Resistance of Sharon Goatgrass (Aegilops sharonensis) to Fungal Diseases of Wheat

Genome-wide association mapping of rust resistance in Aegilops longissima

The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

Unconventional R proteins in the botanical tribe Triticeae

Plant immunity is triggered following the perception of pathogen-derived molecules by plant receptor proteins. Two protein families, membrane-localized receptor-like kinases (RLK) and intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, play key roles in pathogen perception and in the initiation of downstream signaling cascades that lead to defense responses. In addition to RLKs and NLRs, recent research has identified additional protein families that function as plant resistance (R) proteins. In particular, the botanical tribe Triticeae, which includes the globally important crop species wheat and barley, has played a significant role in the discovery of 'unconventional' R proteins. In this review, we will summarize the current knowledge on unconventional R genes in Triticeae and the proteins they encode. The knowledge on unconventional R proteins will not only broaden our understanding of plant-pathogen interactions but also have great implications for disease resistance breeding in crops.

Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.

Characterization, Identification and Evaluation of Wheat-Aegilops sharonensis Chromosome Derivatives

Aegilops sharonensis, a wild relative of wheat, harbors diverse disease and insect resistance genes, making it a potentially excellent gene source for wheat improvement. In this study, we characterized and evaluated six wheat-A. sharonensis derivatives, which included three disomic additions, one disomic substitution + monotelosomic addition and two disomic substitution + disomic additions. A total of 51 PLUG markers were developed and used to allocate the A. sharonensis chromosomes in each of the six derivatives to Triticeae homoeologous groups. A set of cytogenetic markers specific for A. sharonensis chromosomes was established based on FISH using oligonucleotides as probes. Molecular cytogenetic marker analysis confirmed that these lines were a CS-A. sharonensis 2S^sh disomic addition, a 4S^sh disomic addition, a 4S^sh (4D) substitution + 5S^shL monotelosomic addition, a 6S^sh disomic addition, a 4S^sh (4D) substitution + 6S^sh disomic addition and a 4S^sh (4D) substitution + 7S^sh disomic addition line, respectively. Disease resistance investigations showed that chromosome 7S^sh of A. sharonensis might harbor a new powdery mildew resistance gene, and therefore it has potential for use as resistance source for wheat breeding.

Fusarium Head Blight and Rust Diseases in Soft Red Winter Wheat in the Southeast United States: State of the Art, Challenges and Future Perspective for Breeding

Among the biotic constraints to wheat (Triticum aestivum L.) production, fusarium head blight (FHB), caused by Fusarium graminearum, leaf rust (LR), caused by Puccinia triticina, and stripe rust (SR) caused by Puccinia striiformis are problematic fungal diseases worldwide. Each can significantly reduce grain yield while FHB causes additional food and feed safety concerns due to mycotoxin contamination of grain. Genetic resistance is the most effective and sustainable approach for managing wheat diseases. In the past 20 years, over 500 quantitative trait loci (QTLs) conferring small to moderate effects for the different FHB resistance types have been reported in wheat. Similarly, 79 Lr-genes and more than 200 QTLs and 82 Yr-genes and 140 QTLs have been reported for seedling and adult plant LR and SR resistance, respectively. Most QTLs conferring rust resistance are race-specific generally conforming to a classical gene-for-gene interaction while resistance to FHB exhibits complex polygenic inheritance with several genetic loci contributing to one resistance type. Identification and deployment of additional genes/QTLs associated with FHB and rust resistance can expedite wheat breeding through marker-assisted and/or genomic selection to combine small-effect QTL in the gene pool. LR disease has been present in the southeast United States for decades while SR and FHB have become increasingly problematic in the past 20 years, with FHB arguably due to increased corn acreage in the region. Currently, QTLs on chromosome 1B from Jamestown, 1A, 1B, 2A, 2B, 2D, 4A, 5A, and 6A from W14, Ning7840, Ernie, Bess, Massey, NC-Neuse, and Truman, and 3B (Fhb1) from Sumai 3 for FHB resistance, Lr9, Lr10, Lr18, Lr24, Lr37, LrA2K, and Lr2K38 genes for LR resistance, and Yr17 and YrR61 for SR resistance have been extensively deployed in southeast wheat breeding programs. This review aims to disclose the current status of FHB, LR, and SR diseases, summarize the genetics of resistance and breeding efforts for the deployment of FHB and rust resistance QTL on soft red winter wheat cultivars, and present breeding strategies to achieve sustainable management of these diseases in the southeast US.

