All BGRI Abstracts

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MicroRNAs and their mega effects on gene expression in response to leaf rust in wheat (Triticum aestivum L.)

BGRI 2018 Poster Abstract
Summi Dutta Department of BioEngineering, Birla Institute of Technology, Mesra, Ranchi, India
Manish Kumar, Kunal Mukhopadhyay

Bread wheat (Triticum aestivum L.) being the world's most popular edible cereal, plays a major role in global economy. Rust in wheat leaves, caused by Puccinia triticina, affects grain quality and severely retards its production worldwide. Micro(mi)RNAs are considered major components of gene silencing and so have a great role to play during stress. The present study focuses on identification of miRNAs, produced by host to suppress pathogen as well as delivered by pathogens to encounter host defence mechanism. Therefore, these miRNAs may be called as leaf rust responsive microRNAs. Small RNA and degradome libraries were prepared from a pair of near isogenic lines of wheat (HD2329, HD2329+Lr24), one set was mock inoculated while the other set was inoculated with urediniospores of leaf rust pathogen. Using these libraries as input a vast number of miRNAs rather a population of miRNAs were identified derived from wheat that were targeting genes mostly involved in functions like defense response, signal transduction, development, metabolism, and transcriptional regulation.
When reads specifically produced under pathogen inoculation were taken as input with Puccinia triticina genome sequences as reference, only three putative miRNA precursor loci were detected and the molecules produced were called miRNA-like molecules as their precursors lacked one or two criteria essential for a true miRNA precursor. The identified miRNAs were targeting genes like F-box protein, MAP kinase, calmodulin and susceptible antioxidant protein. We further identified the presence of argonaute and dicer like domains in Puccinia proteome available at FungiEnsembl which strengthens presence of RNAi-like activities in Puccinia.
In addition, differential expression of wheat as well as Puccinia small RNAs using stem loop RT-PCR under varying time points of disease progression (0-168 hpi) revealed their direct connection with stress responses.

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Virulence evolution of Puccinia striiformis f.sp. tritici on wheat in Kenya between 1970 to 1992 and 2009 to 2014

BGRI 2018 Poster Abstract
Mercy Wamalwa Egerton University Njoro, Kenya
Ruth Wanyera, James Owuoche, Julian Rodriguez, Annemarie Justesen, Lesley Lesley, Sridhar Bhavani, Cristobal Uauy, Mogens Hovmøller

Emergence of new virulent races of Puccinia striiformis f. sp. tritici (Pst) to stripe (yellow) rust resistance genes in wheat (Triticum aestivum L.) has historically resulted in severe yield losses worldwide. We conducted a study to characterize the virulence profiles of Pst races prevalent in Kenya from historic (1970-1992) and recent collections (2009-2014). Pst isolates collected during surveys in Kenya were characterized at the Global Rust Research Centre (GRRC), Denmark. Yellow rust differential sets (wheat lines with known Yr resistance genes), and strain-specific sequence-characterized-amplified-region (SCAR) markers were used to group the Pst isolates as Pst1 or Pst2. Virulence to Yr1, Yr2, Yr3,Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27, and the seedling resistance in AvocetS were detected. A total of 12 virulence profiles /races were detected in isolates obtained during 1970 to 1992, while six races were detected from samples collected between 2009 to 2014. In both periods, races with virulence profiles Yr2, Yr6, Yr7, Yr8, Yr25, Yr27, Avs and Yr2, Yr6, Yr7, Yr8, Yr17, Yr25, AvS were common. The SCAR results revealed that both Pst1 and Pst2 strains were present in the Pst isolates tested, Pst1 even in isolates from the 1970s. Additional isolates were also identified with neither Pst1 nor Pst2 profiles. From our findings, race analysis is key to understand the race diversity and pre-breeding efforts for effective resistance gene deployment.

