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Rajkumar MS, Jain M, Garg R. Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea. Physiol Plant. 2021;173(4):1573-1586doi: 10.1111/ppl.13507.
Rajkumar, M. S., Jain, M., & Garg, R. (2021). Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea. Physiologia plantarum, 173(4), 1573-1586. https://doi.org/10.1111/ppl.13507
Rajkumar, Mohan Singh, et al. "Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea." Physiologia plantarum vol. 173,4 (2021): 1573-1586. doi: https://doi.org/10.1111/ppl.13507
Rajkumar MS, Jain M, Garg R. Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea. Physiol Plant. 2021 Dec;173(4):1573-1586. doi: 10.1111/ppl.13507. Epub 2021 Jul 28. PMID: 34287918.
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Physiol Plant. 2021 Dec;173(4):1573-1586. doi: 10.1111/ppl.13507. Epub 2021 Jul 28.

Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea.

Physiologia plantarum

Mohan Singh Rajkumar, Mukesh Jain, Rohini Garg

Affiliations

  1. School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
  2. Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, India.

PMID: 34287918 DOI: 10.1111/ppl.13507

Abstract

Salinity stress is one of the major constraints for plant growth and yield. The salinity stress response of different genotypes of crop plants may largely be governed by DNA polymorphisms. To determine the molecular genetic factors involved in salinity stress tolerance in chickpea, we performed a whole genome resequencing data analysis of three each of salinity-sensitive and salinity-tolerant genotypes. A total of 6173 single nucleotide polymorphisms and 920 insertions and deletions differentiating the chickpea genotypes with contrasting salinity stress responses were identified. Gene ontology analysis revealed the enrichment of functional terms related to stress response and development among the genes harboring DNA polymorphisms in their promoter and/or coding regions. DNA polymorphisms located within the cis-regulatory motifs of the quantitative trait loci (QTL)-associated and abiotic stress related genes were identified, which may influence salinity stress response via modulating binding affinity of the transcription factors. Several genes including QTL-associated and abiotic stress response related genes harboring DNA polymorphisms exhibited differential expression in response to salinity stress especially at the reproductive stage of development in the salinity-tolerant genotype. Furthermore, effects of non-synonymous DNA polymorphisms on mutational sensitivity and structural integrity of the encoded proteins by the candidate QTL-associated and abiotic stress response related genes were revealed. The results suggest that DNA polymorphisms may determine salinity stress response via influencing differential gene expression in genotype and/or stage-dependent manner. Altogether, we provide a high-quality set of DNA polymorphisms and candidate genes that may govern salinity stress tolerance in chickpea.

© 2021 Scandinavian Plant Physiology Society.

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