Institutional Publications
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Item Whole genome re-sequencing of soybean accession ec241780 providing genomic landscape of candidate genes involved in rust resistance(Bentham Science Publishers, 2020) Ratnaparkhe, Milind Balkrishna; Marmat, Niharika; Kumawat, Giriraj; Shivakumar, Maranna; Kamble, Viraj Gangadhar; Nataraj, Vennampally; Ramesh, Shunmugiah Veluchamy; Deshmukh, Milind Panjabrao; Singh, Ajay Kumar; Sonah, Humira; Deshmukh, Rupesh Kailasrao; Prasad, Manoj; Chand, Suresh; Gupta, SanjayBackground: In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods: A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results: Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion: The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.Item Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits(PLOS, 2015) Yadav, Chandra Bhan; Bhareti, Priyanka; Muthamilarasan, Mehanathan; Mukherjee, Minakshi; Khan, Yusuf; Rathi, Pushpendra; Prasad, ManojMungbean yellow mosaic India virus (MYMIV) is a bipartite Geminivirus, which causes severe yield loss in soybean (Glycine max). Considering this, the present study was conducted to develop large-scale genome-wide single nucleotide polymorphism (SNP) markers and identify potential markers linked with known disease resistance loci for their effective use in genomics-assisted breeding to impart durable MYMIV tolerance. The whole-genome re-sequencing of MYMIV resistant cultivar 'UPSM-534' and susceptible Indian cultivar 'JS-335' was performed to identify high-quality SNPs and InDels (insertion and deletions). Approximately 234 and 255 million of 100-bp paired-end reads were generated from UPSM-534 and JS-335, respectively, which provided ~98% coverage of reference soybean genome. A total of 3083987 SNPs (1559556 in UPSM-534 and 1524431 in JS-335) and 562858 InDels (281958 in UPSM-534 and 280900 in JS-335) were identified. Of these, 1514 SNPs were found to be present in 564 candidate disease resistance genes. Among these, 829 non-synonymous and 671 synonymous SNPs were detected in 266 and 286 defence-related genes, respectively. Noteworthy, a non-synonymous SNP (in chromosome 18, named 18-1861613) at the 149th base-pair of LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE gene responsible for a G/C transversion [proline (CCC) to alanine(GCC)] was identified and validated in a set of 12 soybean cultivars. Taken together, the present study generated a large-scale genomic resource such as, SNPs and InDels at a genome-wide scale that will facilitate the dissection of various complex traits through construction of high-density linkage maps and fine mapping. In the present scenario, these markers can be effectively used to design high-density SNP arrays for their large-scale validation and high-throughput genotyping in diverse natural and mapping populations, which could accelerate genomics-assisted MYMIV disease resistance breeding in soybean.Item Differential soybean gene expression during early phase of infection with Mungbean yellow mosaic India virus(Springer, 2014) Yadav, Rajiv Kumar; Chattopadhyay, DebasisMungbean yellow mosaic India virus (MYMIV), a bipartite begomovirus, causes yellow mosaic disease to soybean. Studies related to host gene expression in response to begomovirus infection have mostly been performed with systemically infected tissues at a later period of infection. In this study, soybean gene expression analysis has been performed to understand local responses against MYMIV at an early stage of infection before appearance of detectable limit of late viral transcripts. 444 soybean transcripts belonging to eleven functional categories showed significant changes in expression level at two days after infection. MYMIV infection resulted in enhanced expression of genes associated with hypersensitive response, programmed cell death and resistance response pathways and reduced expression of genes for photosynthesis and sugar transport. Comparative expression analysis of selected transcripts in the susceptible and a resistant variety displayed differential expression of host genes involved in intercellular virus movement and long distance signaling of systemic acquired resistance.Item Advances in biotechnological applications in three important food legumes(Springer, 2014) Das, Alok; Parida, Swarup K.Legumes are the third largest family of flowering plants, known for their unique capacity of symbiotic nitrogen fixation. The draft genome sequences of three important food legumes [soybean (Glycine max), pigeonpea (Cajanus cajan) and chickpea (Cicer arietinum)] have been completed. Coupled with a deluge of information on transcriptomics, proteomics and metabolomics, they present a huge amount of genomic resources for the genetic improvement of legume crops. Developed molecular markers, structurally and functionally annotated genes/quantitative trait loci/alleles and regulatory sequences can be utilized in improvement breeding programmes. Further, the genetic transformation of two valuable pulses (chickpea and pigeonpea) has now