Reducing the size of an alien segment carrying leaf rust and stripe rust resistance in wheat

BACKGROUND

Leaf and stripe rusts are two major wheat diseases, causing significant yield losses. The preferred way for protecting wheat from rust pathogens is by introgression of rust resistance traits from wheat-related wild species. To avoid genetic drag due to replacement of large wheat chromosomal segments by the alien chromatin, it is necessary to shorten the alien chromosome segment in primary recombinants.

RESULTS

Here we report on shortening of an alien chromosome segment in wheat that carries leaf and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis). Rust resistant wheat introgression lines were selected and the alien region was mapped using genotyping by sequencing. Single polymorphic nucleotides (SNP) were identified and used to generate diagnostic PCR markers. Shortening of the alien fragment was achieved by induced homoeologous pairing and lines with shortened alien chromosome were identified using the PCR markers. Further reduction of the segment was achieved in tertiary recombinants without losing the rust resistance.

CONCLUSIONS

Alien chromatin in wheat with novel rust resistance genes was characterized by SNP markers and shortened by homoeologous recombination to avoid deleterious traits. The resulting wheat lines are resistant to highly virulent races of leaf and stripe rust pathogens and can be used as both resistant wheat in the field and source for gene transfer to other wheat lines/species.

Identification of New Sources of Resistance to Wheat Stem Rust in Aegilops spp. in the Tertiary Genepool of Wheat

Recent stem rust epidemics in eastern Africa and elsewhere demonstrated that wheat stem rust is a re-emerging disease posing a threat to wheat production worldwide. The cultivated wheat gene pool has a narrow genetic base for resistance to virulent races, such as races in the Ug99 race group. Wild relatives of wheat are a tractable source of stem rust resistance genes. Aegilops species in the tertiary genepool have not been exploited to any great extent as a source of stem rust resistance. We evaluated 1,422 accessions of Aegilops spp. for resistance to three highly virulent races (TTKSK, TRTTF, and TTTTF) of Puccinia graminis f. sp. tritici. Species studied include Ae. biuncialis, Ae. caudata, Ae. comosa, Ae. cylindrica, Ae. geniculata, Ae. neglecta, Ae. peregrina, Ae. triuncialis, and Ae. umbellulata that do not share common genomes with cultivated wheat. High frequencies of resistance were observed as 977 (68.8%), 927 (65.2%), and 850 (59.8%) accessions exhibited low infection types to races TTKSK, TTTTF, and TRTTF, respectively. Contingency table analyses showed strong association for resistance to different races in several Aegilops spp., indicating that for a given species, the resistance genes effective against multiple races. Inheritance studies in selected accessions showed that resistance to race TTKSK is simply inherited.

