Advances in Wheat and Pathogen Genomics: Implications for Disease Control

Keller, Beat; Wicker, Thomas; Krattinger, Simon G.

doi:10.1146/annurev-phyto-080516-035419

Cited by 45 publications

(38 citation statements)

References 110 publications

(35 reference statements)

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“…With the genomic resources developed recently for wheat, many new techniques for gene discovery have been developed. One area has focused on rapid cloning of disease resistance ( R −) genes by using targeted genome sequencing approaches (Keller et al ., ; Periyannan, ). MutRenSeq takes advantage of significantly improved R ‐gene annotations to use an R ‐gene enriched capture method to sequence the majority of R ‐genes in a given plant (Jupe et al ., ; Steuernagel et al ., ; Figure ).…”

Section: New Strategies Accelerate Gene Discovery In Wheatmentioning

confidence: 99%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

2018

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Summary Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in‐field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome‐level assembly of the wheat genome now facilitates a step‐change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene‐editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.

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Section: New Strategies Accelerate Gene Discovery In Wheatmentioning

confidence: 99%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

2018

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“…This transition from genetic to physical maps (from cM to bp) has been one of the rate-limiting steps in many map-based cloning projects, particularly in cereals with large genomes. In wheat for example, hundreds of disease resistance genes have been described and also mapped to a certain extent (McIntosh et al 2008), but only a few dozens of them have been cloned (Keller et al 2018). BAC clones can store a piece of DNA 100 -200 kb in size.…”

Section: Positional Cloning 20 -How To Avoid Spending a Decade On A mentioning

confidence: 99%

Rapid gene cloning in cereals

Bettgenhaeuser

Krattinger

2018

Theor Appl Genet

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The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large re-sequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley. Key message The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops.

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“…Advances in wheat genomics will facilitate rapid gene isolation in wheat and its relatives (Wulff and Moscou 2014). So far, only 25 disease resistance genes have been cloned from wheat and its progenitors in the past fifteen years (Keller et al 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, an enriched genepool will be a crucial resource for identifying avirulence factors from diverse rust races. Such avirulence factors could potentially provide a resource to develop an array of diagnostic tools to forecast pathogen emergence and select suitable gene deployment strategies for rust management (Keller et al 2018;Periyannan 2018). A gene pool with abundant resistance genes is certainly a key resource for gene editing to alter or enhance rust resistance.…”

Section: Discussionmentioning

confidence: 99%

“…Rust resistance is conferred by genes from two distinct groups -all stage resistance (R) genes and adult plant resistance (APR) genes. So far, the majority of the cloned R genes have been shown to encode proteins containing coiled coil, nucleotide binding site and leucine-rich repeat (CC-NBS-LRR or CNL) domains (Pretorius et al 2017a; Keller et al 2018). R genes confer resistance throughout plant development, right from the seedling stage, and are most commonly race specific, although some R genes may confer resistance to multiple races of a single pathogen species.…”

Section: List Of Figuresmentioning

confidence: 99%

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Molecular genetic characterisation of triple rust resistance in Aegilops tauschii

Athiyannan¹

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The major outcomes of this study include:  Understanding the genetic architecture of triple rust resistance in accession CPI110672  Cloning and validation of Sr46b and Yr672 rust resistance candidate genes  Fine mapping a leaf rust resistance (Lr39) gene  Development of breeder-friendly molecular markers for Sr46, Yr672 and Lr39  Marker assisted introgression of Sr46b and Yr672 into a commercial cultivar  Marker assisted pyramiding of Sr33/Sr45/Sr46b resistance genes using speed breeding technology v Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School.

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Advances in Wheat and Pathogen Genomics: Implications for Disease Control

Cited by 45 publications

References 110 publications

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Rapid gene cloning in cereals

Molecular genetic characterisation of triple rust resistance in Aegilops tauschii

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