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.
Umesh Rosyara, Suchismita Mondal, Ravi Singh, Susanne Dreisigacker
Grain yield is the most important economic trait in wheat breeding. The detailed understanding of the genetic architecture of grain yield is crucial and the determining factor to optimize genomics-assisted selection strategies in wheat. First, we performed a marker and haplotype-based genome-wide association study (GWAS) for grain yield (GY) and yield stability coefficient (Pi) on 4,302 advanced breeding lines from five CIMMYT international bread wheat trails grown in multiple (optimally irrigated and stress) environments. All lines were genotyped using genotyping-by-sequencing. A haplotype map was built based on linkage disequilibrium between markers. Twenty-nine markers and 16 haplotypes were associated with GY and Pi across two and three germplasm trials with allelic effects ranging from 2 to 11% across environments. Secondly, we performed genomic prediction, testing eight different prediction models incorporating single markers (base model), haplotypes, epistatic interactions, and significant markers/haplotypes identified in GWAS. Initial results show that by including haplotypes and epistatic interactions among haplotypes (main effect and genome-wide), prediction accuracies range between 0.33-0.49 for GY, a 3 to 22.5% improvement over the base model. Despite the identification of significant marker/haplotype trait associations across traits and environments in GWAS, accounting for these markers in genomic prediction does not improve the prediction models. Our results suggest that the haplotype-based approach can increase prediction ability, but that the knowledge of the genetic architecture of grain yield might not have significant consequence on genomic-assisted selection.
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.
Chris K. Sørensen, Rodrigo Labouriau, Annemarie Justesen, Mogens Hovmøller
Host vernalisation and temperature strongly affect the susceptibility of winter crops to pathogenic fungi. However, how the interaction of these environmental factors influence host susceptibility to Puccinia striiformis, the yellow (stripe) rust fungus, is poorly understood. An experimental system was developed to examine the effect of vernalisation, temperature regime (standard; 18 day/12 night °C and low; 12 day/6 night °C) and plant growth (seedling and adult plant stages) on changes in susceptibility of agronomically important winter wheat and triticale genotypes to P. striiformis races ('Warrior' and 'Kranich') highly predominant in several European countries. Host genotypes exposed to prolonged periods of low temperature, termed vernalisation, reduced disease susceptibility on specific winter host genotypes, although its effect differed considerably by the temperature regime and the P. striiformis race deployed. The influence of vernalisation on host susceptibility was more apparent at low temperature for the 'Warrior' race and at standard temperature for the 'Kranich' race. Triticale genotypes inoculated with the 'Kranich' race were particularly affected by the influence of vernalisation and temperature regime by displaying a shift towards reduced susceptibility at standard temperature. The effect of plant growth stage, i.e., vernalised seedlings versus adult plants, was most evident for the 'Warrior' race at standard temperature and at low temperature for the 'Kranich' race by revealing a lower infection type at the adult plant stage. The research findings presented here contributed to a better understanding of the role of environmental factors in host susceptibility. This, in fact, will aid in the development of more efficient early-warning systems and disease management strategies to the yellow rust fungus and in the decision making for the deployment of winter wheat and triticale genotypes.
Wheat Research Centre, Bangladesh Agricultural Research Institute
Kishwar-E-,Mustarin, Md Mostofa Ali, Reza, Krishna Kanto, Roy, Md. Ashraful, Alam, Md. Rezaul, Kabir, MD Abdil, Hakim, Md Monwar, Hossain, Md Rabiul, Islam, Tim, Krupnik, Md Forhad, Amin, Md. Mosharraf, Hossain, Nure Alam, Siddque, Paritosh Kumar, Malaker, Maricellis, Acevedo, Noresh Chandra Deb, Barma
Disease surveillance and monitoring has been regularly organized by Wheat Research Centre (WRC), in major wheat growing areas of Bangladesh since 2010-11 to track the current status of common diseases, first outbreak of new disease(s), the pathogen hotspot and identify new virulent races. Besides the paper based traditional survey, scientists of WRC are now using different tools like Smartphone/Tablet with supporting applications. Several trainings were arranged under DGGW project on rust tool box in Bangladesh. Among all smartphone applications, RustSurvey is the easiest and handy application which integrates with the SAARC Surveillance Toolbox.