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Survey of wheat stem rust Puccinia graminis f. sp. tritici in Jordan

BGRI 2018 Poster Abstract
Kholoud Alananbeh The University of Jordan
Ayed Al Abdallat, Monther Tahat

Studies on whet stem rust (WSR) in Jordan are considered to be old. There was only one study conducted in the late 1980's by Abu-Blan and Duwayri (1989) to evaluate the infection of wheat cultivars with black stem rust disease (Puccinia graminis f. sp. tritici). Recently, reports of stem rust were published in Israel and Lebanon in 2010 and first report of Ug99 was reported in Egypt in 2014. The objectives of our research are to: (i) survey wheat growing areas for WSR in Jordan during the years 2017-2020, (ii) identification of WSR races isolated from Jordan morphologically and molecularly, (iii) analyze rust populations in terms of their response to known differential sets, pathotype distribution and diversity, (iv) screening the response of Jordanian wheat germplasm to the identified WSR strains, and (vi) study the population diversity of WSR races using RT-PCR and SNP genotyping. In 2017 a total of 270 fields of wheat and barley in the wheat and barley growing areas in Jordan were surveyed from March-May. The survey covered northern, middle, and southern parts of Jordan (arid and semi-arid regions). Altitude, longitude, and latitude data was recorded. Only few WSR pustules (n=4) were collected because the environmental conditions were not suitable for the disease to develop. On the other hand, wheat stripe rust was very common in the wheat growing areas mainly at the southern parts of the country. Other fungal plant pathogens were also reported including smuts, spots, blotches, powdery mildew, crown rot, fusarium head blight, and flag smut.

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Genetic analysis for yield and its components in Afghan bread wheat

BGRI 2018 Poster Abstract
Mohammad Bahman Sadeqi Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-University of Bonn
Mohammad Wali,Salari, Kobra, Yusefi, Mohammad, Yusefi, Gul Mohammad, Ajir, Wakil Ahmad, Sarhadi, Jens, L?on, , , , , , , , , , , , , , , , , ,

Bread wheat is a staple food in Afghanistan. Breeding for improving yield and its components in Afghan bread wheat without using new molecular methods such as marker-assisted selection (MAS) and quantitative trait loci (QTL) mapping approaches is difficult. Therefore study of genetic analysis by focus on yield and its components as first steps is necessary. Genetic analyses were performed on a winter wheat core collection of 20 accessions and commercial varieties sampled from different regions of Afghanistan and twenty agronomic traits were evaluated over three years under fully irrigated, rain-fed and drought treatments. Grain yield was the most important trait to water deficit and was highly correlated with other agronomic traits. The germplasm was structured into two sub-populations. Field plots of the genotypes were treated to one of three treatments including full irrigation, rain supplied and rain-sheltered. A randomized complete block design with three replicate was used every year of the trial. For every agronomic trait, variance components, heritability (h2) and genetic correlations was calculated. Results of the study showed that these genotypes may be good source for national breeding programs. The multiple statistical in this study showed that results of genetics correlation and regression analysis are same. Further analysis of these traits with additional experimental data to attain persuasive conclusion is suggested.

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Mapping and validation of stripe rust resistance loci from wheat cultivar Centrum with SNP markers

BGRI 2018 Poster Abstract
Jingmei Mu State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, P. R. China
Qilin,Wang, Jianhui, Wu, Qingdong, Zeng, Lili, Huang, Dejun, Han, Zhensheng, Kang, , , , , , , , , , , , , , , , , ,

The combination of several additive, partial resistance genes has been proposed as a preferred strategy to breed wheat cultivars with acceptable levels of durable resistance. The German winter wheat cv. Centrum has displayed high levels of adult plant stripe rust resistance (APR) in field environments for many years. One hundred and fifty one F2:7 RILs were developed from a cross between susceptible landrace Mingxian169 and Centrum to determine the inheritance of the APR resistance. The RILs and parents were evaluated for maximum disease severity (MDS) in the field during the 2015-2016 and 2016-2017 cropping seasons. Affymetrix 35K single nucleotide polymorphism (SNP) arrays were used to genotype the RILs and parents. In addition, the 660K SNP array was used to genotype bulked extreme pools and parents for saturation mapping. Four stable QTL were detected in all tested environments using inclusive composite interval mapping (ICIM); namely QYrCEN.nwafu-4AL, QYrCEN.nwafu-4BS, QYrCEN.nwafu-7BL, and QYrCEN.nwafu-7DS. QYrCEN.nwafu-4BS and QYrCEN.nwafu-7DS were contributed by MX169, QYrCEN.nwafu-4AL and QYr-CEN.nwafu-7BL were contributed by Centrum. QYrCEN.nwafu-7BL and QYrCEN.nwafu-4AL appear to represent new APR loci based on map comparisons. QYrCEN.nwafu-4BS contributed by MX169 also seems to represent a new locus. QYrCEN.nwafu-7DS is likely Yr18. Although MX169 was fully susceptible in our nurseries it is positive for the widely used marker csLV34. Reference lines carrying Yr18 are moderately resistant. Our hypothesis is that MX169 probably carries the inhibitor reported in Chinese landrace varieties by Wu et al. (2015, Plant Breeding 134: 634-640). SNP markers within these QTL were converted to KASP markers and validated in a subset of 120 diverse lines. These KASP markers should be useful for marker-assisted selection to improve stripe rust resistance in breeding programs.

