Genome-wide Atlas of Rust Resistance Loci in Wheat

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2024 Jul 9

PMID 38980436

Authors

Jingyang Tong

Cong Zhao

Dan Liu

Dilani T Jambuthenne

Mengjing Sun

Eric Dinglasan

Sambasivam K Periyannan

Lee T Hickey

Ben J Hayes

Affiliations

Soon will be listed here.

Abstract

Rust diseases, including leaf rust, stripe/yellow rust, and stem rust, significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding and deployment of cultivars with genetic resistance is the most effective and sustainable approach to control these diseases. The genetic toolkit for wheat breeders to select for rust resistance has rapidly expanded with a multitude of genetic loci identified using the latest advances in genomics, mapping and cloning strategies. The goal of this review was to establish a wheat genome atlas that provides a comprehensive summary of reported loci associated with rust resistance. Our atlas provides a summary of mapped quantitative trait loci (QTL) and characterised genes for the three rusts from 170 publications over the past two decades. A total of 920 QTL or resistance genes were positioned across the 21 chromosomes of wheat based on the latest wheat reference genome (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple rust loci suggesting they could have pleiotropic effects on two or more rust diseases. We discuss a range of strategies to exploit this wealth of genetic information to efficiently utilise sources of resistance, including genomic information to stack desirable and multiple QTL to develop wheat cultivars with enhanced resistance to rust disease.

Citing Articles

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Stacking beneficial haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance.

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References

Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney R . Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. Mol Plant. 2017; 10(8):1047-1064. DOI: 10.1016/j.molp.2017.06.008. View

Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O . Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol. 2019; 37(2):139-143. DOI: 10.1038/s41587-018-0007-9. View

MacKenzie A, Norman M, Gessese M, Chen C, Sorensen C, Hovmoller M . Wheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery. BMC Plant Biol. 2023; 23(1):590. PMC: 10680240. DOI: 10.1186/s12870-023-04576-2. View

Steuernagel B, Periyannan S, Hernandez-Pinzon I, Witek K, Rouse M, Yu G . Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat Biotechnol. 2016; 34(6):652-5. DOI: 10.1038/nbt.3543. View

Neu C, Stein N, Keller B . Genetic mapping of the Lr20-Pm1 resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat. Genome. 2002; 45(4):737-44. DOI: 10.1139/g02-040. View

Rasheed A, Wen W, Gao F, Zhai S, Jin H, Liu J . Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theor Appl Genet. 2016; 129(10):1843-60. DOI: 10.1007/s00122-016-2743-x. View

Brun H, Chevre A, Fitt B, Powers S, Besnard A, Ermel M . Quantitative resistance increases the durability of qualitative resistance to Leptosphaeria maculans in Brassica napus. New Phytol. 2009; 185(1):285-99. DOI: 10.1111/j.1469-8137.2009.03049.x. View

Luo M, Xie L, Chakraborty S, Wang A, Matny O, Jugovich M . A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat. Nat Biotechnol. 2021; 39(5):561-566. DOI: 10.1038/s41587-020-00770-x. View

Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B . Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci U S A. 2003; 100(25):15253-8. PMC: 299976. DOI: 10.1073/pnas.2435133100. View

10.

Zhang W, Chen S, Abate Z, Nirmala J, Rouse M, Dubcovsky J . Identification and characterization of , a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group. Proc Natl Acad Sci U S A. 2017; 114(45):E9483-E9492. PMC: 5692537. DOI: 10.1073/pnas.1706277114. View

11.

Periyannan S . Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases. New Phytol. 2017; 219(1):45-51. DOI: 10.1111/nph.14928. View

12.

Moore J, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J . A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat Genet. 2015; 47(12):1494-8. DOI: 10.1038/ng.3439. View

13.

Yu G, Matny O, Champouret N, Steuernagel B, Moscou M, Hernandez-Pinzon I . Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. Nat Commun. 2022; 13(1):1607. PMC: 8956640. DOI: 10.1038/s41467-022-29132-8. View

14.

Bentley A . Broken bread - avert global wheat crisis caused by invasion of Ukraine. Nature. 2022; 603(7902):551. DOI: 10.1038/d41586-022-00789-x. View

15.

Zhu Z, Cao Q, Han D, Wu J, Wu L, Tong J . Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895. Theor Appl Genet. 2023; 136(6):142. DOI: 10.1007/s00122-023-04374-2. View

16.

Bolton M, Kolmer J, Garvin D . Wheat leaf rust caused by Puccinia triticina. Mol Plant Pathol. 2008; 9(5):563-75. PMC: 6640346. DOI: 10.1111/j.1364-3703.2008.00487.x. View

17.

Marchal C, Zhang J, Zhang P, Fenwick P, Steuernagel B, Adamski N . BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. Nat Plants. 2018; 4(9):662-668. DOI: 10.1038/s41477-018-0236-4. View

18.

Sucher J, Boni R, Yang P, Rogowsky P, Buchner H, Kastner C . The durable wheat disease resistance gene Lr34 confers common rust and northern corn leaf blight resistance in maize. Plant Biotechnol J. 2016; 15(4):489-496. PMC: 5362690. DOI: 10.1111/pbi.12647. View

19.

Cao S, Xu D, Hanif M, Xia X, He Z . Genetic architecture underpinning yield component traits in wheat. Theor Appl Genet. 2020; 133(6):1811-1823. DOI: 10.1007/s00122-020-03562-8. View

20.

Bouvet L, Holdgate S, James L, Thomas J, Mackay I, Cockram J . The evolving battle between yellow rust and wheat: implications for global food security. Theor Appl Genet. 2021; 135(3):741-753. PMC: 8942934. DOI: 10.1007/s00122-021-03983-z. View