Vignesh Dhandapani - Academia.edu (original) (raw)

Papers by Vignesh Dhandapani

International Journal of Molecular Sciences

Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting th... more Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting the indigenous biodiversity. Invasive plants are generally less affected by pathogens, although the underlying molecular mechanisms responsible for their enhanced resistance are unknown. We investigated expression profiles of three defense hormones (salicylic acid, jasmonic acid, and ethylene) and their associated genes in the invasive weed, Alternanthera philoxeroides, and its native congener, A. sessilis, after inoculation with Rhizoctonia solani. Pathogenicity tests showed significantly slower disease progression in A. philoxeroides compared to A. sessilis. Expression analyses revealed jasmonic acid (JA) and ethylene (ET) expressions were differentially regulated between A. philoxeroides and A. sessilis, with the former having prominent antagonistic cross-talk between salicylic acid (SA) and JA, and the latter showing weak or no cross-talk during disease development. We also found that ...

The involvement of MADS-box transcription factors in the development of seeds, flowers, and fruit... more The involvement of MADS-box transcription factors in the development of seeds, flowers, and fruit is well known. Large numbers of MADS-box genes have been characterized and reported in major plants such as Arabidopsis thaliana (107), Oryza sativa (75), Zea mays (75), and Cucumis sativus (43). However, there is little information about MADS-box genes in the economically and morphologically important genus Brassica. Thus, we performed a series of computational analyses on the recently published Brassica rapa genome and identified 167 potential MADS-box genes. Chromosomal localization of these genes revealed many duplicate genes and 10 tandem repeats from B. rapa chromosomes, though none on A04, A08, and A10. Neighbor-joining phylogenetic analysis was performed between B. rapa, A. thaliana, O. sativa, Z. mays, and C. sativus genes, and type-I and type-II groups were differentiated by their gene clades. Based on their phylogeny and functional characters, type-I group was divided into th...

Journal of Biomedical Materials Research Part B: Applied Biomaterials

Microbiome

Background Research around the weedkiller Roundup is among the most contentious of the twenty-fir... more Background Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results We demonstrate that chronic exposure to ecologically relevant concentrat...

International Journal of Molecular Sciences

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreas... more Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra01...

Whole genome sequencing is instrumental for the study of genome variation in natural populations,... more Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most s...

International Journal of Molecular Sciences

Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quant... more Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quantitative trait loci (QTLs) for clubroot resistance have been identified in Brassica, disease-related damage continues to occur owing to differences in host variety and constant pathogen variation. Here, we investigated the inheritance of clubroot resistance in a double haploid population developed by crossing clubroot resistant and susceptible lines “09CR500” and “09CR501”, respectively. The resistance of “09CR500” to Plasmodiophora brassicae pathotype “Banglim” was controlled as a single dominant gene, with the segregation of resistance and susceptibility being nearly 1:1. PbBrA08Banglim was identified as having a logarithm of odds value of 7.9–74.8, and a phenotypic variance of 26.0–97.1% with flanking marker “09CR.11390652” in A08. After aligning QTL regions to the B. rapa reference genome, 11 genes were selected as candidates. PbBrA08Banglim was located near Crr1, CRs, and Rcr9 loci, ...

Horticulture, Environment, and Biotechnology

Traditional breeding methods usually involve field tests carried out by experienced breeders. How... more Traditional breeding methods usually involve field tests carried out by experienced breeders. However, such methods are costly and time-consuming. Recently, with the development of Next-Generation Sequencing (NGS) technology, molecular markers are being utilized for selection processes in breeding. To implement a high-throughput system using molecular markers in Chinese cabbage ( Brassica rapa subsp. pekinensis ) breeding, we developed single nucleotide polymorphism (SNP) marker sets for background selection and testing F 1 purity using Fluidigm genotyping assays. SNPs were generated using NGS technology on 209 varieties of Chinese cabbage collected from around the world. Those with minor allele frequency ≥ 5% and polymorphism information content ≥ 0.3 were screened, and then based on the physical distribution among the 10 chromosomes, 177 SNPs were selected and synthesized for testing. To obtain marker sets with high selection efficiency, we tested 192 SNPs on 45 types of inbred lines and 29 types of F 1 hybrids. Among the 192 SNPs, we selected 96 markers sets for background selection and 24 marker sets for F 1 purity testing according to the following criteria; the genotype of the parents was homozygous, and the F 1 follows the parents’ genotypes. These SNP sets are suitable for high-throughput systems using the 96.96 and 192.24 integrated fluidic circuit platforms of Fluidigm genotyping assays. These SNP marker sets are not only efficient for selecting of early fixed lines as background selection but are also useful for testing the purity of F 1 hybrids.

Plant Molecular Biology Reporter

Horticulture, Environment, and Biotechnology

3 Biotech, 2018

Sugarcane ( sp.) is predominantly grown in both tropics and subtropics in India, and the subtropi... more Sugarcane ( sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using tri...

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 2, 2017

QTLs and candidate gene markers associated with leaf morphological and color traits were identifi... more QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years. Overall, 158 and 80 QTLs associated with 23 and 14 traits were detected in the DH and RIL populations, respectively. Among them, 23 common robust-QTLs belonging to 12 traits were detected in common loci over the replications. Through comparative analysis, five crucifer genetic blocks corresponding to morphology trait (R, J&U, F and E) and color trait (F, E) were identified in three major linkage groups (A2, A3 and A7). These might be key conserved genomic regions involved ...

