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Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea

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Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum.

Abstract

Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.

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Acknowledgements

This work was supported by Grains Research and Development Corporation through the project DAN00172 and development of the RIL populations in the project DAN00065 and DAN00094. The PhD candidate A. Amalraj was supported by scholarship from the University of Adelaide and Australian Centre for Plant Functional Genomics. Ted Knights (EJ) instigated the development of the RIL populations. Steve Harden, biometrician, NSW DPI, generated designs for field experiments.

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  1. School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia

    Amritha Amalraj, Julian Taylor, Yongle Li & Tim Sutton

  2. NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia

    Sean Bithell, Kevin Moore & Kristy Hobson

  3. South Australian Research and Development Institute, GPO Box 397, Adelaide, SA, 5001, Australia

    Tim Sutton

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  1. Amritha Amalraj
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  2. Julian Taylor
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Correspondence to Tim Sutton.

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Communicated by David A Lightfoot.

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Amalraj, A., Taylor, J., Bithell, S. et al. Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea. Theor Appl Genet 132, 1017–1033 (2019). https://doi.org/10.1007/s00122-018-3256-6

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