taken centre stage, realizing the potential of genetically modified soybean, for enhanced prospects of food production. Together, the advances in biotechnological tools and the research community’s capacity to develop imaginative strategies will help in framing a legume development programme for ensuring the nutritional security of the world.Item Two chimeric regulators of G-protein signaling (RGS) proteins differentially modulate soybean heterotrimeric G-protein cycle(The American Society for Biochemistry and Molecular Biology, 2012) Choudhury, Swarup Roy; Westfall, Corey S.; Laborde, John P.; Bisht, Naveen C.; Jez, Joseph M.; Pandey, SonaHeterotrimeric G-proteins and the regulator of G-protein signaling (RGS) proteins, which accelerate the inherent GTPase activity of Gα proteins, are common in animals and encoded by large gene families; however, in plants G-protein signaling is thought to be more limited in scope. For example, Arabidopsis thaliana contains one Gα, one Gβ, three Gγ, and one RGS protein. Recent examination of the Glycine max (soybean) genome reveals a larger set of G-protein-related genes and raises the possibility of more intricate G-protein networks than previously observed in plants. Stopped-flow analysis of GTP-binding and GDP/GTP exchange for the four soybean Gα proteins (GmGα1-4) reveals differences in their kinetic properties. The soybean genome encodes two chimeric RGS proteins with an N-terminal seven transmembrane domain and a C-terminal RGS box. Both GmRGS interact with each of the four GmGα and regulate their GTPase activity. The GTPase-accelerating activities of GmRGS1 and -2 differ for each GmGα, suggesting more than one possible rate of the G-protein cycle initiated by each of the Gα proteins. The differential effects of GmRGS1 and GmRGS2 on GmGα1-4 result from a single valine versus alanine difference. The emerging picture suggests complex regulation of the G-protein cycle in soybean and in other plants with expanded G-protein networks.Item Conventional and novel Gγ protein families constitute the heterotrimeric G-protein signaling network in soybean(Public Library of Science, 2011) Choudhury, Swarup Roy; Bisht, Naveen C.; Thompson, Rheannon; Todorov, Oleg; Pandey, SonaHeterotrimeric G-proteins comprised of Gα, Gβ and Gγ proteins are important signal transducers in all eukaryotes. The Gγ protein of the G-protein heterotrimer is crucial for its proper targeting at the plasma membrane and correct functioning. Gγ proteins are significantly smaller and more diverse than the Gα and Gβ proteins. In model plants Arabidopsis and rice that have a single Gα and Gβ protein, the presence of two canonical Gγ proteins provide some diversity to the possible heterotrimeric combinations. Our recent analysis of the latest version of the soybean genome has identified ten Gγ proteins which belong to three distinct families based on their C-termini. We amplified the full length cDNAs, analyzed their detailed expression profile by quantitative PCR, assessed their localization and performed yeast-based interaction analysis to evaluate interaction specificity with different Gβ proteins. Our results show that ten Gγ genes are retained in the soybean genome and have interesting expression profiles across different developmental stages. Six of the newly identified proteins belong to two plant-specific Gγ protein families. Yeast-based interaction analyses predict some degree of interaction specificity between different Gβ and Gγ proteins. This research thus identifies a highly diverse G-protein network from a plant species. Homologs of these novel proteins have been previously identified as QTLs for grain size and yield in rice.Item Soybean cultivar resistant to mungbean yellow mosaic India virus infection induces viral RNA degradation earlier than the susceptible cultivar(Elsevier B.V., 2009) Yadav, Rajiv Kumar; Shukla, Rakesh Kumar; Chattopadhyay, DebasisYellow mosaic disease caused by whitefly-transmitted bipartite Geminiviruses is one of the major con- straints on productivity of a number of pulse crops. We have cloned the bipartite genome of Mungbean Yellow Mosaic India Virus isolated from infected Soybean. We report here that agroinfection of Soybean seedlings with a single uncut recombinant binary plasmid containing tandem dimers of both DNA A and DNA B resulted in 100% infectivity in susceptible varieties. To understand the mechanism of natural resistance in a Soybean variety, we compared the abundance of the viral RNAs in a resistant and a susceptible variety at the early time points after agroinfection. Whilst the resistant variety displayed synthesis but rapid degradation of the early viral RNAs; the degradation in the susceptible variety was delayed resulting in accumulation of those transcripts later in infection. Accumulation of the late viral transcripts and DNA replication were detectable only in the susceptible variety. This indicates that rapid degradation of the early viral transcripts, possibly through siRNA mechanism, is one of the probable mechanisms of natural resistance against geminivirus.