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The DNA Replication, Repair, and Recombination Pathway Genes Modulating Yield and Stress Tolerance Traits in Chickpea

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Abstract

DNA replication, repair, and recombination (DRRR) are the fundamental processes required for faithful transmission of genetic information within and between generations. The DRRR genes protect the cells from potential mutations and damage during the developmental phases and stress conditions. Thus, these genes indirectly regulate diverse important agronomic traits in a crop plant. A genome-wide survey of six DRRR pathway genes, namely, DNA replication, Base Excision Repair, Nucleotide Excision Repair, Homologous Recombination, Mismatch Excision Repair, and Non-Homologous End-Joining, identified 157 DRRR genes in chickpea. Phylogenetic analysis of these genes within the legume clades and model plant Arabidopsis identified 42 conserved DRRR genes exhibiting clade-specific evolutionary patterns. Integrating the gene-based association mapping with differential expression profiling identified the natural alleles of the potential DRRR genes, primarily regulating flowering and maturation time and involved in drought tolerance of chickpea. Identifying and understanding DRRR genes’ roles in regulating yield and stress tolerance traits in a vital grain legume like chickpea is requisite for its future crop improvement endeavors. Manipulation of promising functionally relevant DRRR genes will pave the way for simultaneous improvement in multiple beneficial agronomic traits in chickpea.

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Acknowledgements

UB acknowledges the UGC (University Grants Commission), India, for research fellowship awards.

Funding

The financial support for this study was provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013–14).

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UB, HDU, and DB performed the field and laboratory experiments as well as drafted the manuscript. UB, DB, NM, and AS involved in genotyping and data analysis. HDU and UCJ assisted in constitution of an association panel and its field phenotyping. SKP conceived and designed the research study, guided data analysis and interpretation, and participated in drafting and correcting the manuscript critically, and all authors gave the final approval of the version to be published.

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Correspondence to Swarup K. Parida.

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Key Message

Genome-wide survey identified 157 DNA replication repair and recombination (DRRR) genes in chickpea and their homologs within the sequenced legumes. Phylogenetic analysis deciphered clade specific evolutionary pattern of these genes within legumes. Expression profiling and association mapping delineates few crucial DRRR genes regulating yield and stress tolerance traits in chickpea

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Basu, U., Sharma, A., Bajaj, D. et al. The DNA Replication, Repair, and Recombination Pathway Genes Modulating Yield and Stress Tolerance Traits in Chickpea. Plant Mol Biol Rep 40, 119–135 (2022). https://doi.org/10.1007/s11105-021-01303-9

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  1. Udita Basu
  2. Swarup K. Parida