All BGRI Abstracts

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Genomic regions containing multiple disease resistance loci

Joukhadar Department of Animal, Plant and Soil Sciences, La Trobe University, Australia

Climatic changes permit the spread of plant diseases to new areas. To ensure grain production meets the needs of the growing world population, wheat breeding must combine multiple disease resistances in single cultivars in order to maintain current yield potential. Over the last three decades, classical mapping and association studies have identified disease resistance loci for individual diseases, but few studies have investigated loci that confer resistance to multiple diseases. To address this limitation, we extensively surveyed the literature to identify wheat genomic regions harboring resistance to multiple diseases. We identified 174 trait-linked markers distributed across all wheat chromosomes, except chromosome 4A, and the numbers of disease resistance loci in each region ranged from two to ten. Our survey suggests that some regions of the genome contain multiple disease resistance genes, or genes with pleiotropic effects. We are using the Chinese Spring flow sorted chromosome survey contigs to investigate the genic contents of genomic regions containing multiple disease trait loci to address this question.

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Identification of resistance factors against rust fungi: leveraging genetic and genomic tools in Brachypodium - rust fungi pathosystems

Figueroa Department of Plant Pathology, University of Minnesota, USA

During the past 15 years, significant efforts have been directed to develop the grass species Brachypodium distachyon as a genetically tractable model for monocot plants, especially economically valuable cereals such as wheat, barley and oat. Such efforts have led to an increasing availability of genomic, genetic and bioinformatics tools designed to bypass the experimental challenges faced when addressing important biological questions in complex systems. Moreover, such advances may translate in the use of other valuable species of Brachypodium (e.g., B. hybridum), which are not nearly as well characterized as B. distachyon. Given the 2050 global food demands and needs to increase grain production we seek to develop innovative and sustainable approaches to decrease crop yield losses due to rust fungi. One possible strategy is the use of transgenic plants harboring non-host resistance-related genes from closely related species. B. distachyon and B. hybridum can serve as potential sources to engineer plant resistance against highly destructive rust fungi, such as Puccinia graminis and P. coronata. Advancing our understanding of non-host resistance in monocot species has been a slow process. However, the amenability of Brachypodium as a model system offers a means to accelerate scientific discovery of factors controlling non-host pathogen interactions involving stem and crown rust fungi. In a multi-pronged approach, we are leveraging genetic and genomic tools, as well as generating new resources to provide foundational knowledge in order to support plant genetic engineering programs.

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The effector repertoire of Puccinia striiformis subdues host-plant immunity

Wang State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, P. R. China

Rust outbreaks cause severe yield lossespose a serious threat to global food security. As biotrophic pathogens, rust fungi produce effectors to suppress host immunity. In this study, we used a systemic approach to identify and characterize effectors in Puccinia striiformis f. sp. tritici. Among secreted proteins encoded by the Pst genome, we identified 150 putative effectors that are Cys-rich or up-regulated during hostinfection. A systematic screen showed that 14 of them suppressed programmed cell death (PCD) triggered by BAX and INF1 in Nicotiana benthamiana, and all have high intra- and inter-species polymorphisms at the protein level. Although these 14 effectors individually made only minor contributions to Pst virulence, delivery of them into wheat plants via a bacterial type-III secretion system efficiently suppressed PTI and ETI. Interestingly, three of them, Pst_4941, Pst_4884, and Pst_5578, triggered HR-like PCD in the AvSYr1NIL, but only Pst_4941 also caused PCD in the AvSYr7 NIL, suggesting that they may function as avirulence factors. This study suggests that Pst effectors function to suppress PTI and ETI.

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Wheat cv. Kingbird is introduced to address a new stem rust threat in Ethiopia

Tadesse Kulumsa Agricutural Research Center, Ethiopian Institute of Agricultural Research, Ethiopia

Pgt race TKTTF, virulent for the SrTmp gene present in Ethiopian cv. Digalu and first detected in 2012, caused significant yield losses in Digalu during the 2013 and 2014 seasons. No suitable replacement varieties with significant seed volume were available, and alternate solutions were sought. EIAR, with the support of the DRRW project through CIMMYT-Ethiopia, introduced 5 tonnes of adult plant, rust resistant wheat cv. Kingbird from Kenya. Kingbird was evaluated for agronomic performance at seven locations vs. three checks in 2014, and was also evaluated for stem rust reaction in single-race nurseries (TKTTF, TTKSK, TRTTF and JRCQC). With support from USAID/CIMMYT, seed was concurrently multiplied on 37 ha producing 80 tonnes of seed that was distributed to farmers in 2015. Mean grain yield over locations was 2.76 t ha-1. Mean performance of Kingbird was 3.00 t ha-1 compared to 2.79 t ha-1 for Ogolcho, 2.83 t ha-1 for Biqa and 2.42 t ha-1 for Kakaba. Thus Kingbird gave yield advantages of 5 to 22% over the check varieties. Stem rust severities on Kingbird in the single race nurseries ranged from Tr to 15% and reactions ranged from TMR to SMS. The check varieties rated up to 45% severity with S type reactions. Thus Kingbird was superior in terms of yield potential and stem rust resistance as measured in these trials vs. the check varieties. Stem rust resistance of Kingbird is based on Sr2 and Sr57 and is hypothesized to have at least three additional APR loci. Seedling reactions of Kingbird to races TKTTF and Ug99 are characterized as susceptible. Sr57 is pleiotropic and confers partial resistance to all three rusts, powdery mildew, spot blotch, and BYDV. Based on early maturity, yield performance, and stem rust resistance, Kingbird is recommended for low- to mid-altitude wheat-growing areas of Ethiopia.

