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Delineation of genes for a major QTL governing heat stress tolerance in chickpea

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Abstract

Chickpea (Cicer arietinum) is a cool season grain legume experiencing severe yield loss during heat stress due to the intensifying climate changes and its associated gradual increase of mean temperature. Hence, understanding the genetic architecture regulating heat stress tolerance has emerged as an important trait to be addressed for enhancing yield and productivity of chickpea under heat stress. The present study is intended to identify the major genomic region(s) governing heat stress tolerance in chickpea. For this, an integrated genomics-assisted breeding strategy involving NGS-based high-resolution QTL-seq assay, QTL region-specific association analysis and molecular haplotyping was deployed in a population of 206 mapping individuals and a diversity panel of 217 germplasm accessions of chickpea. This combinatorial strategy delineated a major 156.8 kb QTL genomic region, which was subsequently narrowed-down to a functional candidate gene CaHSFA5 and its natural alleles associated strongly with heat stress tolerance in chickpea. Superior natural alleles and haplotypes delineated from the CaHSFA5 gene have functional significance in regulating heat stress tolerance in chickpea. Histochemical staining, interaction studies along with differential expression profiling of CaHSFA5 and ROS scavenging genes suggest a cross talk between CaHSFA5 with ROS homeostasis pertaining to heat stress tolerance in chickpea. Heterologous gene expression followed by heat stress screening further validated the functional significance of CaHSFA5 for heat stress tolerance. The salient outcomes obtained here can have potential to accelerate multiple translational genomic analysis including marker-assisted breeding and gene editing in order to develop high-yielding heat stress tolerant chickpea varieties.

Key message

An integrated next-generation genomic strategy delineates the functionally relevant gene and alleles for a major QTL governing heat stress tolerance in chickpea.

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Acknowledgements

We are thankful to the Central Instrumentation Facility (CIF), Plant Growth Facility (PGF), and DBT-eLibrary Consortium (DeLCON) of NIPGR, New Delhi for providing timely support and access to e-resources for this study.

Funding

Financial support for this study was provided by the research grants from the ICAR and NIPGR, Department of Biotechnology (DBT), Government of India. JKM acknowledge the DBT for research fellowship award.

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Authors and Affiliations

  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

    Jitendra K. Mohanty, Virevol Thakro, Antima Yadav, Pinky Agarwal & Swarup K. Parida

  2. Department of Botany, Panjab University, Chandigarh, 160014, India

    Harsh Nayyar

  3. Indian Institute of Pulses Research (IIPR), Uttar Pradesh, Kanpur, 208024, India

    Girish P. Dixit & Uday Chand Jha

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  1. Jitendra K. Mohanty
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  2. Virevol Thakro
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  3. Antima Yadav
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  4. Harsh Nayyar
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  5. Girish P. Dixit
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  7. Swarup K. Parida
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Contributions

JKM has performed experiments and drafted the manuscript. AY assisted in the yeast-related molecular biology experiments. VT analysed the dataset used. HN, GPD, PA, SKP and UCJ conceived the idea, and guided, 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 or Uday Chand Jha.

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Mohanty, J.K., Thakro, V., Yadav, A. et al. Delineation of genes for a major QTL governing heat stress tolerance in chickpea. Plant Mol Biol 114, 19 (2024). https://doi.org/10.1007/s11103-024-01421-4

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