2015 BGRI Poster Abstracts

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Displaying 201 - 210 of 415

New QTL for leaf rust and stripe rust resistance in four bread wheat and two durum wheat mapping populations

Wheat leaf rust (LR) and stripe rust (YR), caused by the air-borne fungi Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst), respectively, are considered the primary biotic threats to bread wheat and durum wheat production globally. Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by these diseases. Bread wheat lines Francolin #1, Kenya Kongoni, Kundan and Sujata, and CIMMYT-derived durum wheat lines Bairds and Dunkler display an adequate level of adult plant resistance (APR) to both leaf rust and stripe rust in Mexican field environments. Six recombinant inbred line (RIL) populations developed from crosses Avocet/Francolin #1, Avocet/Kenya Kongoni, Avocet/Kundan, Avocet/Sujata, Atred#1/Bairds and Atred#1/Dunkler were phenotyped for leaf rust response at Ciudad Obregon, Mexico, and the bread wheat populations for stripe rust response at Toluca for under artificial inoculations for multiple seasons. The RIL populations and their parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. Known pleotropic APR genes Lr46/Yr29 mapped in all of six populations, and explained 7.4-65.1% and 7.7-66.1% severity variations for LR and YR across different bread wheat populations and accounted for 12.4-60.8% of LR severity variations over two durum wheat populations. In addition, several new APR loci identified on chromosomes 1AS, 1DS, 2BS, 2BL, 3D and 7BL in bread wheat and QTL on chromosome 6BL in durum wheat. Among these loci, QTL on chromosomes 1AS, 3D and 7BL might be represent new co-located/pleotropic loci conferring APR to LR and YR. RILs combining these APR loci can be used as sources of complex APR in both bread wheat and durum wheat breeding. In addition, the closely linked single nucleotide polymorphism (SNP) markers have been converted into breeder-friendly kompetitive allele specific PCR (KASP) markers and their diagnostic verified.

Primary Author: Lan, CIMMYT

Keywords: APR

Genetic characterization of slow rusting resistance to leaf rust in durum wheat cv. Bairds

The CIMMYT durum Bairds is susceptible to leaf rust (LR) at the seedling stage but shows an adequate level of slow rusting adult plant resistance (APR) in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds and the susceptible parent Atred#2 was phenotyped for LR response at Ciudad Obregon, Mexico, during 2013, 2014 and 2015 under artificial epidemics created with Pt race BBG/BP. Genetic analysis indicated that 3-4 additive genes conferred LR resistance. The RILs and parents were also genotyped with the 50K diversity arrays technology (DArT) sequence system and 93 SSR markers. A genetic map comprising 1,150 markers was used to map the resistance loci. Inclusive composite interval mapping analysis detected four quantitative trait loci (QTL) on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTL, designated as QLr.cim-1BL, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, explained 20.1-60.7%, 6.4-13.1%, 4.3-11.2%, and 7.1-28.0%, respectively, of the variation in leaf rust severity. QLr.cim-1BL was close to the previously reported APR gene Lr46, whereas QLr.cim-6BL, detected in all three seasons, is a new resistance locus in durum wheat. The four QTL combined showed a significant additive effect on resistance with a disease severity of 18-20%, whereas RILs carrying the individual QTL showed mean leaf rust severities ranging from 56 to 98%. Three QTL, except for QLr.cim-2BC, were derived from Bairds. The final LR severity of Bairds ranged from 15-25% across three years. This cultivar can be used as a source for complex APR in durum wheat breeding.

Primary Author: Lan, International Maize and Wheat Improvement Center (CIMMYT), México