Resistance of Aegilops longissima to the Rusts of Wheat

Stem rust (caused by Puccinia graminis f. sp. tritici), leaf rust (P. triticina), and stripe rust (P. striiformis f. sp. tritici) rank among the most important diseases of wheat worldwide. The development of resistant cultivars is the preferred method of controlling rust diseases because it is environmentally benign and also cost effective. However, new virulence types often arise in pathogen populations, rendering such cultivars vulnerable to losses. The identification of new sources of resistance is key to providing long-lasting disease control against the rapidly evolving rust pathogens. Thus, the objective of this research was to evaluate the wild wheat relative Aegilops longissima for resistance to stem rust, leaf rust, and stripe rust at the seedling stage in the greenhouse. A diverse collection of 394 accessions of the species, mostly from Israel, was assembled for the study, but the total number included in any one rust evaluation ranged from 308 to 379. With respect to stem rust resistance, 18.2 and 80.8% of accessions were resistant to the widely virulent U.S. and Kenyan P. graminis f. sp. tritici races of TTTTF and TTKSK, respectively. The percentage of accessions exhibiting resistance to the U.S. P. triticina races of THBJ and BBBD was 65.9 and 52.2%, respectively. Over half (50.1%) of the Ae. longissima accessions were resistant to the U.S. P. striiformis f. sp. tritici race PSTv-37. Ten accessions (AEG-683-23, AEG-725-15, AEG-803-49, AEG-1274-20, AEG-1276-22, AEG-1471-15, AEG-1475-19, AEG-2974-0, AEG-4005-20, and AEG-8705-10) were resistant to all races of the three rust pathogens used in this study. Distinct differences in the geographic distribution of resistance and susceptibility were found in Ae. longissima accessions from Israel in response to some rust races. To P. graminis f. sp. tritici race TTKSK, populations with a very high frequency of resistance were concentrated in the central and northern part of Israel, whereas populations with a comparatively higher frequency of susceptibility were concentrated in the southern part of the country. The reverse trend was observed with respect to P. striiformis f. sp. tritici race PSTv-37. The results from this study demonstrate that Ae. longissima is a rich source of rust resistance genes for wheat improvement.

Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis

KEY MESSAGE

We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F6 recombinant inbred line and an F2 population, two genes were identified that mapped to the short arm of chromosome 1Ssh, designated as Sr-1644-1Sh, and the long arm of chromosome 5Ssh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.

Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors

MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.

Resistance of Aegilops Species from Israel to Widely Virulent African and Israeli Races of the Wheat Stem Rust Pathogen

Widely virulent races of the stem rust pathogen (Puccinia graminis f. sp. tritici) such as those isolated from Africa (e.g., TTKSK, isolate synonym Ug99) threaten wheat production worldwide. To identify Aegilops accessions with effective resistance to such virulent stem rust races, up to 10 different species from Israel were evaluated against African races TTKSK, TTKST, and TTTSK and the Israeli race TTTTC as seedlings in the greenhouse. A wide diversity of stem rust reactions was observed across the Aegilops spp. and ranged from highly resistant (i.e., infection type 0) to highly susceptible (infection type 4). The frequency of resistance within a species to races TTTTC and TTKSK ranged from 7 and 14%, respectively, in Aegilops searsii to 98 and 100% in AE. speltoides. In all, 346 accessions were found resistant to the three African races and 138 accessions were resistant (or heterogeneous with a resistant component) to all four races. The species with broadly resistant accessions included Ae. longissima (59 accessions), Ae. peregrina (47 accessions), Ae. sharonensis (15 accessions), Ae. geniculata (9 accessions), Ae. kotschyi (5 accessions), and Ae. bicornis (3 accessions). Few geographical trends or correlations with climatic variables were observed with respect to stem rust resistance in the Aegilops spp. The exception was Ae. longissima infected with race TTTTC, where a high frequency of resistance was found in central and northern Israel and a very low frequency in southern Israel (Negev desert region). This geographical trend followed a pattern of annual precipitation in Israel, and a significant correlation was found between this variable and resistance in Ae. longissima. Although difficult, it is feasible to transfer resistance genes from Aegilops spp. into wheat through conventional wide-crossing schemes or, alternatively, a cloning and transformation approach. The broadly resistant accessions identified in this study will be valuable in these research programs.

Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis Eig) into bread wheat (Triticum aestivum L.)

Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cultivar Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.

Elevating crop disease resistance with cloned genes

Essentially all plant species exhibit heritable genetic variation for resistance to a variety of plant diseases caused by fungi, bacteria, oomycetes or viruses. Disease losses in crop monocultures are already significant, and would be greater but for applications of disease-controlling agrichemicals. For sustainable intensification of crop production, we argue that disease control should as far as possible be achieved using genetics rather than using costly recurrent chemical sprays. The latter imply CO₂ emissions from diesel fuel and potential soil compaction from tractor journeys. Great progress has been made in the past 25 years in our understanding of the molecular basis of plant disease resistance mechanisms, and of how pathogens circumvent them. These insights can inform more sophisticated approaches to elevating disease resistance in crops that help us tip the evolutionary balance in favour of the crop and away from the pathogen. We illustrate this theme with an account of a genetically modified (GM) blight-resistant potato trial in Norwich, using the Rpi-vnt1.1 gene isolated from a wild relative of potato, Solanum venturii, and introduced by GM methods into the potato variety Desiree.

Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section

Aegilops sharonensis Eig (Sharon goatgrass) is a wild diploid relative of wheat within the Sitopsis section of Aegilops. This species represents an untapped reservoir of genetic diversity for traits of agronomic importance, especially as a source of novel disease resistance. To gain a foothold in this genetic resource, we sequenced the cDNA from leaf tissue of two geographically distinct Ae. sharonensis accessions (1644 and 2232) using the 454 Life Sciences platform. We compared the results of two different assembly programs using different parameter sets to generate 13 distinct assemblies in an attempt to maximize representation of the gene space in de novo transcriptome assembly. The most sensitive assembly (71,029 contigs; N50 674 nts) retrieved 18,684 unique best reciprocal BLAST hits (BRBH) against six previously characterised grass proteomes while the most specific assembly (30,609 contigs; N50 815 nts) retrieved 15,687 BRBH. We combined these two assemblies into a set of 62,243 non-redundant sequences and identified 139 belonging to plant disease resistance genes of the nucleotide binding leucine-rich repeat class. Based on the non-redundant sequences, we predicted 37,743 single nucleotide polymorphisms (SNP), equivalent to one per 1,142 bp. We estimated the level of heterozygosity as 1.6% in accession 1644 and 30.1% in 2232. The Ae. sharonensis leaf transcriptome provides a rich source of sequence and SNPs for this wild wheat relative. These sequences can be used with existing monocot genome sequences and EST sequence collections (e.g. barley, Brachypodium, wheat, rice, maize and Sorghum) to assist with genetic and physical mapping and candidate gene identification in Ae. sharonensis. These resources provide an initial framework to further build on and characterise the genetic and genomic structure of Ae. sharonensis.

Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (S(sh)) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6S(sh)) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

Why genetically modified crops?

This paper is intended to convey the message of the talk I gave at the Theo Murphy meeting at the Kavli Centre in July 2010. It, like the talk, is polemical, and conveys the exasperation felt by a practitioner of genetically modified (GM) plant science at its widespread misrepresentation. I argue that sustainable intensification of agriculture, using GM as well as other technologies, reduces its environmental impact by reducing pesticide applications and conserving soil carbon by enabling low till methods. Current technologies (primarily insect resistance and herbicide tolerance) have been beneficial. Moreover, the near-term pipeline of new GM methods and traits to enhance our diet, increase crop yields and reduce losses to disease is substantial. It would be perverse to spurn this approach at a time when we need every tool in the toolbox to ensure adequate food production in the short, medium and long term.

Characterization of a partial wheat-Thinopyrum intermedium amphiploid and its reaction to fungal diseases of wheat

Partial amphiploids between wheat (Triticum aestivum L.) and Thinopyrum species play an important role in the transfer and use of traits from alien species. A wheat-Thinopyrum intermedium partial amphiploid, TAI8335, and its alien parent were characterized by a combination of genomic in situ hybridization (GISH) and cytological observations. Evidence from GISH indicated that the donor parent Th. intermedium possessed seven pairs of S, seven J(s) and 21 J chromosomes. Mitotic observation showed that the majority of TAI8335 plants had 56 chromosomes, but a few had 54 to 55, in some cases with two to three additional telochromosomes. The chromosomes in most pollen mother cells of plants with 2n = 56 formed 28 bivalents, averaging 27.12 in 223 cells, suggesting a basic cytological stability. Sequential GISH patterns using genomic Pseudoroegneria spicata and genomic Th. intermedium DNA as probes revealed that TAI8335 had fourteen chromosomes derived from Th. intermedium and its alien genome consisted of one pair of S-, three pairs of J(s) - and one pair of J-genome chromosomes as well as two translocated chromosome pairs, one being a Robertsonian translocation and another an intercalary translocation, both of which involved J and S genome. Two of the telochromosomes in the aneuploid plants originated from the J genome and one from wheat. Disease screening demonstrated this line was highly resistant to leaf rust, stem rust, stripe rust and powdery mildew. This study showed that the partial amphiploid TAI8335 appears to serve as a novel source for the transfer of resistance genes for multiple fungal pathogens to wheat.

