University of Mohammed V/ICARDA
HAFSSA,KABBAJ, AYED, AL ABDALLAT, GREGOR, GORJANC, JESSE, POLAND, MIKAEL, MILOUDI NACHIT, AHMED, AMRI, BOUCHRA, BELKADI, KARIM, FILALI MALTOUF, FILIPPO, BASSI MARIA, , , , , , , , , , , ,
Durum wheat (Triticum durum Desf.) is a major stable crop and it represents a base of the Mediterranean diet. This region is subject to a Mediterranean climate, which is extremely unpredictable with severe changes in moisture and temperature occurring each crop season. This unpredictability is summarized by breeders as GxE and the identification of traits controlling this interaction is quintessential to ensure stability in production season after season. To study the genetics of yield stability, four RILs populations derived from elite x elite crosses were assessed for yield and 1,000-kernel weights across five diverging environments in Morocco and Lebanon. These 550 RILs were characterized with 4,909 polymorphic SNPs via genotyping by sequencing. A consensus map was derived by merging the individual genetic maps of each population. Finally, imputation was used to fill all the missing haplotypes and reach a reduction of missing data to below 8%. Several significant QTLs were identified to be linked to TKW, grain yield and a stability index, namely AMMI wide adaptation index (AWAI). A second approach to identify loci controlling stability was the use of a global panel of 288 elites, accessions and landraces tested in 15 diverging environment. Multi-locations data were compiled via GxE models to derive the AWAI stability index. In addition, this panel was characterized with 8,173 polymorphic SNPs via Axiom 35K array. Significant associations were identified for all traits, including QTLs unique to AWAI. The sum of the identified QTLs can now be pyramid via marker assisted selection and molecular designed crosses in order to obtain very stable cultivars.
Hawassa Agriculture Research Centre
Agdew Bekele, Waga Mazengia, Shimekt Maru
Shortage of seed of rust resistant varieties is a challenge of small holder farmers in wheat production. To successfully address this issue, one of the essential elements in wheat production system is farmer's access to quality seed of improved varieties. This paper presents the experience of on-farm basic and pre-basic seed production of newly released rust resistant wheat varieties. For the first time in the country, On-Farm basic and pre-basic seed production of wheat varieties was carried out in two districts/woredas (Silti and Soddo) of two specific locations (Loke faka and Wacho) where the Edget Farmers' Seed Multiplier and Marketing Union was licensed to produce some crop varieties (cereals and pulse), beginning in the 2011/2012 cropping season. Model farmers from primary cooperatives were selected based on the past experience they had with the union in producing certified seed. Selected farmers and relevant experts were trained on how earh seed of wheat is produced. Accordingly seed multiplication of four wheat varieties was conducted with frequent monitoring and evaluation at the course of multiplication.
As a result sufficient and quality basic seed of newly released wheat varieties was produced on-farm in both Loke and Wacho locations for own utilization and seed market. The result of the experiment revealed that it was possible to multiply quality wheat seed provided that partnership (with GOs and/or NGOs) is well-built and cooperative farmers do farm management practices as per the recommendations. On-farm seed production can be sustainable if the strong partnership exists among stakeholders, and wheat seed growers are given premium prices for their seed which is supported by the legal frame work that encourages the seed production of early generations. More importantly, the result of this experiment has a useful implication on government policies and strategies and government institutions' practice on farm early seed generation production and marketing.
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.
