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Fandade V, Singh P, Singh D, Sharma H, Thakur G, Saini S, Kumar P, Mantri S, Bishnoi OP, Roy J. Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat (Triticum spp). Gene 2024; 896:148039. [PMID: 38036075 DOI: 10.1016/j.gene.2023.148039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Wheat (Triticum aestivum L.) is a crucial global staple crop, and is consistently being improved to enhance yield, disease resistance, and quality traits. However, the development of molecular markers is a challenging task due to its hexaploid genome. Molecular marker system such as simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) are helpful for breeding, but SNP has limitations due to its development cost and its conversion to breeder markers. The study proposed an in-silico approach, by utilizing the low-cost transcriptome sequencing of two parental lines, 'TAC 75' and 'WH 1105', to identify polymorphic SSRs for mapping in a recombinant inbred line (RIL) population. This study introduces a new approach to bridge wheat genetics intricacies and next-generation sequencing potential. It presents a comprehensive genome-wide SSR distribution using IWGSC CS RefSeq v2.1 genome assembly and to identify 189 polymorphic loci through in-silico strategy. Of these, 54.76% showed polymorphism between parents, surpassing the traditional low polymorphic success rate. A RIL population screening validated these markers, demonstrating the fitness of identified markers through chi-square tests. The designed SSRs were also validated for genetic diversity analysis in a subset of 37 Indian wheat genotypes and cross-transferability in the wild/relative wheat species. In diversity analysis, a subset of 38 markers revealed 95 alleles (2.5 allele/locus), indicating substantial genetic variation. Population structure analysis unveiled three distinct groups, supported by phylogenetic and PCoA analyses. Further the polymorphic SSRs were also analyzed for SSR-gene association using gene ontology analysis. By utilizing the developing seed transcriptome data within parental lines, the study has enhanced the polymorphic SSR identification precision and facilitated in the RIL population. The undertaken study pioneers the use of transcriptome sequencing and genetic mapping to overcome challenges posed by the intricate wheat genome. This approach offers a cost-effective, less labour-intensive alternative to conventional methods, providing a platform for advancing wheat breeding research.
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Affiliation(s)
- Vikas Fandade
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Pradeep Singh
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Dalwinder Singh
- Department of Anatomy and cell biology, University of Western Ontario, London, Canada.
| | - Himanshu Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Garima Thakur
- Protection for Plant Varieties and Farmers Rights Authority, New Delhi, India.
| | - Shivangi Saini
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Prashant Kumar
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Shrikant Mantri
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - O P Bishnoi
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar- 125004, India.
| | - Joy Roy
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
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Analysis of SSR and SNP markers. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Kumar P, Parveen A, Sharma H, Rahim MS, Mishra A, Kumar P, Shah K, Rishi V, Roy J. Understanding the regulatory relationship of abscisic acid and bZIP transcription factors towards amylose biosynthesis in wheat. Mol Biol Rep 2021; 48:2473-2483. [PMID: 33834358 DOI: 10.1007/s11033-021-06282-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Starch is biosynthesized during seed development and this process is regulated by many bZIP proteins in bread wheat. Abscisic acid (ABA), an important phyto-hormone involved in various physiological processes mediated by bZIPs in plants including seed development. The 'Group A' TabZIP transcription factors play important roles in the ABA signaling pathway in Arabidopsis, rice and other cereal crops but their role in regulation of amylose biosynthesis in wheat is limited. In this study 83 'Group A' TabZIPs were characterized by gene expression analysis in wheat amylose mutants. A set of 17 TabZIPs was selected on the basis of differential expression (> 2 fold) in low and high amylose mutants from RNA-seq data and validated by qRT PCR. Based on qRT PCR and correlation analysis out of the 17 TabZIPs six differentially expressed candidate TabZIPs were identified, involving in high amylose biosynthesis. The TabZIP175.2, identified as upregulated in all high amylose lines and TabZIP90.2, TabZIP129.1, TabZIP132.2, TabZIP143 and TabZIP159.2 were found downregulated in all low amylose lines, after exogenous supply of ABA. Proximal promoter analysis of starch pathway genes revealed the presence of ABA-responsive elements (ABREs) that are putative binding sites for bZIPs. Collectively, these findings indicated the involvement of putative six candidate TabZIPs as transcriptional regulators of amylose related genes via an ABA-dependent pathway in wheat. This study could help the investigators to make an informed decision to edit wheat genome for high/low amylose content using gene-editing technologies.
