Glimpse of some of my research activities
Strawberry and tomato: Genetics of disease resistance
Strawberry and tomato are the important specialty crops with major production in Florida and California. Our recent research on genetic mapping of tomato Ty-6 gene for resistance to tomato yellow leaf curl virus is out now (Gill et al., Theoretical & Applied Genetics, 2019). Another work on fine mapping of strawberry Pc2 gene against Phytophthora crown rot is getting ready for publication.
Draft genome sequence of Puccinia novopanici (Switchgrass rust)
Puccinia novopanici is an important biotrophic fungal pathogen that causes rust disease in switchgrass. Lack of genomic resources for P. novopanici has hampered the progress towards developing effective disease resistance against this pathogen. Therefore, we have sequenced the whole genome of P. novopanici and generated a framework to understand pathogenicity mechanisms, identify effectors, repeat element invasion, genome evolution, and comparative genomics among Puccinia species in the future. For more details, refer to Gill et al., Phytopathology, 2019. (Image: Switchgrass cv. Summer leaves infected with P. novopanici (Left); P. novopanici infection structures on switchgrass leaf (Right).
Draft genome sequence of Puccinia novopanici (Switchgrass rust)
Puccinia novopanici is an important biotrophic fungal pathogen that causes rust disease in switchgrass. Lack of genomic resources for P. novopanici has hampered the progress towards developing effective disease resistance against this pathogen. Therefore, we have sequenced the whole genome of P. novopanici and generated a framework to understand pathogenicity mechanisms, identify effectors, repeat element invasion, genome evolution, and comparative genomics among Puccinia species in the future. For more details, refer to Gill et al., Phytopathology, 2019. (Image: Switchgrass cv. Summer leaves infected with P. novopanici (Left); P. novopanici infection structures on switchgrass leaf (Right). Phosphite on disease suppression and dsRNA based silencing
We explored the use of Phi in controlling fungal pathogens Puccinia emaculata and Phakopsora pachyrhizi the causal agents of the switchgrass rust and the Asian soybean rust, respectively. Phi primes host defenses and efficiently inhibits growth of both fungal pathogens. Transcriptomic studies were conducted on host and pathogen for each patho-system. A few Phi targets identified through RNAseq in P. emaculata were functionally characterized by rust inoculation of switchgrass leaves sprayed with double stranded (ds) RNAs. For more details, refer to Gill et al., The Plant Journal, 2018. (Image: Venn diagram of differentially expressed genes in Puccinia emaculata and Phakopsora pachyrhizi identified via RNAseq analyses).Genetic mapping and cloning
The inherent ability of a plant to protect against various biotic and abiotic stresses is environmentally safe and sustainable way of plant production. Therefore, it is very important to capture the natural germplasm diversity and identify novel traits and sources of resistance against various stresses. The underlying genes/genomic regions/QTL’s (Quantitative Trait Loci) for a specific trait can be identified using genetic mapping approaches and transferred to cultivated varieties of agricultural crops. I performed a comprehensive genetic analysis of six mutants showing susceptibility of wheat and barley stem rust (Puccinia graminis f.sp. tritici) and developed high-resolution genetic map of rpr2 mutant. One such team effort also led to map based cloning of one of the resistance gene, Rpg5 in barley. (Image: Genetic map of chro. 6H of barley; For more details, refer to Gill et al., Theoretical and Applied Genetics, 2016; Brueggeman et al., PNAS, 2008).
Lignin content and disease resistance
Downregulation of lignin in alfalfa is associated with increased availability of cell wall polysaccharides for biofuel production. However, association of lignin content with disease resistance against root pathogens has not been explored in detail. We tested alfalfa lines downregulated for lignin content for resistance to Phymatotrichum root rot and Fusarium wilt caused by Phymatotrichopsis omnivora and Fusarium oxysporum f. sp. medicaginis, respectively, and found them more resistant against these diseases. Improved disease resistance is associated with increased accumulation and/or spillover of flux towards the (iso)flavonoid pathway. Refer to Gill et al., Plant, Cell & Environment, 2017. (Image: disease development on alfalfa lines after F. oxysporum f. sp. medicaginis inoculations).
Forward genetics and transposon tagging based gene identification
Transposable elements are being used by scientists to tag genes in plants. In Medicago truncatula, a model legume, Tnt1 retrotransposon based mutant population is available. Using forward genetics screening of ~2500 mutants against Asian soybean rust, we identified several mutants. One such mutant, epr (enhanced penetration of rust), showed small germ tubes and enhanced penetration of P. pachyrhizi on leaf surface. Genetic co-segregation analysis identified a Cytochrome p450 gene which co-segregates with the epr phenotype. (Image: Gene structure of Cyp450 and SEM analysis of mutant and wild-type plants; Up-coming publication).
Downregulation of lignin in alfalfa is associated with increased availability of cell wall polysaccharides for biofuel production. However, association of lignin content with disease resistance against root pathogens has not been explored in detail. We tested alfalfa lines downregulated for lignin content for resistance to Phymatotrichum root rot and Fusarium wilt caused by Phymatotrichopsis omnivora and Fusarium oxysporum f. sp. medicaginis, respectively, and found them more resistant against these diseases. Improved disease resistance is associated with increased accumulation and/or spillover of flux towards the (iso)flavonoid pathway. Refer to Gill et al., Plant, Cell & Environment, 2017. (Image: disease development on alfalfa lines after F. oxysporum f. sp. medicaginis inoculations).
