Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Naveenkumar Athiyannan; Michael Abrouk; Willem H. P. Boshoff; Stéphane Cauet; Nathalie Rodde; Dave Kudrna; Nahed Abdullah Mohammed; Jan Bettgenhaeuser; Kirsty S. Botha; Shannon S. Derman; Rod Anthony Wing; Renée Prins; Simon G. Krattinger

doi:10.1038/s41588-022-01022-1

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Naveenkumar Athiyannan, Michael Abrouk, Willem H. P. Boshoff, Stéphane Cauet, Nathalie Rodde, Dave Kudrna, Nahed Abdullah Mohammed, Jan Bettgenhaeuser, Kirsty S. Botha, Shannon S. Derman, Rod Anthony Wing, Renée Prins, Simon G. Krattinger

Research output: Contribution to journal › Article › peer-review

83 Scopus citations

Abstract

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future

Original language	English (US)
Pages (from-to)	227-231
Number of pages	5
Journal	Nature Genetics
Volume	54
Issue number	3
DOIs	https://doi.org/10.1038/s41588-022-01022-1
State	Published - Mar 14 2022

Bibliographical note

KAUST Repository Item: Exported on 2023-01-20
Acknowledged KAUST grant number(s): OSR-CRG2018-3768
Acknowledgements: We are grateful to L. Zhou and V. Venkataraman for technical assistance, and the King Abdullah University of Science and Technology (KAUST) Bioscience Core Lab for sequencing support. We thank H. Šimková from the Institute of Experimental Botany, Czech Republic, for technical advice. This publication is based on work supported by the South African Winter Cereal Trust (Grant WCT/W/2020/04) and the KAUST Office of Sponsored Research (OSR) under award no. OSR-CRG2018-3768.

ASJC Scopus subject areas

Genetics

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10.1038/s41588-022-01022-1

https://repository.kaust.edu.sa/bitstream/10754/676423/1/s41588-022-01022-1.pdf

Cite this

@article{efe427888f65438cb5fb8e89b140492c,

title = "Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning",

abstract = "The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future",

author = "Naveenkumar Athiyannan and Michael Abrouk and Boshoff, {Willem H. P.} and St{\'e}phane Cauet and Nathalie Rodde and Dave Kudrna and Mohammed, {Nahed Abdullah} and Jan Bettgenhaeuser and Botha, {Kirsty S.} and Derman, {Shannon S.} and Wing, {Rod Anthony} and Ren{\'e}e Prins and Krattinger, {Simon G.}",

note = "KAUST Repository Item: Exported on 2023-01-20 Acknowledged KAUST grant number(s): OSR-CRG2018-3768 Acknowledgements: We are grateful to L. Zhou and V. Venkataraman for technical assistance, and the King Abdullah University of Science and Technology (KAUST) Bioscience Core Lab for sequencing support. We thank H. {\v S}imkov{\'a} from the Institute of Experimental Botany, Czech Republic, for technical advice. This publication is based on work supported by the South African Winter Cereal Trust (Grant WCT/W/2020/04) and the KAUST Office of Sponsored Research (OSR) under award no. OSR-CRG2018-3768.",

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AU - Athiyannan, Naveenkumar

AU - Abrouk, Michael

AU - Boshoff, Willem H. P.

AU - Cauet, Stéphane

AU - Rodde, Nathalie

AU - Kudrna, Dave

AU - Mohammed, Nahed Abdullah

AU - Bettgenhaeuser, Jan

AU - Botha, Kirsty S.

AU - Derman, Shannon S.

AU - Wing, Rod Anthony

AU - Prins, Renée

AU - Krattinger, Simon G.

N1 - KAUST Repository Item: Exported on 2023-01-20 Acknowledged KAUST grant number(s): OSR-CRG2018-3768 Acknowledgements: We are grateful to L. Zhou and V. Venkataraman for technical assistance, and the King Abdullah University of Science and Technology (KAUST) Bioscience Core Lab for sequencing support. We thank H. Šimková from the Institute of Experimental Botany, Czech Republic, for technical advice. This publication is based on work supported by the South African Winter Cereal Trust (Grant WCT/W/2020/04) and the KAUST Office of Sponsored Research (OSR) under award no. OSR-CRG2018-3768.

PY - 2022/3/14

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N2 - The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future

AB - The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future

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JO - Nature Genetics

JF - Nature Genetics

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ER -

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Abstract

Bibliographical note

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