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Affiliation(s)
- Pankaj Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Koushik Shah
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.
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Genome-wide identification and expression profiling of basic leucine zipper transcription factors following abiotic stresses in potato (Solanum tuberosum L.). PLoS One 2021; 16:e0247864. [PMID: 33711039 PMCID: PMC7954325 DOI: 10.1371/journal.pone.0247864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important food crop that is grown and consumed worldwide. The growth and productivity of this crop are severely affected by various abiotic stresses. Basic leucine zipper (bZIP) transcription factors (TFs) in plants are well known for their function during growth and development. However, systematic and in-depth identification and functional characterization of the bZIP gene family of potato is lacking. In the current study, we identified a total of 90 bZIPs (StbZIP) distributed on 12 linkage groups of potato. Based on the previous functional annotation and classification of bZIPs in Arabidopsis, wheat, and rice, a phylogenetic tree of potato bZIPs was constructed and genes were categorized into various functional groups (A to I, S, and U) as previously annotated in Arabidopsis thaliana. Analyses of the transcript sequence (RNA-seq) data led to identifying a total of 18 candidate StbZIPs [four in roots, eight in the tuber, six in mesocarp and endocarp] that were expressed in a tissue-specific manner. Differential expression analysis under the various abiotic conditions (salt, mannitol, water, and heat stress) and treatment with phytohormones (ABA, GA, IAA, and BAP) led to the identification of forty-two [thirteen under salt stress, two under mannitol stress, ten under water stress, and eighteen under heat stress], and eleven [eight and three StbZIPs upon treatment with ABA, and IAA, respectively] candidate StbZIPs, respectively. Using sequence information of candidate StbZIPs, a total of 22 SSR markers were also identified in this study. In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.
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Kumar P, Kumar P, Sharma D, Verma SK, Halterman D, Kumar A. Genome-wide identification and expression profiling of basic leucine zipper transcription factors following abiotic stresses in potato (Solanum tuberosum L.). PLoS One 2021. [PMID: 33711039 DOI: 10.1371/journal.pone.0247864]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Potato (Solanum tuberosum L.) is an important food crop that is grown and consumed worldwide. The growth and productivity of this crop are severely affected by various abiotic stresses. Basic leucine zipper (bZIP) transcription factors (TFs) in plants are well known for their function during growth and development. However, systematic and in-depth identification and functional characterization of the bZIP gene family of potato is lacking. In the current study, we identified a total of 90 bZIPs (StbZIP) distributed on 12 linkage groups of potato. Based on the previous functional annotation and classification of bZIPs in Arabidopsis, wheat, and rice, a phylogenetic tree of potato bZIPs was constructed and genes were categorized into various functional groups (A to I, S, and U) as previously annotated in Arabidopsis thaliana. Analyses of the transcript sequence (RNA-seq) data led to identifying a total of 18 candidate StbZIPs [four in roots, eight in the tuber, six in mesocarp and endocarp] that were expressed in a tissue-specific manner. Differential expression analysis under the various abiotic conditions (salt, mannitol, water, and heat stress) and treatment with phytohormones (ABA, GA, IAA, and BAP) led to the identification of forty-two [thirteen under salt stress, two under mannitol stress, ten under water stress, and eighteen under heat stress], and eleven [eight and three StbZIPs upon treatment with ABA, and IAA, respectively] candidate StbZIPs, respectively. Using sequence information of candidate StbZIPs, a total of 22 SSR markers were also identified in this study. In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.
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Affiliation(s)
- Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Madison, Wisconsin, United States of America
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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