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Characterization of a stripe rust resistance gene in wheat landrace AUS 27969 from the Watkins collection

Kandiah The University of Sydney, Plant Breeding Institute, Australia

Landraces and wild relatives of wheat are rich repositories of new rust resistance genes. Landraces are preferred over wild relatives for the absence of deleterious effects associated with large alien segments. A common wheat landrace, AUS 27969 (ex Portugal), from the Watkins Collection was resistant under field conditions and produced seedling infection type (IT) 2C against the widely virulent Australian Puccinia striiformis f. sp. tritici (Pst) pathotype 134 E16 A+ Yr17+ Yr27+. AUS 27969 was crossed with the susceptible genotype Avocet S (AvS) and the distribution of F3 lines conformed to monogenic segregation [40 non-segregating resistant (NSR), 93 segregating (Seg), and 37 non-segregating susceptible (NSS); ?2 = 1.61, P2d.f. >0.05] when tested with the same pathotype at the seedling stage. The population is currently being selfed to F6. DNA from NSR and NSS lines will be sent for high throughput analysis to identify the genomic region carrying the resistance gene. Resistance-linked SNPs will be mapped on the F6 RIL population. The resistance gene will be backcrossed into modern Australian wheat backgrounds.

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Genetic characterization of stripe rust resistance in a common wheat landrace AWCC618

Gessese The University of Sydney Plant Breeding Institute, Australia

Stripe rust of wheat was estimated to cause losses of A$127 m annually in Australia. Although stripe rust can be controlled through the use of chemicals, breeding for resistance is considered to be the best means of control. Identification and characterization of diverse sources of resistance is essential to achieve durable stripe rust control. A common wheat landrace AWCC618 showed resistance (IT 1CN) to Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. AWCC618 was crossed with the susceptible genotype Avocet S (AvS) to determine the genetic basis of resistance. Seedling tests on 123 AWCC618/AvS F3 families using Australian Pst pathotype 134 E16 A+ 17+ 27+ indicated monogenic inheritance of resistance (22HR:68SEG:33HS; χ21:2:1=3.34, non-significant at P=0.05 and 2 d.f.). The resistance locus was temporarily named YrAW3. Selective genotyping of eight homozygous resistant (HR) and eight homozygous susceptible (HS) F3 families using the 90K SNP Infinium assay tentatively located YrAW3 on chromosome 6A. The AWCC618/AvS population was advanced to F6 for detailed mapping of the target region. YrAW3 appears to be a new locus. AWCC618 was crossed with three current Australian cultivars to transfer YrAW3 to modern wheat backgrounds. Backcross-derivatives will also be useful for validation of linked markers.

 

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Monitoring the South African leaf rust population through a combined phenotyping and SSR genotyping approach

Selinga Department of Plant Sciences, University of the Free State, South Africa
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Leaf rust is a common wheat disease in South Africa. Annual surveys conducted by the Agricultural Research Council - Small Grain Institute (ARC-SGI) during the last 35 years used infection type (IT) data on a defined differential set to identify individual field isolates. Results from these surveys confirmed that the South African Pt population is affected by both local evolution and foreign introductions. A good correlation was found between avirulence/virulence phenotypes and simple sequence repeat (SSR) genotypes in the South African Pt population. We therefore evaluated whether identification of field isolates by SSR analysis would complement the traditional IT analysis using 47 field isolates collected during the 2013 growing season. Of the 39 phenotyped isolates, 35 were correctly genotyped while three were incorrectly genotyped only because the corresponding race was not included as a control. Five isolates that could not be phenotyped due to non-viable spores were successfully genotyped. The dominant race 3SA145 (North American race annotation CCPS) was represented by nine different genotypes sharing 82% genetic similarity. The SSR data further showed that the field isolates formed part of two distinct lineages with little admixture between them. This study confirmed the supporting value of SSR genotyping to traditional race analysis in monitoring the South African Pt population. 

