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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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Kumar J, Mishra A, Kumar A, Kaur G, Sharma H, Kaur S, Sharma S, Devi K, Garg M, Pandey AK, Bishnoi M, Pareek A, Roy J. Whole genome re-sequencing of indian wheat genotypes for identification of genomic variants for grain iron and zinc content. Mol Biol Rep 2022; 49:7123-7133. [PMID: 35717473 DOI: 10.1007/s11033-022-07593-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/16/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Whole-genome sequencing information which is of abundant significance for genetic evolution, and breeding of crops. Wheat (Triticum spp) is most widely grown and consumed crops globally. Micronutrients are very essential for healthy development of human being and their sufficient consumption in diet is essential for various metabolic functions. Biofortification of wheat grains with iron (Fe) and zinc (Zn) has proved the most reliable and effective way to combat micronutrient associated deficiency. Genetic variability for grain micronutrient could provide insight to dissect the traits. METHODS AND RESULTS In the current study, 1300 wheat lines were screened for grain Fe and Zn content, out of which only five important Indian wheat genotypes were selected on the basis of Fe and Zn contents. These lines were multiplied during at the National Agri-Food Biotechnology Institute (NABI) and re-sequenced to identify genomic variants in candidate genes for Fe and Zn between the genotypes. Whole genome sequencing generated ̴ 12 Gb clean data. Comparative genome analysis identified 254 genomic variants in the candidate genes associated with deleterious effect on protein function. CONCLUSIONS The present study demonstrated the fundamental in understanding the genomic variations for Fe and Zn enrichment to generate healthier wheat grains.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ashish Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Satveer Kaur
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Shivani Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Kirti Devi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Monika Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India.
| | - Ajay K Pandey
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India. .,School of Life Sciences, Jawaharlal Nehru University, Delhi, India.
| | - Mahendra Bishnoi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India.
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Kaur G, Shukla V, Meena V, Kumar A, Tyagi D, Singh J, Kandoth PK, Mantri S, Rouached H, Pandey AK. Physiological and molecular responses to combinatorial iron and phosphate deficiencies in hexaploid wheat seedlings. Genomics 2021; 113:3935-3950. [PMID: 34606916 DOI: 10.1016/j.ygeno.2021.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 01/16/2023]
Abstract
Iron (Fe) and phosphorus (P) are the essential mineral nutrients for plant growth and development. However, the molecular interaction of the Fe and P pathways in crops remained largely obscure. In this study, we provide a comprehensive physiological and molecular analysis of hexaploid wheat response to single (Fe, P) and its combinatorial deficiencies. Our data showed that inhibition of the primary root growth occurs in response to Fe deficiency; however, growth was rescued when combinatorial deficiencies occurred. Analysis of RNAseq revealed that distinct molecular rearrangements during combined deficiencies with predominance for genes related to metabolic pathways and secondary metabolite biosynthesis primarily include genes for UDP-glycosyltransferase, cytochrome-P450s, and glutathione metabolism. Interestingly, the Fe-responsive cis-regulatory elements in the roots in Fe stress conditions were enriched compared to the combined stress. Our metabolome data also revealed the accumulation of distinct metabolites such as amino-isobutyric acid, arabinonic acid, and aconitic acid in the combined stress environment. Overall, these results are essential in developing new strategies to improve the resilience of crops in limited nutrients.
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Affiliation(s)
- Gazaldeep Kaur
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India; Department of Biotechnology, Panjab University, Punjab, India
| | - Vishnu Shukla
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Varsha Meena
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Anil Kumar
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India; Department of Biotechnology, Panjab University, Punjab, India
| | - Deepshikha Tyagi
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Jagtar Singh
- Department of Biotechnology, Panjab University, Punjab, India
| | - Pramod Kaitheri Kandoth
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Shrikant Mantri
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States of America; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, United States of America
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute, Department of Biotechnology, Sector 81, Knowledge City, Mohali 140306, Punjab, India.
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