Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Yinghui Li; Zhen Zhen Wei; Hanan Sela; Liubov Govta; Valentyna Klymiuk; Rajib Roychowdhury; Harmeet Singh Chawla; Jennifer Ens; Krystalee Wiebe; Valeria Bocharova; Roi Ben-David; Prerna B. Pawar; Yuqi Zhang; Samidha Jaiwar; István Molnár; Jaroslav Doležel; Gitta Coaker; Curtis J. Pozniak; Tzion Fahima

doi:10.1016/j.xplc.2023.100646

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Yinghui Li, Zhen Zhen Wei, Hanan Sela, Liubov Govta, Valentyna Klymiuk, Rajib Roychowdhury, Harmeet Singh Chawla, Jennifer Ens, Krystalee Wiebe, Valeria Bocharova, Roi Ben-David, Prerna B. Pawar, Yuqi Zhang, Samidha Jaiwar, István Molnár, Jaroslav Doležel, Gitta Coaker, Curtis J. Pozniak, Tzion Fahima

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

Abstract

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Original language	English
Article number	100646
Journal	Plant Communications
DOIs	https://doi.org/10.1016/j.xplc.2023.100646
State	Accepted/In press - 2023

Bibliographical note

Funding Information:
T.F. was supported by the Israel Science Foundation , grant numbers 2289/16 , 1366/18, and 2342/18 , and the United States– Israel Binational Science Foundation ( 2019654 ). C.J.P. was supported by the Genome Canada –funded project 4D Wheat. I.M. and J.D. 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 ). G.C. and T.F. were supported by the United States National Science Foundation ( 1937855 ) and the United States Department of Agriculture ( 2020-67013-32577 ). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India.

Funding Information:
T.F. was supported by the Israel Science Foundation, grant numbers 2289/16, 1366/18, and 2342/18, and the United States–Israel Binational Science Foundation (2019654). C.J.P. was supported by the Genome Canada–funded project 4D Wheat. I.M. and J.D. 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). G.C. and T.F. were supported by the United States National Science Foundation (1937855) and the United States Department of Agriculture (2020-67013-32577). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India.

Publisher Copyright:
© 2023 The Authors

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Plant Science
Cell Biology

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10.1016/j.xplc.2023.100646

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Li, Y., Wei, Z. Z., Sela, H., Govta, L., Klymiuk, V., Roychowdhury, R., Chawla, H. S., Ens, J., Wiebe, K., Bocharova, V., Ben-David, R., Pawar, P. B., Zhang, Y., Jaiwar, S., Molnár, I., Doležel, J., Coaker, G., Pozniak, C. J., & Fahima, T. (Accepted/In press). Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69. Plant Communications, Article 100646. https://doi.org/10.1016/j.xplc.2023.100646

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title = "Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69",

abstract = "Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.",

author = "Yinghui Li and Wei, {Zhen Zhen} and Hanan Sela and Liubov Govta and Valentyna Klymiuk and Rajib Roychowdhury and Chawla, {Harmeet Singh} and Jennifer Ens and Krystalee Wiebe and Valeria Bocharova and Roi Ben-David and Pawar, {Prerna B.} and Yuqi Zhang and Samidha Jaiwar and Istv{\'a}n Moln{\'a}r and Jaroslav Dole{\v z}el and Gitta Coaker and Pozniak, {Curtis J.} and Tzion Fahima",

note = "Funding Information: T.F. was supported by the Israel Science Foundation , grant numbers 2289/16 , 1366/18, and 2342/18 , and the United States– Israel Binational Science Foundation ( 2019654 ). C.J.P. was supported by the Genome Canada –funded project 4D Wheat. I.M. and J.D. 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 ). G.C. and T.F. were supported by the United States National Science Foundation ( 1937855 ) and the United States Department of Agriculture ( 2020-67013-32577 ). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India. Funding Information: T.F. was supported by the Israel Science Foundation, grant numbers 2289/16, 1366/18, and 2342/18, and the United States–Israel Binational Science Foundation (2019654). C.J.P. was supported by the Genome Canada–funded project 4D Wheat. I.M. and J.D. 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). G.C. and T.F. were supported by the United States National Science Foundation (1937855) and the United States Department of Agriculture (2020-67013-32577). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

doi = "10.1016/j.xplc.2023.100646",

language = "English",

journal = "Plant Communications",

issn = "2590-3462",

publisher = "Cell Press",

}

Li, Y, Wei, ZZ, Sela, H, Govta, L, Klymiuk, V, Roychowdhury, R, Chawla, HS, Ens, J, Wiebe, K, Bocharova, V, Ben-David, R, Pawar, PB, Zhang, Y, Jaiwar, S, Molnár, I, Doležel, J, Coaker, G, Pozniak, CJ & Fahima, T 2023, 'Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69', Plant Communications. https://doi.org/10.1016/j.xplc.2023.100646

TY - JOUR

T1 - Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

AU - Li, Yinghui

AU - Wei, Zhen Zhen

AU - Sela, Hanan

AU - Govta, Liubov

AU - Klymiuk, Valentyna

AU - Roychowdhury, Rajib

AU - Chawla, Harmeet Singh

AU - Ens, Jennifer

AU - Wiebe, Krystalee

AU - Bocharova, Valeria

AU - Ben-David, Roi

AU - Pawar, Prerna B.

AU - Zhang, Yuqi

AU - Jaiwar, Samidha

AU - Molnár, István

AU - Doležel, Jaroslav

AU - Coaker, Gitta

AU - Pozniak, Curtis J.

AU - Fahima, Tzion

N1 - Funding Information: T.F. was supported by the Israel Science Foundation , grant numbers 2289/16 , 1366/18, and 2342/18 , and the United States– Israel Binational Science Foundation ( 2019654 ). C.J.P. was supported by the Genome Canada –funded project 4D Wheat. I.M. and J.D. 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 ). G.C. and T.F. were supported by the United States National Science Foundation ( 1937855 ) and the United States Department of Agriculture ( 2020-67013-32577 ). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India. Funding Information: T.F. was supported by the Israel Science Foundation, grant numbers 2289/16, 1366/18, and 2342/18, and the United States–Israel Binational Science Foundation (2019654). C.J.P. was supported by the Genome Canada–funded project 4D Wheat. I.M. and J.D. 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). G.C. and T.F. were supported by the United States National Science Foundation (1937855) and the United States Department of Agriculture (2020-67013-32577). Y.L. was supported by a fellowship provided by the Planning and Budgeting Committee (PBC) of the Israel Council for Higher Education for Outstanding Post-doctoral Fellows from China and India. Publisher Copyright: © 2023 The Authors

PY - 2023

Y1 - 2023

N2 - Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

AB - Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

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U2 - 10.1016/j.xplc.2023.100646

DO - 10.1016/j.xplc.2023.100646

M3 - Article

AN - SCOPUS:85168707410

SN - 2590-3462

JO - Plant Communications

JF - Plant Communications

M1 - 100646

ER -

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

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