse collection of bread wheat, durum wheat, wild relatives, and ditelosomic lines. Sequence analysis in bread wheat led to the identification of four alleles, which could be distinguished by number of SNPs. Sequence comparison between monocot bread wheat and dicot Arabidopsis thaliana revealed that the HKT1;5 gene is conserved at level of exonic regions; however, the presence of transposable elements especially in intronic regions is further intriguing towards evolutionary relatedness. Two paralogous or major alleles observed in Triticum monoccum and Aegilops tauschii were further categorized as sub-alleles based on their SNPs comparison. This gene was absent in T. urartu in accordance with existing evidence, while it was found in A. speltoides (an allelic variant) with a few base pairs insertion in the exon1 region causing a frameshift mutation with an altered amino acids and genomic database mining unveiled additional alleles in this species. Ditelosomic lines with 4DL and 4DS chromosomes revealed a higher similarity with bread and durum wheat respectively. Phylogenetic studies of HKT1;5 orthologs from different Poaceae species revealed the occurrence of five different ortholog groups with taxonomic consistency. Phenotyping based salinity stress experiment distinguished the unknown lines for salinity tolerance and sensitiveness in comparison with known reference lines and possible allelic comparison was made. The salinity stress analysis further revealed that some known drought/heat tolerance lines showed slightly better salinity tolerance with mean values and variability of traits than known saline tolerant wheat line at controlled ambient.

genetics↗

bioRxiv2022

Gene editing for accelerated breeding in wheat

Diseases adversely affect grain yield of crop plants. Leaf rust is a major disease of wheat. As race-specific resistance breaks down, introduction of newer sources of resistance often from older accessions is necessary. Linkage drag from the donor accessions adversely impacts grain yield. As a result, CIMMYT breeding effort has shifted to using durable resistance, also referred to as race non-specific host resistance, which allows slow rusting but maintains grain yield. One of the key genes for durable resistance is Lr67 and the resistant form of this gene is absent in CIMMYT elite lines. Hence, we have initiated efforts to convert the susceptible copy of Lr67 into its resistant form directly in these elite lines using gene editing. This would eliminate backcrossing and thus save time as well as eliminate linkage drag that would accompany the resistant copy of the gene if it were to be introgressed from an older accession. As first steps, we have isolated and sequenced the genomic copies from each of the A, B, and D genome of the Lr67 gene from three elite lines and an experimental line. Identification of more than 50 single nucleotide polymorphisms (SNPs) in the open reading frames (ORF) among these lines would be useful in designing the guide RNA molecules with precision. Further, we have streamlined genetic transformation of these elite lines, a prerequisite step for gene editing.

molecular biology↗

bioRxiv2022

Identification and evolutionary analysis of a Triticeae tribe specific novel non-autonomous DNA transposon in DREB related Dehydration Responsive Factor1 gene.

A non-autonomous DNA transposon was identified in the DRF1 gene, belonging to the DREB gene family, the presence of this element was initially assessed in the Triticum durum DRF1 gene and subsequently it was also identified in Aegilops speltoides and Triticum urartu DRF1 genes. The DRF1 gene consists of four exons and three introns, the transposon carrying core element is inserted between the first and the third introns. Our studies identified inverted repeats, target site duplications and the presence of many internal reverse and direct short tandem and long tandem repeats, that all represent signals of a transposable element. Based on transposon specific sequence and position of the terminal inverted repeats, a possible transposition mechanism was inferred. As the identified transposable element does not possess a sequence coding for a transposase enzyme, it represents a non-autonomous element. The transposon encompasses a core element with two small, transcribed regions (Exon 2 and Exon 3) that are combined by alternative splicing during gene expression and an intron (intron2). A possible role of this non-autonomous DNA transposon in the alternative splicing regulation was investigated by a genomics approach. Divergence time analysis supported the relatively recent evolution of this transposon in Triticeae comparing to other tribes and further there is no footprints or highly disrupted footprints sequence such as TIR, TSD in other earlier evolved Poaceae member species were observed, which revealed the novelty and well-preserved nature of these signals in Triticeae. While other monocots (apart from Poaceae) and dicots, including Arabidopsis thaliana, neither showed this transposon insertion and nor revealed the existence of alternative spliced gene transcripts. In Poaceae members the core element is well preserved with disturbed transposon and transposon signals, while the tribe Triticeae especially wheat, its progenitors have intact DRF1 transposon and its signals.

evolutionary biology↗