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Khassanova G, Oshergina I, Ten E, Jatayev S, Zhanbyrshina N, Gabdola A, Gupta NK, Schramm C, Pupulin A, Philp-Dutton L, Anderson P, Sweetman C, Jenkins CL, Soole KL, Shavrukov Y. Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1354413. [PMID: 38766473 PMCID: PMC11099236 DOI: 10.3389/fpls.2024.1354413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.
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Affiliation(s)
- Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Irina Oshergina
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Nursaule Zhanbyrshina
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Ademi Gabdola
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Narendra K. Gupta
- Department of Plant Physiology, Sri Karan Narendra (SNK) Agricultural University, Jobster, Rajastan, India
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Antonio Pupulin
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Lauren Philp-Dutton
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Colin L.D. Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
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