Keywords: leaf rust, durum wheat, genetics

Contig reduction in genomic assembly of Pst isolates from Western Canada

We earlier assembled the genomes of Pst isolates collected in western Canada using assembly of Illumina paired-end sequences. Two isolates, LSW3_2012_SP2 and SWS484_SPF, were assembled with ?15,150 and ?11,700 contigs each when compared to references North American PST-78 and Chinese CYR32, respectively. In order to reduce the number of contigs and therefore obtain a longer display of contiguous genes, we used the PacBio and Illumina Mate Pair (MP) technologies to achieve that goal using the two isolates. We had to modify our current protocol for DNA isolation from Pst spores to obtain DNA fragments of ?35 Kb suitable for construction of large insert genomic sequencing libraries. Libraries of 8-10 Kb and 3.5-6 Kb were used for PacBio and Illumina MP analyses, respectively. We obtained a 26x coverage of the Pst genome with the PacBio results with an mean size of 7,400 bp and 6,500 bp for the two libraries, and a 190x coverage with the Illumina MP sequencing information. We are using the Ray assembler with the datasets and the 50x Illumina paired end sequencing information from previously independently associated isolates LSW3_2012_SP2 and SWS484_SPF. The quality of our assembly will be compared to the contigs and supercontigs available for the reference isolates PST-78 and CYR32. These results will also enable us to establish the physical relationship among isolate-specific genes. Finally, the impact of the large insert libraries on the proportion of short paired-end unassembled reads will be discussed as it was 78% and 50% for LSW3_2012_SP2 and SWS484_SPF, respectively, after assembly of 100 bp paired-end reads.

Primary Author: Laroche, Agriculture and Agri-Food Canada, Lethbridge Research Centre, Canada

Keywords: Canada, genomic assembly

Regulation of Pst and wheat genes in incompatible and compatible reactions

We evaluated Pst-wheat interaction at the transcriptome level between Pst isolate LSW3_2012_SP2 and Avocet/Yr5 (R), and Avocet S (S). For the compatible interaction we used a dataset of 9.3 M Illumina paired-end clean reads in which ?300,000 reads mapped against nearly 9,000 contigs of the PST-78 reference transcriptome, whereas 3.5 M reads mapped against a partial wheat transcriptome of 13,300 contigs. Pst transcripts in the infected wheat tissues amounted to about 10% of the mapped transcripts. In the incompatible reaction, we used a dataset of 13.2 M clean reads and ?27,000 reads mapped against nearly 2,900 Pst transcriptome contigs while 7.7 M reads mapped against 18,800 wheat transcripts. These results show an important differential regulation of genes in both the fungal pathogen and the wheat host. More than 3 times the number of distinct Pst transcripts was identified in the compatible reaction than the incompatible reaction. Genes differentially regulated between the incompatible and compatible reactions will be compared in terms of functionality and GO term classification. To validate Pst transcripts involved in the infection process, we adapted a leaf rust haustorial isolation protocol for characterization of proteins and modified it to protect the integrity of RNA in enriched Pst haustoria. A list of potential effectors present in LSW3_2012_SP2 and verified in haustoria-enriched tissues will be presented.

Primary Author: Laroche, Agriculture and Agri-Food Canada, Lethbridge Research Centre, Canada

Keywords: Pst, genes, reactions

Using ‘speed breeding’ to harness rust resistance: faster, cheaper and easier

A new method for rapid generation advance, called ‘speed breeding’, has considerable advantages over DH technology for spring wheat because it provides increased recombination during line development and enables selection in early generations for some traits. The system has been refined over the past 8 years at The University of Queensland, utilizing controlled temperature regimes and 24-hour light to accelerate plant growth and development. The low-cost management system enables up to 6 plant generations of wheat annually – just like Arabidopsis. Currently, three of the six wheat breeding companies in Australia are exploiting speed breeding, and elite lines developed using the technology are in the final stages of yield evaluation. Recently, we developed methods adapted for use in the speed breeding system, which permit year-round high-throughput screening for adult plant resistance (APR) to rust pathogens that attack wheat. In this presentation, we describe the protocols, explain how phenotypes are related to field-based measures and highlight how the system can even handle diverse germplasm, such as winter types and landraces. Our ‘triple rust’ screening methodology enables selection for APR to all three rust pathogens and crossing of selected plants within a single plant generation. We applied the technique to rapidly introgress rust resistance into several Australian cereal cultivars. The technology is also a useful tool to accelerate rust research efforts. RIL populations designed for mapping novel APR genes can be developed within 12–18 months. Experiments to understand gene function in terms of temperature stability and onset of resistance can be performed year-round and if combined with sequencing technologies, such as RNAseq, transcripts involved in rust defence can be rapidly identified and harnessed via the speed breeding system. We will also reveal our current activities aiming to integrate the system with other plant breeding technologies to maximise genetic gain for wheat.

