University of the Free State, South Africa
Nelzo Ereful, Botma Visser, Lesley Boyd, Zakkie Pretorius
Adult plant resistance (APR) to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is often conferred by multiple minor genes and has the potential to be durable. A preceding project identified two Kenyan wheat lines (W1406 and W6979) from the Genome Resource Unit (Norwich, UK) that exhibit APR to Pgt. The aim of this study was to investigate the APR response to Pgt race PTKST in W1406 and W6979 compared to 37-07, a susceptible control line. Histological investigation of inoculated flag leaf sheaths indicated a significant and quantifiable decrease in Pgt colony size in the APR lines at 120 hours post inoculation (hpi). Molecular analysis supported the observed fungal biomass decrease in the APR lines at 120 hpi. RNAseq analysis identified 169 transcripts differentially expressed in W1406 and 166 transcripts in W6979 when comparing 24 and 72 hpi to 0 hpi. In W1406 transcripts encoding putative pectinesterases, lipid-transfer proteins and leucine-rich repeat-like proteins were induced at 72 hpi. In W6979 only a corresponding putative pectinesterase encoding transcript was identified. Although the induced defence response in the two APR lines exhibited some dissimilarity, it potentially involves cell wall modification in both lines. Two independent sets of peroxidases were induced at 24 and 72 hpi in both lines, suggesting independent signalling events. Expression analysis suggests the occurrence of two phases of gene expression, one at 24 hpi and another at 72 hpi; the latter seeming to correspond to the inhibition of Pgt growth, manifesting as the observed APR phenotype.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
Yuan Tian, Yan Meng, Hengbo Ma, Lili Huang, Zhensheng Kang
Stripe rust, caused by Puccinia striiformis Westend f.sp. tritici, is currently one of the most prevalent and damaging disease on wheat. Up to now, some genes in wheat which are resistant to wheat stripe rust have been cloned, but little is known about the corresponding avirulence gene according to the gene-for-gene hypothesis. A population containing 118 progeny isolates population acquired by selfing an isolate, PL17-7, with virulence to Yr26 was derived. Seventy-two progeny isolates were different in genotype depending on 92 simple sequence repeat (SSR) markers. The progeny population segregated for avirulence to Yr6 at one locus (3 avirulent :1 virulent ratio). The parental isolate and 72 of 118 progeny isolates were resequenced to find candidate avirulence genes corresponding to Yr6. Overall, 7.6 million reads per sample were obtained and mapped to the draft genome of a Chinese Pst isolate CY32. The median depth of coverage was 63.6 fold. For each isolate, between 97.6% and 98.1% of the sequence reads were mapped to the race CY32 genome, which covered between 87.3% and 95.4% of the reference genome bases. An average of 97357 single nucleotide polymorphisms (SNP) per isolate was found, which covered 8.1% of the reference genome. Different SNPs and Indels were found when isolates virulent and avirulent to wheat cultivar containing Yr6 were grouped into two groups. Though screening discrepant SNP and indel in these two groups, candidate avirulence genes corresponding to Yr6 may be found.
CSIRO Agriculture and Food, Australia
Timothy Hewitt, Peng Zhang, Zacharias A. Pretorius, Narayana Upadhyaya, Rohit Mago, Sambasivam Periyannan, Xiuying Kong, Burkhard Steuernagel, Brande H. Wulff, Evans S. Lagudah
Multiple rust resistance gene combinations are considered as a practical solution for providing durable rust resistance and preventing resistance breakdown arising from single gene deployment. The stem rust resistance locus Sr26, originally derived from Thinopyrum ponticum and introgressed into wheat as a chromosome translocation, is one of the very few genes conferring durable resistance for almost 40 years to all known races of stem rust, including the highly virulent stem rust race Ug99 (TTKSK) and its derivatives (Dundas et al. 2015). To understand the underlying mechanisms of its unusual long-term effectiveness and to explore allelic diversity in different Th. ponticum accessions for other functional alleles that may offer new sources of resistance, we used comparative genomics and gene capture techniques (Resistance gene enrichment sequencing, RenSeq) as complementary strategies for isolating the target gene (Steuernage et al. 2016). Sr26 region was first mapped using NB-LRR (Nucleotide-binding site and leucine-rich repeat) sequences from the orthologous gene members located on the long arm of chromosome 6D from Aegilops tauschii (the D-genome donor of wheat) reference genome. Subsequently, we revealed a cluster of NB-LRR sequences located at the distal end of the Th. ponticum introgression segment that were absent in the smallest interstitial Sr26 deletion mutant. Therefore, we substantially narrowed down the genetic interval for Sr26. In addition to this approach, we subjected the mutant population to RenSeq pipeline. A candidate gene of Sr26 has been successfully identified to be a NBS-LRR type resistance gene. Validation of the gene candidate by complementation studies is currently in progress. In order to enhance durable resistance, genetic stocks of Sr26 from different backgrounds as well as a panel of Sr26-APR (Adult Plant Resistance) gene combinations have been generated to further investigate the resistance response of Sr26 in combination with different multi-pathogen APR genes.
Institut National de la Recherche Agronomique INRA Morocco
Kumarse Nazari, David Hodson, Tine Thach, Julian Rodriguez Algaba, Mogens Støvring Hovmøller
Wheat rusts, notably yellow rust, are amongst the most damaging diseases on wheat in Morocco. The objective of this survey was to assess the incidence and severity of wheat rust diseases across Morocco. The survey was carried out during April-May 2017 where growth stage of wheat ranged from anthesis to physiological maturity. The severity and response rating for the adult plant field reaction to rusts were based on the modified Cobb scale. A total of 117 bread wheat fields were inspected. The survey revealed that the most prevalent disease was yellow rust (96 out of 117 fields). Leaf rust, SLD (Septoria Like Diseases) and to some extent root rot complex were less prevalent. Leaf rust was only observed in 8 out of 117 inspected fields and exhibited low severity. Stem rust was observed in only one field. Following the drought of 2016, the 2017 growing season was an epidemic year for yellow rust in Morocco. It was detected across all regions and 50% of inspected fields were highly infected. Those that were lightly or not infected were sprayed with fungicides up to two times. Almost all commercial bread wheat cultivars in Morocco are highly susceptible to yellow rust. Appearance of new virulent races is leading to the breakdown of resistance in major cultivars e.g., Arrihan, which had very few pustules of yellow rust in 2013 was highly susceptible in the last three years. Samples of yellow rust from 2016 revealed a new virulent race in all samples, temporarily designated Pst (new) [virulence pattern: [Yr-,2,3,-,-,6,7,8,9,-,-,17,-,25,-,32,Sp,AvS,-]. Thirty-four samples submitted to GRRC in 2017 were all of the same genotype, identical to the new race already detected in 2016. The results demonstrate that surveillance and genotyping/race phenotyping of samples may be important for early-warning and anticipatory breeding strategies.
Omsk State Agricultural University, Omsk, Russia
Elena Salina, Yuriy Zelenskiy, Alma Kokhmetova, Mehran Patpour, Mogens Hovmøller, Pablo Olivera, Les Szabo, Yue Jin, Marcel Meyer, Chris Gilligan, Matthew Hort, Dave Hodson, Alexey Morgunov
Short season, high latitude spring wheat is grown on 7 million ha in Western Siberia and 10 million ha in Northern Kazakhstan. Despite relatively low wheat yields (1.5 t/ha), the region is extremely important for regional and global food security. Leaf rust dominates, occurring three years out of five, especially in favorable years with higher rainfall. Since 2010, stem rust has been observed at an increasing number of sites. The first large-scale stem rust outbreak occurred in 2015 and affected about 0.5-1 million ha in Omsk, Western Siberia. In 2016, 2 million ha were affected in the Omsk and Altay regions, while 1 million ha in the Kostanay and Northern Kazakhstan regions were affected in 2017. Estimated yield losses reached 25-35% each year. Factors associated with the outbreaks included: higher rainfall in late June and July; cultivation of susceptible varieties; and an increased area planted to winter wheat, which serves as a source of inoculum. Sampling and race analysis revealed a diverse pathogen population, indicative of a sexual recombination. A total of 51 races were identified from 31 samples taken in 2015 and 2016. All races were avirulent on Sr31. The majority of varieties released and cultivated in the region are susceptible to stem rust and require replacing. A recent study of 150 local resistant varieties and breeding lines indicated that the genetic basis of resistance was limited to Sr25, Sr31, Sr36, Sr6Ai, Sr6Ai#2, and additional unknown major genes. Adult-plant resistance to stem rust was observed in less than 20% of the germplasm. The potential impact of these large stem rust outbreaks on other wheat growing regions is being investigated by analyzing spore wind dispersal patterns. Further research is required to understand and mitigate the sudden appearance of stem rust as a disease of economic importance.
Study at Omsk State Agrarian University was supported by the Russian Science Foundation (project No. 16-16-10005).
Emel Ozer, Mehmet Karaman, Mozaffar Roustaii, Jalal Kamali
Erratic weather patterns associated with climate change pose unique challenges for wheat breeders playing a key part in the fight to ensure global food security. Within the rainfed winter wheat areas of Turkey and Iran this erratic weather patterns may prevent attaining maximum potential increases in winter wheat genetic gains. This is primarily related with the fact that the ranking of tested varieties may greatly change from one year to the other. Erratic weather patterns may interfere with breeders decision on the ideotype(s) they should aim for during selection. To support breeding decisions, this study aimed at optimizing major traits through modelling different combinations of environments and defining probabilities of the range of variation of traits (phenology and pant height) that maximized grain yields. Optimal phenology was found to be highly related with the temperatures at which the winter wheat varieties were exposed at around heading time (20 days before and after heading). Specifically later winter wheat varieties were exposed to higher temperature both before and after heading and this exposure had a negative effect on grain filling duration and final grain yield. Finally, the use of at least five different wheat varieties in one production field (with different phenology and plant height) was compared to a field with monoculture to test for improved resilience. It was concluded that by selecting one best wheat variety in a wide range of environments it was possible to maximize grain yield and that using a set of diverse varieties was not beneficial.
Northwest A&F University
Xiaoguo Zhu, Zhensheng Kang
RNA interference (RNAi) is a powerful genetic tool to accelerate research in plant biotechnology and to control biotic stresses by manipulating target gene expression. However, the potential of RNAi in wheat to efficiently and durably control the devastating stripe rust fungus Puccinia striiformis f. sp. tritici (Pst), remained largely under explored, so far. To address this issue, we generated transgenic wheat lines expressing double-stranded RNA targeting PsFUZ7 transcripts of Pst. We analyzed expression of PsFUZ7 and related genes, and resistance traits of these transgenic wheat lines. We show that PsFUZ7 is an important pathogenicity factor that regulates infection and development of Pst. A PsFUZ7 RNAi construct stably expressed in two independent transgenic lines of wheat confers strong resistance to Pst. Pst hyphal development is strongly restricted, and necrosis of cells in plant resistance responses was induced significantly. We conclude that trafficking of RNA molecules from wheat plants to Pst may lead to a complex molecular dialogue between wheat and the rust pathogen. Moreover, we confirm the RNAi-based crop protection approaches can be used as a novel control strategy against rust pathogens in wheat.
Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Egypt.
Wasif Youssif, Mohamed Hasan
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, [Pst] is a widespread and damaging disease of wheat (Triticum aestivum L.), causing significant losses in yield and quality. During the 2015, eight stripe rust physiological races were identified in greenhouse tests i.e. 0E0, 6E4, 70E20, 128E28, 134E244, 143E245, 250E174, and 450E214. Race 0E0 was the most common and avirulent race, and races 143E245, and 450E214 had high virulence on most of tested Yr resistance gene wheat lines. In the same season, an unusual stripe rust infection occurred in spring wheat at Sakha region in Egypt. Some of the most important commercial cultivars such as (Misr 2, Giza 168 and Sakha 61), known as resistant to the previously characterized races of Pst in Egypt have become susceptible under field conditions. Infections of stripe rust was observed on some wheat lines with Yr genes previously known to be resistant, such as Yr1, Yr17 and Yr32, in a yellow-rust trap nursery at Sakha (30.601400? N, 31.510383? E), northern Egypt. Independent race analysis of collected samples from four governorates i.e. Kafrelsheikh, Al-Sharqia, Dakahleia and Damietta at Sakha Agricultural Research Station in Kafrelsheikh confirmed the detection of a new Pst race in Egypt. Aggressive races with virulence to Yr27 were detected on differentials with Yr27 (Yr27/6*Avocet S), and (Ciano 97) during the 2012 in Egypt. In addition, the Warrior race (virulent on: Yr1, Yr2, Yr3, Yr4, Yr6, Yr7, Yr9, Yr17, Yr25, Yr32, and YrSp) was observed in the 2015 crop season, which indicated continued changes in the Pst the population. In Europe, the Warrior race first identified in 2011 in the United Kingdom, has caused significant change in yellow rust susceptibility of several varieties of both wheat and triticale. In a conclusion, some of wheat cultivars, known to be resistant, were shifted to susceptible due to these new races.
CREA Research Centre for Genomics and Bioinformatics
,International Durum Wheat Genome Sequencing Consortium
The domestication of wild emmer wheat ~10,000 years ago by early agrarian societies have led to the selection of domesticated emmer and subsequently of durum wheat through a process of selection for non-brittle rachis and free-threshing forms. Durum wheat and became established as a prominent crop only ~1,500-2,000 years ago. We have completed the 10.45 Gb assembly of the 14 chromosomes of the modern DW cultivar 'Svevo' and provides, via comparison with the wild emmer assembly, an account of the genome-wide modifications imposed by 10,000 years of selection and breeding on the genome architecture of tetraploid wheat. A number of regions that were under selection during the domestication of wild emmer or the subsequent selection of durum wheat have been identified. Furthermore, we have projected on the durum wheat genome about 1,500 QTLs for morphological phenological and quality traits, grain yield components and disease resistance reported from published biparental mapping or GWAS. NBS-LRR genes are prominently involved in signaling and plant disease resistance. The durum wheat genome contains more than 66,000 genes and among them we annotated about 1,500 complete NBS-LRR genes. A similar number was found in the wild emmer genomes, nevertheless the comparison of the two genomes has identified some NBS-LRR genes specific for durum wheat. The availability of the complete genome of durum wheat will speed up the identification and the isolation of new resistance genes as well as the breeding for high-yielding and more resilient cultivars.
National Research Council of Canada (NRC)-Saskatoon
Kerry Boyle, Tammy Francis, Peng Gao, Brittany Polley, Christine Sidebottom, Brent McCallum, Harpinder Randhawa, Tom Fetch, Randy Kutcher, Sylvie Cloutier, Pierre R. Fobert
Most rust resistant genes in wheat are race-specific (R), with relatively few genes conferring resistance only at the adult stage that have been described as slow rusting genes (APR). Pyramiding multiple R, APR or APR+R genes has been used successfully over many years to achieve durable rust resistance. To further enhance this strategy, a genetic genomics approach was exploited to identify genes with different resistant mechanisms and the most effective gene pyramids.
Several new combinations of rust genes were created and tested in the Thatcher background, revealing synergistic ("booster") effects involving Lr21 with Lr16. With QTL mapping approach, we found that genes combined from 7D, 1B and 7B conferred an almost immune response to leaf rust, while genes from 7D, 1B and 3B provided an almost immune response to stripe rust. With a genomics approach, a large scale transcriptome analysis was conducted on key rust resistant genes including six R genes, three APR genes and one gene pyramid with Lr34+Lr16 over a time series during the infection process of both seedlings and adult plants. Detailed transcriptome analysis of gene expression associated with different major and minor leaf rust genes, alone or in combination, identified common and unique aspects of defense responses. For example, Lr9 is different from the other three leaf rust genes tested, with resistance triggered at a very early stage, consistent with pre-haustorial resistance. R genes Lr21 and Lr16 were also significantly different compared to other R and APR genes. With gene co-expression network analysis, a shared unique gene module mediated by Lr34 and Lr67 was also identified. This large transcriptome dataset also allowed the development of a rust-wheat interactome atlas for rust functional genomics research in wheat.