A disease surveillance program on wheat blast was organized in Mid February 2017 followed by hands on training in collaboration with CIMMYT and CU, USA. Out of 103 sites surveyed, 33 sites were found infected with wheat blast. Overall disease incidence was comparatively lower than the previous season with low disease severity (5-10%). Surveillance program on rust diseases was also conducted in early March 2016. Among 102 rust survey sites stem rust and yellow rust was not found, but leaf rust occurred with varying levels of severity depending on field locations, sowing times and cultivars grown. About 52% of the 102 fields investigated had leaf rust, and almost 73% of the infected fields showed low (<20%), 21% moderate (20-40%) and only 6% showed high (more than 40%) disease severity. Timely (15-30 November) planted crops largely escaped or had less disease compared to those planted late in the season. The predominant cultivar Prodip as well as BARI Gom 25 and 26 showed zero to high disease levels with MSS type reactions. BARI Gom 21, 28, 29 and 30 were free from leaf rust infection. Furthermore, Spot blotch was found in most of the region with low to high level field incidence depending on crop growth stage.
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.
University of Sydney Plant Breeding Institute
Naeela Qureshi, Vallence Nsaiyera, Pakeer Kandiah, Mesfin Gesesse, Mandeep Randhawa, Mumta Chhetri, Bosco Chenayek, James Kolmer, Miroslav Valarik, Zaroslav Dolezel, Beat Keller, Matthew Hayden, Justin Faris, Harbans Bariana, Vanessa Wells
Dr. Norman Borlaug stated that rust never sleeps and this enables rust pathogens to produce new strains capable of putting rust resistance genes to rest. These pathogens continue to pose threats to global wheat production. Wheat breeders have made significant progress to control rust outbreaks using conventional selection technologies; however, some critical shifts in pathogen populations have let them down. Rapid evolution in molecular marker technologies in the last 15 years and refinement of phenomic facilities have expedited the process of discovery and characterisation of rust resistance genes to underpin the development and validation of markers closely linked with genetically diverse sources of resistance. A high proportion of the formally named rust resistance genes were characterized in the 21st century and markers closely linked with these genes have been developed and validated. The marker tagged sources of resistance to three rust diseases have equipped the wheat breeding community with tools to deploy combinations of all stage and adult plant resistance genes in future wheat cultivars. The question that whether we have enough resistance genes discovered to compete against the ever-awake rust pathogens. In our opinion, we cannot be complacent and discovery needs to continue to ensure food security. This presentation will discuss the role of advances in phenomic and genomic technologies to achieve durable rust control in wheat.
Ayub Agricultural Research Institute, Faisalabad
Different biotic and abiotic stresses are hampering wheat yield across different geographic regions. Among biotic stresses, wheat rusts are principal cause of yield reduction. Whereas among abiotic stresses, drought is the principle cause of reduction in growth and lowering yield potential. So developing rust resistance and drought tolerance in wheat germplasm is needed, which requires assessment of genetic potential of current cultivars against these stresses to identify variation among existing germplasm. Screening of genotypes under naturally prevailing races of rust species is the better and inexpensive approach. In the present study 65 genotypes including five checks (AARI-11, Chakwal- 50, Aas- 11, Morocco and Galaxy-13) were evaluated for adult plant response to wheat rusts and water deficit conditions. Experimental material was planted in four blocks each having new entries along with repetition of five checks in augmented design. Data was recorded on morphological traits including plant height, peduncle length, spike length, productive tillers per meter, flag leaf area, number of spikelet per spike, grains per spike, single head weight, 1000 grain weight, days to maturity and grain yield per acre. Significant variation was observed among genotypes for all the studied traits. On the basis of performance G39 and G36 were better than commercial drought check Chakwal-50 in almost all the traits. However rust screening under natural rust infestation revealed that although Morocco showed susceptible (S) response yet only six genotypes were susceptible to yellow rust whereas all others were resistant. In case of leaf rust 29 were completely resistance, 25 were moderately resistant, seven were moderately susceptible and only four were completely susceptible to currently active races of leaf rust. However, in the case of stem rust, 61 genotypes showed complete resistance to stem rust, two showed moderately resistance and two were moderately susceptible. Information obtained from this study would be favorable for breeding rust resistant and drought tolerant cultivars.
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.