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Characterization of wheat germplasm for leaf rust resistance using molecular markers and multi-location field testing

BGRI 2018 Poster Abstract
Muhammad Ismail The University of Agriculture, Peshawar, Pakistan
Muhammad Khan, Aamir Iqbal, Sher Nawab, Sohail Ahmed, Muhammad Imtiaz, Sajid Ali

Resistance breeding for wheat leaf rust requires testing of breeding materials under field conditions, which must be complemented with diagnostic molecular makers. A set of 28 exotic wheat lines from advanced CIMMYT material along with three check varieties (Siran, Atta-Habib, Ghanimat-e-IBGE) were tested at three contrasting locations (Peshawar, Mansehra and Lakki-Marwat) and were genotyped with markers linked to three Lr genes (LrPr, Lr37, and Lr34). The overall leaf rust pressure was low during the wheat season of 2015-16, with the maximum disease observed at Lakki-Marwat (up to 70%), followed by Peshawar (up to 50%) and the minimum disease at Mansehra (up to 30%). Despite the overall low leaf rust pressure, the germplasm behaved variably in terms of leaf rust resistance as revealed through average co-efficient of infection (ACI). According to ACI value, 16 out of 28 genotypes were completely resistant, while few genotypes showed partial resistance. The maximum CI value was recorded for wheat line W-SA-87, which was 55 at Lakki Marwat, 33 at Peshawar and 15 at Mansehra, while 18 lines had CI value of zero across the three locations. Variability existed in yield parameters with W-SA-84, W-SA-78 and W-SA-79 producing the better grain yield. Genotyping with Lr linked markers viz., STS-7 (LrPr), SC-Y15 (linked with Lr37) and csLV34 (linked with Lr34) revealed that among the tested lines LrPr was the most frequent (83.8%), present in 26 lines; followed by Lr37 (77.4%), present in 24 lines, while Lr34 was present in 16 lines (71.1%). All three genes were detected in 45% of the germplasm. Cluster analysis grouped the germplasm in four clusters based on both phenotypic and molecular markers data. The information generated in the present study would be valuable in resistance breeding for a better control of leaf rust disease in Pakistan.

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A new warrior race of Puccinia striiformis f.sp tritici in Syria

BGRI 2018 Poster Abstract
Mohammad Kassem Aleppo University, Aleppo , Syria
Bassam,Souliman, Naem, Al-Housien, Mohammad Shafick, Hakiem, Miloudi.M, Nachit, , , , , , , , , , , , , , , , , , , , , ,

Wheat yellow rust, caused by Puccinia triticina f. sp. tritici, is the major problem in wheat production in most parts of West Asia. Monitoring of the pathogen virulence factors and their changes provides basic information for the development of an early warning system. Wheat yellow rust has become increasingly important in the Syrian central and coastal areas during the last three years, The objective of this study was to identify races of the pathogen. Yellow rust samples collected at sites in the central and the coastal plains, were analyzed on differential host genotypes with known seedling resistance genes. According to the results of race determination, races 230E150, 166E150, 230E142 and 462E128 were identified. The race 462E128 designated the Warrior race, was identified at several sites across the Syrian central plains at the end of the 2017 growing season (early and Mid-May) when yellow rust exploded suddenly on a number of varieties, despite their previous high resistance ratings. The infections rapidly reached significant levels, in spite of the high temperature (up to 33?C) and the absence of rainfall or irrigation. This new virulent race (462E128) has been able to attack wheat lines with several major resistance gene(s) including: Spaldings Prolific (SP), Yr 3+4, Triticum spelta (Yr5), which remained effective until 2016 in Syria, Virulence to lthe resistance genes Yr1, Yr2, Yr2+, Yr3V, Yr3ND, Yr4+, Yr6, Yr6+, Yr7, Yr7+, Yr9, Yr9+, Yr11, Yr12, Yr18, Yr24, Yr26 Spaldings Prolific (YrSP), Anza (YrA+) Spaldings Prolific (SP), Yr 3+4, Triticum spelta (Yr5) and Selkirk (YrSK) was also found. Virulence to Carstens V (CV), Yr 15/6* Avocet S and Yr 5/6* Avocet S; was not found. According to our findings, the Warrior race has increased in frequency within the mix of yellow rust races in these areas in Syria . It is expected that the Warrior yellow rust race will cause damage on resistant wheat cultivars in 2018.

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GWAS of field and seedling response to individual Pgt races reveals combinations of race-specific genes in spring wheat

BGRI 2018 Poster Abstract
Erena Edae University of Minnesota
Michael Pumphrey, Matthew Rouse

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis was conducted on 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for three years (2013, 2015 and 2016) at Rosemount, Minnesota. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. Markers presumably linked to Sr6 and Sr7a were associated with both seedling and field resistance to specific races. A field resistance QTL on chromosome arm 2DS was detected for response to races RCRSC and TPMKC. A QTL specific to field resistance was detected for QFCSC and TPMKC on 2BL. The markers that showed strong association signals may be useful to pyramid and track race-specific stem rust resistance genes in wheat breeding programs. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found that combinations of genes conferring resistance to specific P. graminis f. sp. tritici races accounts for the prevalent stem rust resistance in North American spring wheat.

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Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

BGRI 2018 Poster Abstract
Mengxing Wang State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
Hui,Liu, Guangwei, Xing, Xiaojun, Nie, Song, Weining, , , , , , , , , , , , , , , , , , , , , ,

RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 50-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations.

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Wheat rusts status and population structure across Pakistan during wheat growing seasons 2015-16 and 2016-17

BGRI 2018 Poster Abstract
Sajid Ali The University of Agriculture, Peshawar, Pakistan
Muhammad,Khan, Safi, Kathi, Zahoor, Swati, Manzoor, Hussain, Annemarie, Justesen, Muhamamd, Imtiaz, , , , , , , , , , , , , , , , , ,

Considering the importance of wheat rust diseases in Pakistan and the recent identification of yellow rust pathogen (Puccinia striiformis f. sp. tritici) centre of diversity in Pakistan, the present study was designed to assess the status of three wheat rusts across the country during 2015-16 and 2016-17 and analyze the population structure of P. striiformis f. sp. tritici . A total of 451 fields (from 68 districts) were surveyed during 2016 and 480 fields (from 69 districts) during 2017. A high yellow rust pressure was present during 2016 throughout Pakistan, while it was predominant only in the Northern half during 2017. Leaf rust was present in the central part of the country, while stem rust was only found in the south. In Sindh province (located in the south), yellow rust was reported unexpectedly with high severity (>60%) on varieties like Kiran and Galaxy during both the years. A set of 513 samples of P. striiformis were genotyped with microsatellite markers to assess the population diversity and spatial structure. and infer on the cause of epidemics in the Sindh province. Population genetics analyses confirmed a recombinant population structure across all locations except the Sindh province, where relatively lower diversity and lack of recombination signature was revealed. At least five genetic groups were identified in the overall population, which were found across all locations, except Sindh province where one of the genetic groups was predominant. The P. striiformis population from Sindh province with low diversity that caused unexpected epidemics in a relatively warmer region needs to be further investigated for specific adaptation traits. Our results confirmed the high diversity across Pakistan, which lies in the Himalayan centre of diversity of the pathogen. This high diversity was present in locations without the presence of alternate host (Berberis spp.) and could potentially be associated with regular migrants from the Berberis zone into the whole country.

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