 

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Characterization of seedling and adult plant resistance to leaf rust in African wheat germplasm

Kankwatsa The University of Sydney, Plant Breeding Institute, Australia

Many of the catalogued leaf rust resistance genes in wheat deployed in agriculture have been overcome by variants of Puccinia triticina (Pt), the causal pathogen of leaf rust. Discovery and characterization of new sources of resistance in various germplasms using multipathotype tests and molecular markers could permit future diversification of the genetic base of leaf rust resistance in wheat. In searching for new sources of leaf rust resistance, 140 wheat lines from 14 African countries were tested with 8 Australian Pt pathotypes. Seedling tests revealed that 41% of the lines were susceptible to all pathotypes, 31% were postulated to carry either one of 10 resistance genes (Lr1, Lr2a, Lr3a, Lr13, Lr18, Lr23, Lr24, Lr26, Lr37 or Lr73) or one of five gene combinations (Lr2a+Lr3a, Lr1+Lr13, Lr1+Lr23, Lr1+Lr13+Lr73 and Lr23+Lr73). Twenty-eight percent of the lines were postulated to carry uncharacterized seedling resistance genes. Based on average coefficients of infection (ACI), 101, 25 and 11 lines showed high (ACI 0-19), moderate (ACI 21-38) and low (ACI 41-56) levels adult plant resistance, respectively, whereas three lines were moderately susceptible to susceptible (ACI 63-76). Genotyping of 74-78 lines that were anticipated to carry APR genes, using the molecular markers: csLV34 (linked to Lr34) and KASP SNP markers SNP1G22 and SNPT10 (linked to Lr46 and Lr67), respectively, revealed the presence of Lr34, Lr46 and Lr67 in 11, 22 and 14 wheat lines, respectively. The identities of the APR in the remaining 22 lines are unknown, and potentially represent new resistance sources. Genetic analyses of these uncharacterized APR sources are underway to select single gene lines and allow fine mapping.

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Brachypodium distachyon as a model to study nonhost resistance to wheat stripe rust

Gilbert CSIRO Plant Industry, Australia

The model grass Brachypodium distachyon has been used to study nonhost resistance mechanisms to the wheat stripe rust pathogen, Puccinia striiformis f. sp tritici. Numerous B. distachyon accessions were screened with an array of UK and Australian P. striiformis isolates and distinct infection phenotypes identified, ranging from complete resistance to partial susceptibility. Three mapping families were established - BdTR10H x TEK4, BdTR13K x Bd21 and ABR6 x Bd21 - and immunity was dominantly inherited when they were tested with one Australian and three UK isolates. Depending upon the mapping family, between one and three genes for stripe rust resistance were present and designated Yrr1 to Yrr3. Yrr1, which is present in all three families, was effective against all isolates and was fine mapped to a 100 kilobase region containing six candidate genes. Interestingly, no candidate was homologous to a known resistance gene. Yrr2, which is present in the BdTR13K x Bd21 and ABR6 x Bd21 families, is race-specific and was mapped to a 1 megabase region that contains multiple, classic NBS-LRR resistance gene candidates. Yrr3, which is present in the ABR6 x Bd21 family and effective against all isolates, was mapped to a 400 kilobase region also containing NBS-LRR gene candidates. Agrobacterium-mediated transformation of Yrr1 candidates is underway in Brachypodium for complementation, and in common wheat to test for interspecies transfer of characterized resistance.

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Achieving durable rust resistance in wheat through deployment of major and minor genes

Thapa Agriculture Botany Division, Nepal Agricultural Research Council (NARC), Nepal

Stripe rust and leaf rust have been major constraints to wheat production in Nepal since the 1960s. Several rust epidemics causing hardship for Nepalese wheat growers were due to race changes. Breeding for rust resistance was initiated with establishment of the National Wheat Research Program in 1972, but concerted searches for durable resistance came later with the introduction of wheat genetic resources from CIMMYT, Mexico. The early wheat varieties Nepal 297, Siddhartha, Vinayak, BL1473, BL 1022 and Annapurna series with leaf rust and stripe rust resistance genes Lr13, Lr23, Lr26 and Yr9, and Yr27 in the 1970s and 1980s succumbed to new races within a few years of release. However, Bhrikuti (CMT/COC75/3/PLO/FURY/ANA) with both major and minor gene combinations (Lr10, Lr14a, Lr26/Yr9/Sr31+ and Lr34/Yr18) and released in 1994 was unaffected by Yr9 virulence in 1997 and Yr27 virulence in 2004. This variety with >20 years of leaf rust and stripe rust protection continues to be the most popular wheat variety in Nepal. Three other varieties, Gautam (Siddhartha/Ning8319//Nepal 297) released in 2004, WK 1204 (SW89-3064/Star) released in 2007, and Pasang Lhamu (PGO/SERI) released in 1997 with Lr16, Lr26/Yr9/Sr31, Lr34/Yr18, Lr46/Yr29, Yr7, and Sr2 also remain resistant. The Ug99 resistant varieties Vijay (NL748/NL837), Danphe(KIRITATI//2*PBW65/2*SERI.1B) and Tilottama (Francolin#1 = Waxwing*2/Vivitsi) also possesses APR to the three rusts. Nepalese wheat researchers work closely with the CIMMYT Global Wheat Program and DRRW/BGRI to utilize knowledge and APR germplasm. Strong networks for participatory varietal selection involving women farmers in both the hills and terai help in faster adoption and in establishing varietal diversity. In summary, Nepalese wheat breeders have successfully used APR in protecting wheat crops.

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