Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases

Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker‐assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long‐lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.I acknowledge the Australian Research Council (Discovery Early Career Research Award-DE170100151) and the Grains Research and Development Corporation, Australia, for their ongoing research support

An overview of genetic rust resistance: From broad to specific mechanisms

Global agriculture is under threat due to the rapid evolution and spread of pathogenic fungi that cause rust diseases. For instance, the recently evolved races of wheat stem rust (Puccinia graminis f. sp. tritici) and stripe rust (P. striiformis f. sp. tritici) fungus in parts of Africa, Asia, and Europe are a menace to food security due to their ability to spread rapidly and overcome resistance in common wheat varieties [1]. Similarly, new variants of Asian soybean rust (Phakopsora pachyrhizi) detected in Brazil and the United States pose a major constraint to soybean cultivation [2]. Since genetic resistance can provide effective and chemical-free disease control, many efforts are directed towards isolating rust-resistance genes in crop plants and understanding how to best deploy them for durable resistance [3]. In addition, related nonhost species are increasingly being utilised to identify new sources of resistance [4, 5]. Here, we summarise current knowledge of rust resistance, focussing on race-specific, non–race-specific, and nonhost resistance mechanisms.Work in the authors’ laboratory is supported by the Grains Research and Development Corporation (https://grdc.com.au/) grant # CSP0016

Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust

Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci

The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley

In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley’s genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley

Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture

Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel

Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases

Contents I. II. III. IV. V. VI. VII. VIII. References Summary: Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides. Copyrigh

A rapid phenotyping method for adult plant resistance to leaf rust in wheat

Background: Leaf rust (LR), caused by Puccinia triticina and is an important disease of wheat (Triticum aestivum L.). The most sustainable method for controlling rust diseases is deployment of cultivars incorporating adult plant resistance (APR). However, phenotyping breeding populations or germplasm collections for resistance in the field is dependent on weather conditions and limited to once a year. In this study, we explored the ability to phenotype APR to LR under accelerated growth conditions (AGC; i.e. constant light and controlled temperature) using a method that integrates assessment at both seedling and adult growth stages. A panel of 21 spring wheat genotypes, including disease standards carrying known APR genes (i.e. Lr34 and Lr46) were characterised under AGC and in the field