Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing

Abstract

Key message

Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D.

Abstract

Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.

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Acknowledgements

We thank Marie Kubaláková, Romana Šperková and Jitka Weiserová for technical assistance with chromosome flow sorting and chromosome DNA amplification. This work was carried out under the Sustainable Crop Production Research for International Development (SCPRID) grant. The financial support provided by the Department of Biotechnology, Ministry of Science and Technology, Government of India (Grant No. BT/IN/UK/08/PC/2012), and the UK Biotechnology and Biological Sciences Research Council (Grants No. BB/JO12017/1 and BB/P016855/1) is gratefully acknowledged. MB, PC and CU gratefully acknowledge the support provided by Monsanto Beachell Borlaug International Scholars Programme (MBBISP). IM, KH, JV, JD and MV were supported by the ERDF project ‘Plants as a tool for sustainable global development’ (No. CZ.02.1.01/0.0/0.0/16_019/0000827). IM also gratefully acknowledges the support from a Marie Curie Fellowship Grant ‘AEGILWHEAT’ (H2020-MSCA-IF-2016-746253) under the H2020 framework programme of the European Union and from the Hungarian National Research, Development and Innovation Office (K116277). MB also gratefully acknowledges Dr Kuldeep Singh, Director, NBPGR, New Delhi, for his guidance in writing the project proposal for MBBISP.

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MB carried out the phenotyping of the germplasm, analysed both genotype and phenotype data and wrote the draft of the manuscript; NA helped in the assembly of flow-sorted chromosome sequence and SNP detection; PIK helped in phenotyping, DNA extraction and harvesting of high-resolution mapping population; SK maintained the germplasm and populations in the field and facilitated rust screening; JV and JD sorted the chromosomes, IM sequenced the 5U chromosome; MV and KH sequenced chromosomes 5D of WL711 and pau16057; CU helped in analysis of 5U chromosome data, marker generation and supervised the study; PC conceived the idea, designed and supervised the study, prepared the draft of the manuscript and submitted it. All the authors have read the manuscript and approved it.

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Correspondence to Parveen Chhuneja.

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Bansal, M., Adamski, N.M., Toor, P.I. et al. Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing. Theor Appl Genet 133, 903–915 (2020). https://doi.org/10.1007/s00122-019-03514-x

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