Forward genetics and transposon tagging based gene identificationTransposable elements are being used by scientists to tag genes in plants. In Medicago truncatula, a model legume, Tnt1 retrotransposon based mutant population is available. Using forward genetics screening of ~2500 mutants against Asian soybean rust, we identified several mutants. One such mutant, epr (enhanced penetration of rust), showed small germ tubes and enhanced penetration of P. pachyrhizi on leaf surface. Genetic co-segregation analysis identified a Cytochrome p450 gene which co-segregates with the epr phenotype. (Image: Gene structure of Cyp450 and SEM analysis of mutant and wild-type plants; Up-coming publication).
Host vs nonhost disease resistance
Depending upon the nature of plant-pathogen interactions, plants generally have two main defense mechanisms, host resistance and nonhost resistance. Host resistance is generally controlled by single R genes and less durable compared to nonhost resistance. In contrast, nonhost resistance is believed to be a multi-gene trait and more durable. Due to the durability of nonhost resistance over host resistance, nonhost resistance holds great promise for agriculture. Despite their classification into two classes, host and nonhost resistance share more similarities than differences in their mechanisms and resistance process. (Image: Host vs nonhost resistance; Gill et al., Phytopathology, 2015).
Depending upon the nature of plant-pathogen interactions, plants generally have two main defense mechanisms, host resistance and nonhost resistance. Host resistance is generally controlled by single R genes and less durable compared to nonhost resistance. In contrast, nonhost resistance is believed to be a multi-gene trait and more durable. Due to the durability of nonhost resistance over host resistance, nonhost resistance holds great promise for agriculture. Despite their classification into two classes, host and nonhost resistance share more similarities than differences in their mechanisms and resistance process. (Image: Host vs nonhost resistance; Gill et al., Phytopathology, 2015).
Development of Brachypodium-Puccinia emaculata nonhost pathosystem
Switchgrass rust, caused by Puccinia emaculata, is an important disease of switchgrass, a potential biofuel crop in the United States. We characterized P. emaculata interactions with six monocot nonhost species and identified Brachypodium distachyon as a suitable nonhost model to study switchgrass rust. Brachypodium exhibit type I nonhost resistance against P. emaculata. Brachypodium accessions also exhibit variations in resistance response against P. emaculata. Brachypodium nonhost resistance against P. emaculata may involve various defense pathways based on our transcript profiling data of defense related genes. (Image: P. emaculata infection process on Brachypodium; Gill et al., BMC Plant Biology, 2015).
Switchgrass rust, caused by Puccinia emaculata, is an important disease of switchgrass, a potential biofuel crop in the United States. We characterized P. emaculata interactions with six monocot nonhost species and identified Brachypodium distachyon as a suitable nonhost model to study switchgrass rust. Brachypodium exhibit type I nonhost resistance against P. emaculata. Brachypodium accessions also exhibit variations in resistance response against P. emaculata. Brachypodium nonhost resistance against P. emaculata may involve various defense pathways based on our transcript profiling data of defense related genes. (Image: P. emaculata infection process on Brachypodium; Gill et al., BMC Plant Biology, 2015).
Targeted genome editing (CRISPR-Cas9 system)
CRISPR-Cas9 based targeted genome editing is a new cutting edge molecular technology to generate desired changes in plant genomes. In M. truncatula,tThe Tnt1-based loss-of-function mutant population is widely used by researchers worldwide. Recently, I developed a novel approach to exploit CRISPR-Cas9 based transcriptional activation in combination with Tnt1 mutagenesis to develop gain of function mutagenesis. I also routinely use CRISPR-Cas9 system to generate targeted mutations in gene/s of interest. (Image: Flow chart of CRISPR-Cas9 and Tnt1 based activation tagging; Up-coming publication).
CRISPR-Cas9 based targeted genome editing is a new cutting edge molecular technology to generate desired changes in plant genomes. In M. truncatula,tThe Tnt1-based loss-of-function mutant population is widely used by researchers worldwide. Recently, I developed a novel approach to exploit CRISPR-Cas9 based transcriptional activation in combination with Tnt1 mutagenesis to develop gain of function mutagenesis. I also routinely use CRISPR-Cas9 system to generate targeted mutations in gene/s of interest. (Image: Flow chart of CRISPR-Cas9 and Tnt1 based activation tagging; Up-coming publication).
In Brassica spp. oil and meal quality are the important breeding objectives. I worked on Brassica rapa and Brassica nigra and developed a novel micro-propagation based approach for rapid multiplication of S-allele (self-incompatibility allele) homozygous lines in Brassica rapa to facilitate hybrid development (Gill et al., 2006). Another focus was to generate variability in diploid proginator, Brassica nigra using mutagenesis, selection and back-crossing. (Images: (top) Micropropagation of s-allele homozygotes; Gill et al., J. of Oilseeds Research,2006; (bottom) Breeding strategies).
Abiotic (drought) and biotic (insect) stress tolerance
Abiotic stress especially drought stress is the most frequent abiotic stress that crop plant face in the world. Drought tolerance is one of the breeding objective for most crops. We have developed alfalfa plants with improved drought avoidance parameters and insect (thrip) resistance. The mechanism of abiotic and biotic stress tolerance in these alfalfa lines has now been identified.
Abiotic stress especially drought stress is the most frequent abiotic stress that crop plant face in the world. Drought tolerance is one of the breeding objective for most crops. We have developed alfalfa plants with improved drought avoidance parameters and insect (thrip) resistance. The mechanism of abiotic and biotic stress tolerance in these alfalfa lines has now been identified.
My work on M. truncatula have also identified mutants that are more susceptible to water stress (Images: (top) Alfalfa thrip resistant and susceptible plants. (bottom) Infrared imaging showing leaf water loss in susceptible and tolerant M. truncatula plants).
If you wish to know more about my research and interests, please drop me an email.
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