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Characterization of ‘QTL-hotspot’ introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea

Barmukh, R., Roorkiwal, M., Dixit, G.P., Bajaj, P., Kholova, J., Smith, M.R., Chitikineni, A., Bharadwaj, C., Sreeman, S.M., Rathore, A., Tripathi, S., Yasin, M., Vijayakumar, A.G., Rao Sagurthi, S., Siddique, K.H.M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Foyer, C. (2022) Characterization of ‘QTL-hotspot’ introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. Journal of Experimental Botany . Art. erac348.

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‘QTL-hotspot’ is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of ‘QTL-hotspot’ on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the ‘QTL-hotspot’ region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the ‘QTL-hotspot’ region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.

Item Type: Journal Article
Murdoch Affiliation(s): Centre for Crop and Food Innovation
State Agricultural Biotechnology Centre
Publisher: Oxford University Press
Copyright: © 2022 The Authors.
United Nations SDGs: Goal 12: Responsible Consumption and Production
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