Primary Author: Lee Hickey, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Australia


Global Pgt Initiative: An international genetic resource to combat stem rust

An important component of the management of wheat stem rust is an understanding of the population diversity of the pathogen, Puccinia graminis f. sp. tritici (Pgt). The discovery of “Ug99” resulted in renewed efforts on pathogen surveys, sample collections and pathotyping of Pgt, with a primary focus on Africa. In the last few years these efforts have been expanded to include other targeted regions, however a global effort is needed. The aims of the “Global Pgt Initiative” is: to capture and maintain living cultures that collectively reflect the entire global diversity of Pgt in the years 2014 - 2016; pathotype and genotype this collection; develop DNAbased diagnostic tools that will be able to rapidly detect shifts in Pgt populations, and provide an early warning system of the vulnerability of wheat to new virulent strains; and provide a genetic baseline for comparison of Pgt populations over time, both forward and backwards. This initiative will provide the wheat rust community with a geographically distributed, well characterized, living culture collection that represents the global diversity of Pgt; a global open access knowledge bank on Pgt pathotypes and genotypes; and advanced molecular diagnostic tools for rapid detection and tracking of Pgt populations. The Global Pgt Initiative represents the most comprehensive effort to capture and characterize the global diversity of Pgt and provide a unique resource to the global wheat rust community.

Primary Author: Les Szabo, USDA-ARS, Cereal Disease Laboratory


Virulence of Puccinia striiformis f. sp. tritici Population to 18 NILs in Yunnan Province, China

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) is the most destructive disease of wheat worldwide. Breeding and planting resistant cultivars is the most economic, effective, as well as environmental methods to control the disease. Yunnan is a severe epidemic zone in China, which provides new incursions for other parts of China. Study on virulence of the Pst population and effectiveness of resistance genes, will provide information for breeding and rational use of resistance genes. One hundred and thirty-six136 isolates collected from 9 regions of Yunnan were tested using a set of 18 Yr NILs with genes Yr1, Yr5, Yr6, Yr7, Yr8, Yr9, Yr10, Yr15, Yr17, Yr24, Yr27, Yr32, Yr43, Yr44, YrSP, YrTr1, YrExp2, YrTyTye. Stripe rust races were named by octal code. The results showed that the Pst population in Yunnan is highly variable in races and virulence. A total of 64 races were identified and the top two most frequent races were 550273 (Virulence/Avirulence formula: 1, 6, 7, 9, 27, 43, 44, SP, Exp2, Tye / 5, 8, 10, 15, 17, 24, 32, Tr1 and 550073(Virulence/Avirulence Formula: 1, 6, 7, 9, 43, 44, SP, Exp2, Tye / 5, 8, 10, 15, 17, 24, 27, 32,Tr1), with frequency of 28.68% and 11.76%, respectively. The remaining races had frequencies less than 5.0%. No virulence were found for Yr5, Yr10, Yr15, and Yr32. The frequencies of virulence to Yr24, YrTr1, Yr8, and Yr17 ranged from 0.74% to 11.76%. The frequency of virulence to Yr27 was 52.94%; and virulence to Yr1, Yr6, Yr7, Yr9, Yr43, Yr44, YrSP, YrExp2, and YrTye ranged from 79.94% to 91.91%. The results will guide the breeding and wheat production. (This study was supported by National Natural Science Foundation of China, Grant No. 31260417 and 31560490)

Primary Author: Li, Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, China

Keywords: virulence

Combining population genetic structure and upper air flow trajectories to reveal the origin and migration of Puccinia striiformis f. sp. tritici

