Ebrahiem Babiker, Tyler Gordon, Sam Stoxen, Matthew Rouse, Yue Jin, Shiaoman Chao, John Bonman
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a threat to wheat production worldwide. To manage this important disease, new sources of genetic resistance are needed and common wheat landraces are a potential source of such resistance. Landrace accessions from the USDA-ARS National Small Grains Collection were evaluated for seedling resistance to the Ug99 race group. To identify accessions most likely to carry novel resistance genes, a bulked segregant analysis (BSA) approach was used. Seven resistant accessions were crossed to a susceptible parent line and F3 families were tested against Pgt race TTKSK. The resistant plants were identified and grouped into two bulks per population. The bulks, along with the parents and F1 progeny, were genotyped with the 90K wheat iSelect SNP genotyping platform. Four of the populations appeared to segregate in a 1:1 phenotypic resistant/susceptible ratio, one in a 1:2 ratio, and two in 1:3 ratios. However, chi squared tests indicated the ratios were statistically the best fit for only two of the 1:1 segregating populations and one of the 1:3 segregating populations. Initial BSA results indicate the markers associated with reduced stem rust infection are located on wheat chromosomes 1DL and 2B. These mapping populations are being advanced for further evaluation to ascertain if novel resistance to the Ug99 stem rust race group is present.
Barani Agricultural Research Station, Kohat
Fida Mohammad, Muhammad Imtiaz
Stripe rust is one of the major limiting factors in wheat production. An objective-based breeding program was initiated at Barani Agricultural Research Station (BARS), Kohat in 2013/14 to transfer APR genes from CIMMYT and ICARDA spring wheat lines into wheat germplasm well adapted in Khyber Pakhtunkhwa (KPK). Nine high yielding but stripe rust susceptible KPK wheat varieties were crossed in various combination with 17 CIMMYT and ICARDA wheat lines carrying resistance genes. The resultant 79 F1s were backcrossed with respective susceptible parents followed by single plant selection in F2 generation. During 2015/16, 367 segregating populations/lines were screened in multi-environment stripe rust tests within Khyber Pakhtunkhwa. Sixty-nine out of 367 lines showing adequate resistance were again screened for strip rust resistance at hot spot and in yield trial at BARS, Kohat during 2016/17. Seventeen lines showed considerable resistance and were higher yielding than check cultivars. Lines exhibiting adequate resistance will be further tested in advanced yield trial at provincial and national level for possible release of new varieties 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.
Bogale Nigir, Cherinet Alem, Yosef G. Kidane, Mario Enrico Pè, Matteo Dell'Acqua
Septoria tritici blotch (STB) is a devastating fungal disease affecting durum and bread wheat cultivation worldwide. The search for resistance sources in untapped genetic resources may speed up breeding for STB resistance. Ethiopian durum wheat landraces represent a valuable source of allelic diversity for several traits, including disease resistance. In this study, we measure STB phenotypes under natural infection on two interconnected populations: i) a diversity panel comprising 318 Ethiopian durum wheat lines, mostly farmer varieties, and ii) a nested association mapping (NAM) population developed from a subset of the diversity panel. Phenology, yield and yield component traits were concurrently measured in the populations. We evaluated the distribution of STB resistance in Ethiopian genetic materials and the relationship existing between STB resistance and agronomic traits. STB resistance sources were found in landraces as well as in NAM lines. The genetic material was genotyped with more than 13 thousand genome-wide SNP markers to describe the linkage disequilibrium and genetic structure existing within the panels. The genotyping information was combined with phenotypes to identify marker-trait associations and loci involved in STB resistance. We identified several loci, each explaining up to 10% of the phenotypic variance for disease resistance. We developed KASP markers tagging the most interesting loci to allow the uptake of our results in a breeding perspective. Our results showed that the Ethiopian untapped allelic diversity bears a great value for studying the molecular basis of STB resistance and for breeding for resistance in local and international material.
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.