Genomics & Informatics, 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational... more MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

International Journal of Molecular Sciences

Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting th... more Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting the indigenous biodiversity. Invasive plants are generally less affected by pathogens, although the underlying molecular mechanisms responsible for their enhanced resistance are unknown. We investigated expression profiles of three defense hormones (salicylic acid, jasmonic acid, and ethylene) and their associated genes in the invasive weed, Alternanthera philoxeroides, and its native congener, A. sessilis, after inoculation with Rhizoctonia solani. Pathogenicity tests showed significantly slower disease progression in A. philoxeroides compared to A. sessilis. Expression analyses revealed jasmonic acid (JA) and ethylene (ET) expressions were differentially regulated between A. philoxeroides and A. sessilis, with the former having prominent antagonistic cross-talk between salicylic acid (SA) and JA, and the latter showing weak or no cross-talk during disease development. We also found that ...

The involvement of MADS-box transcription factors in the development of seeds, flowers, and fruit... more The involvement of MADS-box transcription factors in the development of seeds, flowers, and fruit is well known. Large numbers of MADS-box genes have been characterized and reported in major plants such as Arabidopsis thaliana (107), Oryza sativa (75), Zea mays (75), and Cucumis sativus (43). However, there is little information about MADS-box genes in the economically and morphologically important genus Brassica. Thus, we performed a series of computational analyses on the recently published Brassica rapa genome and identified 167 potential MADS-box genes. Chromosomal localization of these genes revealed many duplicate genes and 10 tandem repeats from B. rapa chromosomes, though none on A04, A08, and A10. Neighbor-joining phylogenetic analysis was performed between B. rapa, A. thaliana, O. sativa, Z. mays, and C. sativus genes, and type-I and type-II groups were differentiated by their gene clades. Based on their phylogeny and functional characters, type-I group was divided into th...

Journal of Biomedical Materials Research Part B: Applied Biomaterials

Microbiome

Background Research around the weedkiller Roundup is among the most contentious of the twenty-fir... more Background Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results We demonstrate that chronic exposure to ecologically relevant concentrat...

International Journal of Molecular Sciences

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreas... more Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra01...

Whole genome sequencing is instrumental for the study of genome variation in natural populations,... more Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most s...

International Journal of Molecular Sciences

Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quant... more Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quantitative trait loci (QTLs) for clubroot resistance have been identified in Brassica, disease-related damage continues to occur owing to differences in host variety and constant pathogen variation. Here, we investigated the inheritance of clubroot resistance in a double haploid population developed by crossing clubroot resistant and susceptible lines “09CR500” and “09CR501”, respectively. The resistance of “09CR500” to Plasmodiophora brassicae pathotype “Banglim” was controlled as a single dominant gene, with the segregation of resistance and susceptibility being nearly 1:1. PbBrA08Banglim was identified as having a logarithm of odds value of 7.9–74.8, and a phenotypic variance of 26.0–97.1% with flanking marker “09CR.11390652” in A08. After aligning QTL regions to the B. rapa reference genome, 11 genes were selected as candidates. PbBrA08Banglim was located near Crr1, CRs, and Rcr9 loci, ...

Horticulture, Environment, and Biotechnology

Traditional breeding methods usually involve field tests carried out by experienced breeders. How... more Traditional breeding methods usually involve field tests carried out by experienced breeders. However, such methods are costly and time-consuming. Recently, with the development of Next-Generation Sequencing (NGS) technology, molecular markers are being utilized for selection processes in breeding. To implement a high-throughput system using molecular markers in Chinese cabbage ( Brassica rapa subsp. pekinensis ) breeding, we developed single nucleotide polymorphism (SNP) marker sets for background selection and testing F 1 purity using Fluidigm genotyping assays. SNPs were generated using NGS technology on 209 varieties of Chinese cabbage collected from around the world. Those with minor allele frequency ≥ 5% and polymorphism information content ≥ 0.3 were screened, and then based on the physical distribution among the 10 chromosomes, 177 SNPs were selected and synthesized for testing. To obtain marker sets with high selection efficiency, we tested 192 SNPs on 45 types of inbred lines and 29 types of F 1 hybrids. Among the 192 SNPs, we selected 96 markers sets for background selection and 24 marker sets for F 1 purity testing according to the following criteria; the genotype of the parents was homozygous, and the F 1 follows the parents’ genotypes. These SNP sets are suitable for high-throughput systems using the 96.96 and 192.24 integrated fluidic circuit platforms of Fluidigm genotyping assays. These SNP marker sets are not only efficient for selecting of early fixed lines as background selection but are also useful for testing the purity of F 1 hybrids.

Plant Molecular Biology Reporter

Horticulture, Environment, and Biotechnology

3 Biotech, 2018

Sugarcane ( sp.) is predominantly grown in both tropics and subtropics in India, and the subtropi... more Sugarcane ( sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using tri...

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 2, 2017

QTLs and candidate gene markers associated with leaf morphological and color traits were identifi... more QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years. Overall, 158 and 80 QTLs associated with 23 and 14 traits were detected in the DH and RIL populations, respectively. Among them, 23 common robust-QTLs belonging to 12 traits were detected in common loci over the replications. Through comparative analysis, five crucifer genetic blocks corresponding to morphology trait (R, J&U, F and E) and color trait (F, E) were identified in three major linkage groups (A2, A3 and A7). These might be key conserved genomic regions involved ...

Genomics & Informatics, 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational... more MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.