Genetics of resistance to wheat leaf rust, stem rust, and powdery mildew in Aegilops sharonensis

Aegilops sharonensis (Sharon goatgrass) is a wild relative of wheat and a rich source of genetic diversity for disease resistance. The objectives of this study were to determine the genetic basis of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis and also the allelic relationships between genes controlling resistance to each disease. Progeny from crosses between resistant and susceptible accessions were evaluated for their disease reaction at the seedling and/or adult plant stage to determine the number and action of genes conferring resistance. Two different genes conferring resistance to leaf rust races THBJ and BBBB were identified in accessions 1644 and 603. For stem rust, the same single gene was found to confer resistance to race TTTT in accessions 1644 and 2229. Resistance to stem rust race TPMK was conferred by two genes in accessions 1644 and 603. A contingency test revealed no association between genes conferring resistance to leaf rust race THBJ and stem rust race TTTT or between genes conferring resistance to stem rust race TTTT and powdery mildew isolate UM06-01, indicating that the respective resistance genes are not linked. Three accessions (1644, 2229, and 1193) were found to carry a single gene for resistance to powdery mildew. Allelism tests revealed that the resistance gene in accession 1644 is different from the respective single genes present in either 2229 or 1193. The simple inheritance of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis should simplify the transfer of resistance to wheat in wide crosses.

A walk on the wild side: mining wild wheat and barley collections for rust resistance genes

Leaf rust, stem rust, and stripe rust are among the most important diseases of wheat and barley worldwide and are best controlled using genetic resistance. To increase the diversity of rust resistance in wheat and barley, a project was initiated to identify and characterise rust resistance genes from the wild species of Aegilops sharonensis (Sharon goatgrass) and Hordeum vulgare ssp. spontaneum (wild barley), respectively. One hundred and two accessions of Sharon goatgrass from Israel and 318 Wild Barley Diversity Collection (WBDC) accessions from the Fertile Crescent, Central Asia, North Africa, and the Caucasus region were evaluated for resistance to leaf rust, stem rust, and/or stripe rust. Sharon goatgrass exhibited a wide range of infection types (ITs) in response to leaf rust, stem rust, and stripe rust. The percentage of resistant accessions in Sharon goatgrass was 58.8–78.4% for leaf rust, 11.8–69.6% for stem rust, and 46.1% for stripe rust, depending on the race used and the plant growth stage. Genetic studies with Sharon goatgrass revealed oligogenic resistance to leaf rust and stem rust. Wild barley also exhibited a wide range of ITs to leaf rust and stem rust; however, the overall frequency of resistance was lower than for Sharon goatgrass. The percentage of resistant accessions in wild barley was 25.8% for leaf rust and 5.7–20.1% for stem rust, depending on the race used. Resistance to the new virulent stem rust race TTKS (i.e. Ug99), present in eastern Africa, was found in both Sharon goatgrass (70% of accessions) and wild barley (25% of 20 accessions tested). Association mapping for stem rust resistance was applied in the WBDC using Diversity Arrays Technology (DArT) markers. Using the highly conservative P value threshold of 0.001, 14 and 15 significant marker associations were detected when the number of subpopulations (K value) was set for 10 and 8, respectively. These significant associations were in 9 and 8 unique chromosome bins, respectively. Two significant marker associations were detected for resistance to the wheat stem rust race MCCF in the same bin as the rpg4/Rpg5 complex on chromosome 7(5H). The presence of a major stem rust resistance gene in this bin on chromosome 7(5H) was validated in a bi-parental mapping population (WBDC accession Damon × cv. Harrington) constructed with DArT markers. The results from this study indicate that Sharon goatgrass and wild barley are rich sources of rust resistance genes for cultivated wheat and barley improvement, respectively, and that association mapping may be useful for positioning disease resistance genes in wild barley.