Plant Pathology Division, Nepal Agricultural Research Council
Baidya Nath Mahto, Durba Bahadur, Thapa Roshan, Basnet Nautan Raj, Gautam Sesh, Raman Upadhyaya
Disease surveillance is very important in establishing the status of disease response in crops. During the 2014 to 2016 wheat seasons, foliar blight (spot blotch caused by Bipolaris sorokiniana and tan spot caused by Pyrenophora tritici-repentis) was recorded as severe across the entire whole plains region. Foliar blight was moderate in the mid hills, especially the Kathmandu valley. Leaf rust was severe (10MS - 100S) at several places in the mid hills. This could be due either to climatic conditions or varieties susceptible to the prevailing pathotypes. Yellow rust was also recorded up to 100S in the Kathmandu valley. Newly released varieties Gaura and Dhaulagiri showed yellow rust incidence of 20MS to 40S. Stem rust was sporadic and light and was observed very late in the season (tR - 10MR) in far western districts and the Kathmandu valley. Powdery mildew was moderate and localized. Loose smut was found at low levels throughout the mid hills. In 2014, Karnal bunt (caused by Tilletia indica) was also recorded in far western regions. Five different pathotypes of P. triticina (121R63-1, 21R55, 21R63 and 0R9) and one Pst pathotype (110S119) have prevailed during the last few years. Wheat genotypes were evaluated at Khumaltar and those reputed to have Yr27, Yr27+, Yr27+Yr18, Yr31+APR, Yr9, Yr10 and Yr15 were resistant. Similarly, genotypes containing Lr34+ had lower leaf rust severities than others.
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).
University of Eldoret
Julius Ochuodho, Ruth Wanyera, Sridhar Bhavani, Les Szabo
Stem rust Ug99 and related race group are one of the major constraints of wheat production in Kenya. The challenge has been largely due to rapid evolution of races within lineage defeating resistance genes resulting in boom and burst cycles. Understanding of the pathogen population structure in major wheat growing regions in Kenya gives comprehensive information of the predominant races as well as capturing new races which may have potential of causing epidemics. Such information can have significant impact on effective gene stewardship in breeding resistant varieties. Using 11 Pgt Simple Sequence Repeats (SSR) markers we analyzed 104 single uredinial-pustule samples. Allele frequency distribution ranged from 2 to 6 per locus with an average of 3.27 per locus. Observed heterozygosity ranging from 0.297-1.000 (mean HO=?0.809) was significantly different (P< 0.001) than the expected heterozygosity (0.264 to 0.507; mean HE=?0.407) indicating that the population is asexual. Analysis of molecular variance (AMOVA) showed that the majority of the variation occurred within the samples (98%) rather than between regions (2%). Analysis of 104 samples identified 21 multiple locus genotypes (MLGs). MLG.19 was observed across the three region analyzed that is Central Rift, North Rift and Mount Kenya while MLG.18 was predominant in Mount Kenya. Based on SSR genotypes of reference isolates, Pgt clade IV (race TKTTF) was associated with MLG.16 in Central Rift Kenya while clade I (race TTKSK) had a unique MLG.10. These results indicated two main groups corresponding to Clade I (Ug99 race group) and Clade IV (race TKTTF race group). This minimum spanning network analysis pattern points to the Pgt population being asexual due to mutation. These preliminary results suggest that Pgt population in Kenya is asexual in nature. Further analysis is being conducted to ascertain geographical structure as well as compare the results with the 2011 data.
CIMMYT International, South Asia, Regional Office, Kathmandu
Gurbinder Gill, Madan Bhatta, Andrew McDonald, Arun Joshi
The experience of seed system development works in Nepal shows that lack of business orientation is one of the key challenges for the growth of Nepalese seed enterprises (SEs). We implemented a business mentorship activity focusing on SEs in the project - Cereal System Initiative for South Asia. The business mentoring (BM) was implemented covering 10 SEs during 2014 to 2017 using discovery sensitization and facilitation mode. The key actions were, SWOT analysis, mentorship to develop strategic business plan, technical facilitation for seed quality improvement through maintenance breeding and on-farm farmer participatory trials as well as large plot demonstrations of recently released and pre-released wheat varieties. This resulted in 45% average increase in the volume of seed sold by individual SEs in three years. Five SEs started maintenance breeding in wheat and by third year, over 50% of the seed sold by the enterprises consisted of newly released varieties compared to 20% before mentoring. The improved performance of SEs prompted seed quality control authority of Nepal to issue a license to two of these private seed companies for maintenance breeding cum foundation seed production. As a consequence, foundation seed production of these entities increased by 60% in three years, and two of them have also started maintenance breeding in rice from 2017. The facilitation in developing business plan by SEs helped them to attract financial resources from different sources in upgrading seed processing, storage and laboratory facilities. Moreover, the National Wheat Research Program of Nepal has proposed the release of a new wheat variety BL 4341 through integration of on-farm trials and seed production data of these SEs. This new variety is resistant to major diseases, yields 7% higher than the popular cultivar NL 297 which was released 32 years ago and needed replacement due to susceptibility to wheat rusts
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.