Pathogen migration is a source of new pathogens and pathotypes to a particular region. Studies on origin and migration of pathogens were difficult in the past, but DNA sequence data and new analytical approaches now enable us to analyze population genetic structures from which we can determine possible migration routes. The Himalayan and neighboring regions (Gansu, China) were earlier suggested as putative centers of origin for Puccinia striiformis f. sp. tritici (Pst) and sampling locations for Chinese isolates were strongly focused in South Gansu. Previous field surveys indicated that Yunnan might be the primary source of the Gansu population in China. Using samples collected in 2008 and 2011 we compared the Pst population structures of Yunnan and south Gansu for SNPs in housekeeping genes Cdc2, Ef-1? and Mapk1, and the trajectories of upper air flow during wheat growing seasons from 2005 to 2013. The ancestral haplotype was detected in the Yunnan population, which had higher a mutation rate than the Gansu population, but the latter contained more recombination events. Both populations were highly diverse. There was massive air flow between Yunnan and Gansu with trajectories being mainly from Yunnan to Gansu. We propose a putative dispersal route of Pst from Yunnan to South Gansu, making Yunnan the center of origin for Pst in China, whereas Gansu is a secondary center of origin. It is proposed that Pst migrates from South Asia to Yunnan under the influence of westerly weather patterns, and subsequently spreads to other parts in China. DNA sequence comparisons should be undertaken to compare Pst populations of South Asia and China in order to confirm these hypotheses.

Primary Author: Li, Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, China

Keywords: China, stripe rust, rust migration

Berberis holstii is functional as an alternate host of Puccinia graminis in Ethiopia

Berberis holstii, native to the highlands of East Africa, is susceptible to Puccinia graminis and P. striiformis in artificial inoculations. However, it is not known whether these pathogens complete their sexual cycles in the region. In an attempt to understand the role of B. holstii in pathogen variation and epidemiology of wheat stem rust and stripe rust, we investigated the functionality of B. holstii as an alternate host. Natural aecial infections on B. holstii were observed and sampled in August at Mt. Kenya and Narok (Kenya), and June to December at North Shewa (Ethiopia) from 2008. Aeciospores from the collections were inoculated to a panel of cereal species, including Line E and ‘Morocco’ wheat, 'Hiproly’ barley, 'Prolific' rye, and ‘Marvelous’ oat. For the majority of aecial samples, aeciospore viability was lost during shipment and storage; thus inoculations were not successful. Inoculations using relatively fresh samples collected at North Shewa in 2012 and 2014, resulted in stem rust infections on Line E, Prolific, Hiproly, and Marvelous. DNA assays using real-time PCR confirmed the presence of P. graminis in these samples. While it is likely that the pathogen infecting Line E, Prolific and Hiproly is P. graminis f. sp. secalis (Pgs), the inoculation and DNA assays did not provide sufficient resolution to distinguish Pgs from Pgt. Stem rust infections on Marvelous were assumed to involve Pg f. sp. avenae. Experiments are in progress to characterize isolates derived from these samples, and to determine if other rust fungi are present in these samples. Based on these preliminary data, we conclude that P. graminis completes its sexual cycle in Ethiopia. The contribution of the sexual cycle to the observed variation within the Pgt population in the region remains unclear. 


Primary Author: Lim, Department of Plant Pathology, University of Minnesota, USA

Keywords: Ethiopia, barberry, alternate host

A plasma membrane localized Cu-only superoxide dismutase boosts stripe rust fungus infection by scavenging host-derived ROS

Infection of pathogens in plants induces production and accumulation of reactive oxygen species (ROS). ROS are not only involved in plant defense responses, but directly restrict or kill pathogens. To counteract this attack, it is necessary for pathogens to remove host-produced ROS. However, the mechanisms protecting pathogens against host-derived oxidative stress are little known. In this study, a superoxide dismutase (SOD) gene, PsSOD2, was cloned from Puccinia striiformis f. sp. tritici (Pst). Quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PsSOD2 is an in-planta induced gene active in the early stage of Pst infection. Prokaryotic expression and biochemical characterization revealed that PsSOD2 encoded a Cu-only SOD. The predicted signal peptide for protein secretion was functional in an invertase-mutated yeast strain. Transient expression in Nicotiana benthamiana suggested that PsSOD2 is localized in plasma membrane and dependent on glycophosphatidyl inositol (GPI) anchor at the C terminus. Furthermore, Size exclusion chromatography and bimolecular fluorescence complementation validated dimerization of PsSOD2. Overexpression of PsSOD2 in N. benthamiana significantly decreased ROS production triggered by flg22. Knockdown of PsSOD2 using a host-induced gene silencing (HIGS) system reduced the virulence of Pst, which was correlated to ROS accumulation in HIGS plants. These results suggest that PsSOD2 is a pivotal virulence factor that is localized in hyphal plasma membrane to promote Pst infection by scavenging host-derived ROS.

Primary Author: Liu, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling