Sathguru Management Consultants
Kanan Vijayaraghavan, Venugopal Chintada, Rituparna Majumder, Richa Kapur, K. Aishwariya Varadan
South Asia has the highest "wheat dependent" low income community in the world. Stem rust and blast are recognized as the most damaging disease of wheat in the region producing 19% of the world's wheat. In order to combat the potential threat the national research centers were geared up to track the real time movement of wheat diseases, generate disease incidence data and create an enabling environment to boost wheat research in the region through streamlined efforts and enhanced SAARC tool box deployed six years ago.
Recent data (2016-17) from the tool box has shown a significant increase in the data records captured in this region compared to previous years. This has been possible because of heightened awareness amongst the scientists and with the continuous capacity building through pre-season and in-season surveillance trainings organized by Sathguru in collaboration with National Wheat Research Institutes at various levels.
The model is helping partner institutes to be self-sufficient for generating, maintaining wheat disease surveillance data in national and global databases and exchanging real time information with stakeholders. The application have been widely deployed and competently being used by 95% of rust surveillance teams in the wheat fields of SAARC region.
The study will focus on how national research center's judicious decision of carrying out diligent surveillance during the season contributed to safeguarding wheat crops in their respective nations through increased vigilance on emergence of new races and targeted introduction of regionally resistant varieties. Further using this data scientist's can aim to strategize their wheat research for identification of resistant varieties and eventually resulting in increased productivity addressing food security of the region.
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.
Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, Israel
Dina Raats, Lin Huang, Valeria Bocharova, Jorge Dubcovsky, Abraham Korol, Tzion Fahima
Wild emmer wheat (Triticum dicoccoides, (DIC)) is an important source of resistance to stripe rust due to presence of Puccinia striiformis in its natural habitats with high humidity and relatively low temperatures that are favorable for stripe rust development. Previously, we showed that DIC accessions from northern Israel were highly resistant to stripe rust. According to the rust responses of three DIC accessions (G25, H52, G303) and mapping of the resistance to relatively close, but different, genetic positions on chromosome 1BS, three different resistance genes were assumed to be present. However, the development of additional critical recombinants and new higher resolution genetic maps for these three genes in subsequent work led us to place YrH52 and YrG303 in the same genetic interval as Yr15, suggesting that the three putative genes are allelic or identical. The recent cloning of Yr15 allowed us to test this hypothesis using an EMS mutagenesis approach. We sequenced the Yr15 locus in five yrH52 and three yrG303 susceptible mutants and identified missense point mutations associated with the susceptible phenotype in each one. Thus, YrH52 and YrG303 may not be new genes. Further work is under way to determine if these genes are allelic or identical.
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).
Agriculture & Agri-Food Canada
Wheat cultivar McNair 701 carries resistance gene SrMcN and is used as a differential line to identify Pgt races using the international letter code nomenclature. The inheritance and location of the resistance gene has not been characterized. We developed a doubled haploid (DH) population from cross LMPG/McNair 701 to study the genetics and chromosomal location of SrMcN. A DH population inoculated with race QCCJB segregated 100 resistant : 94 susceptible, a 1:1 ratio (?2=0.186, P=0.666, NS) indicative of segregation at a single locus. This gene was mapped to chromosome 2DL using the Infinium 90k platform. The map position of SrMcN was similar to that of Sr54, one of two genes previously found in Norin 40. Comparison of stem rust seedling reactions using 12 diverse Pgt races indicated that McNair 701 and an Sr54 line derived from Norin 40 had an identical pattern of responses and similar low infection types (IT=12-) to races LCBNB and QCCJB. Based on the chromosomal location on 2DL and identical seedling responses to Sr54, it is likely that the resistance gene in McNair 701 formerly known as SrMcN is Sr54. This finding will be confirmed by a test of allelism.
National Institute of Agricultural Research
Nsarellah Nasserlhaq, Wuletaw Tadesse, Ahmed Birouk
In the context of climate change, drought is one of the most important and complex abiotic stresses affecting crop production worldwide. The adoption of an appropriate technological package, principally drought tolerant varieties, may overcome these challenges to meet global food security needs for the rapidly growing human population, particularly in developing countries. Therefore, this research was carried out to identify efficient phenotypic and genetic selection criteria to identify drought tolerant wheat varieties. In this perspective, 200 diverse elite bread wheat lines from ICARDA and CIMMYT were evaluated under four Moroccan environments during the 2015 and 2016 seasons for yield and 15 agro-physiological traits. The same set of genotypes was genotyped using 15k SNPs. Significant environment and genotype environment interaction effects were observed for yield. Average yield reached 3.18t/ha and ranged from 2.45 to 4.27t/ha. The secondary traits were mostly dominated by the environment effect (p<0.001). Based on correlation and regression analysis between grain yield and phenotypic data, the biomass, grain number per m<sup>2</sup> and to a lesser extent fertile spikes number and thousand kernel weights (depending of drought scenarios) can be more reliable traits than yield for the identification of drought tolerant genotypes. Moreover, the ground cover and canopy temperature depression can be used as supplementary criteria for more accurate selection. Slow selection on the basis of phenotypic traits may be accelerated and improved by using molecular markers. The genetic analysis highlighted significant SNPs and identified new QTLs linked to yield and the most efficient phenotypic traits under drought conditions. These findings could be useful for breeding drought-resistant wheat cultivars using marker-assisted selection to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield.
University of Queensland, St. Lucia
Adnan Riaz, Jonathan Powell, Timothy Fitzgerald, Kemal Kazan, Neena Mitter, Evans Lagudah, Lee T. Hickey
The Lr34/Yr18/Sr57/Pm38/Ltn1 multi-resistance locus has been deployed and remained effective in wheat cultivars for more than 100 years. The durability and pleiotropic nature makes Lr34 a unique and highly valuable resource for rust resistance breeding. Despite its functional annotation as an ABC transporter, the mode of action is unknown. Considering this, we aimed to decipher molecular factors and signaling components essential for Lr34 function using RNA-seq of Chara resistant (Lr34) and Chara mutant (heavy ion irradiation, HII) susceptible wheat lines. Screening of Chara and Chara HII lines with Lr34-specific markers confirmed the integrity of Lr34 in both lines; however, phenotyping confirmed rust and powdery mildew susceptibility in the Chara HII lines. Plants were grown under controlled conditions and infected with Puccinia triticina pathotype 76-1,3,5,7,9,10,12,13+Lr37 at the flag leaf stage. Flag leaves were sampled at 0, 24, 48, 72, 96 and 168 hours post inoculation (hpi) from mock and infected plants. Based on real-time PCR analysis of basal defense genes and the Lr34 gene, we selected 72 hpi for RNA-seq with four biological replicates per condition. The samples were sequenced on an Illumina Hiseq 4000 at the Beijing Genomics Institute, China. A total of 9.0 Gb of sequence (2.25 Gb/library) from 16 libraries for four conditions was obtained. Differential expression analysis was performed using the Tuxedo analysis pipeline with standard parameters. Analysis revealed deletion of DNA fragments with collinear gene order on chromosomes 1A, 2D, 5A, 5B, 5D and 7D of Chara HII mutants. To determine the significance of the deletions we performed bulk segregant analyses on segregating F2 populations of Chara ? Chara HII crosses. Analyses revealed key genomic regions associated with Lr34-functional resistance and we are in the process of validating candidate genes using qPCR.
The University of Sydney
Davinder Singh, Peter Dracatos
Following the introduction of wheat stripe rust into Australia in 1979, an uncharacterized resistance (YrA) was identified in both Australian and International spring wheats. Genetic analyses of YrA indicated it was a pair of complementary genes, which were mapped to chromosomes 3DL and 5BL and designated Yr73 and Yr74, respectively. While selection Avocet 'R' carries both genes, selection Avocet 'S' carries Yr73 only. P. triticina pathotype (pt.) 104-1,2,3,(6),(7),11 +Lr37 ("104-VPM"), first detected in Australia in 2002, most likely arose via mutation from pt. 104-1,2,3,(6),(7),11 ("104"), with added virulence for Lr37. Interestingly, while both pathotypes are avirulent on Lr13, 104-VPM shows a much lower Infection Type (IT, ";1") than pt. 104 ("X++3") on several genotypes carrying Lr13 (e.g.Avocet 'R', Avocet 'S'). Other Lr13 genotypes (e.g. cv. Hereward) respond similarly to both pts ("X++3"). Genetic analyses of 4 doubled haploid (DH) populations based on intercrosses between Avocet 'R' and genotypes lacking Lr13 segregated in a 1:7 ratio to pt. 104-VPM (";1" : all other ITs). Two populations fixed for Lr13 (viz. Hereward/ Avocet 'R' and Estica/Avocet 'R') segregated 1:3 to pt. 104-VPM (";1" : all other ITs). This segregation pattern fitted a model where two complementary genes interact with Lr13 to generate the low (IT ";1") IT. Mapping of a Teal/Avocet 'R' DH population using 92 lines and 9,035 DArT-Seq markers identified three QTLs: chromosome 2BS (Lr13); chromosome 3DL (co-located with Yr73); chromosome 1DS. These results suggest that Yr73 acts in a complementary manner with a gene on chromosome 1DS to confer leaf rust resistance (IT "X"), and that these complementary genes are additive with Lr13. It appears that Yr73 is a modifier of two independent genes in wheat, one conferring resistance to stripe rust (Yr74 on chromosome 5BL), and one conferring resistance to leaf rust (LrAv on chromosome 1DS).
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.
Institute of Plant Biology and Biotechnology
Makpal Atishova, Aygul Madenova, Kanat Galymbek, Jenis Keyshilov, Hafiz Muminjanov, Alexey Morgounov
Wheat rust diseases are a major cause of yield losses of this crop. Yellow (Puccinia striiformis f. sp. tritici) rust is of the most widespread and dangerous disease of wheat and is the major factor that adversely affects wheat yield and quality. The use of genetic host resistance is the most effective, economical and environmentally safe method of controlling stripe rust that allows elimination of fungicides and minimize crop losses from this disease. Due to the threat of the development of epiphytoties of rust disease it is necessary to identify new donors of resistance to yellow rust and to develop resistant wheat breeding material. In the present study, attention was drawn to the effective yellow rust resistance genes Yr5, Yr10 and Yr15, which were identified in the process of molecular screening of wheat germplasm. Genetic analysis using S23M41 molecular marker linked to Yr5 revealed the presence of this gene in 17 out of 136 promising lines. Thirteen genotypes screened with Xbarc8 generated the DNA fragment associated with Yr15. Three advanced lines with Yr10 were identified using the SCAR marker. Three lines carrying two Yr genes (Yr5 and Yr15) were detected. Combination of Yr5 and Yr10 were found in 15 wheat lines. We identified a number of wheat genotypes highly resistant to stripe rust, which could be further evaluated to release new resistant varieties or to be used in the breeding program.