USDA-ARS, Pullman, WA, USA
Lu Liu, Meinan Wang, Junyan Feng, Deven See, Shiaoman Chao
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is the most destructive disease of wheat in the US Pacific Northwest. Durable high-temperature adult-plant (HTAP) resistance to stripe rust has been emphasized for breeding wheat cultivars and the resistance level has been gradually increased since the early 1960s. Wheat cultivar Madsen has been widely grown, intensively used in breeding programs, and has exhibited durable and high level resistance to stripe rust since its release in 1988. To map its resistance genes and determine the genetic basis of durable and high-level of resistance, Madsen was crossed with susceptible cultivar Avocet S, and 156 recombinant inbred lines (RILs) were developed. The RILs and parents were tested with races PSTv-37 and PSTv-40 in seedling stage at low temperatures in the greenhouse and in adult-plant stage in the fields of Pullman and Mount Vernon, WA in 2015 and 2016 under natural infection of the pathogen. The RILs were genotyped with single-nucleotide polymorphism (SNP) markers derived from genotyping by sequencing and the 90K Illumina iSelect wheat SNP chip. A linkage map was constructed with 1,348 SNP loci. QTL analysis identified three genes for all-stage resistance on chromosomes 1AS (QYrMad.wgp-1AS), 1BS (QYrMad.wgp-1BS), and 2AS (QYrMad.wgp-2AS); and two QTL for HTAP resistance on 3B (QYrMad.wgp-3B) and 6B (QYrMad.wgp-6B). QYrMad.wgp-2AS was the most significant QTL, explaining 16.03-71.23% phenotypic variation depending upon the race or environment, followed by QYrMad.wgp-6B that was consistently detected in all field experiments and explained 6.7-35.9% of the phenotypic variations. Based on the chromosomal locations and the results from other studies, QYrMad.wgp-2AS contains Yr17 and a HTAP resistance QTL, and QYrMad.wgp-1AS is a new QTL. The interactions among these QTL were mostly additive. The combination of the five QTL for different types of resistance provides the durable and high level resistance to stripe rust.
Ethiopian institute of agricultural research
Dr. Netsanet B. Heyi, Dr. Getaneh W. Wolderufael, Tsegab T.
Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a major production constraint in most wheat growing areas of Ethiopia. The stem rust pathogen is capable of rapidly developing new virulence to resistance genes. The highlands of Ethiopia are considered a hot spot for Pgt diversity. The present study was conducted to investigate the virulence diversity and spatial distribution of races of Pgt in the major wheat growing areas of Ethiopia. The physiologic races of Pgt were determined on seedlings of the standard wheat stem rust differentials following the international system of nomenclature. Stem rust race analyses were carried out both at Ambo Plant Protection Center and the Cereal Disease Laboratory in Minnesota. 426 stem rust samples were collected from major wheat growing of the country in the 2016 cropping season and 185 viable samples were analyzed. Stem rust races TKTTF, TTKSK, TTTTF, JRCQC and RRTTF were identified. Among the identified races, TKTTTF was dominant at a frequency of 78.7% followed by TTKSK (10.6%). Race TTTTF was found for the first time in Ethiopia in 2016. Only one resistance gene in the differential set, Sr24, was effective against all isolates. Stem rust resistance gene Sr31 was found to confer resistance to most of the races prevalent in Ethiopia with the exception of Ug99. Sr24 could be used in combination with other resistance genes in breeding for resistance to stem rust in Ethiopia.
University of Minnesota
Caixia Lan, Ravi Singh, Matthew Rouse, Muhammad Imtiaz, James Anderson
The rapid appearance of new races of rust pathogens with virulence for the major seedling resistance genes in wheat has intensified the focus to discover adult plant resistance (APR) genes in wheat and utilize them in breeding programs for sustainable wheat production. The experimental breeding line 'Copio' developed by the International Maize and Wheat Improvement Centre (CIMMYT) in Mexico has exhibited high levels of APR to all three rusts including the African stem rust Ug99 race group. To dissect the mechanism of APR in Copio it was crossed with APAV#1, which is susceptible to all three rusts and a population of 176 F4:F5 recombinant inbred lines (RILs) was developed at CIMMYT. Both parental lines were found to be susceptible (IT >3) at the seedling stage to races TTKSK and TKTTF, which ensures the field data from Africa will be applicable for APR mapping. Seedling tests were also conducted on the RIL population using the predominant Pakistani race RRTTF, and Chi-squared tests indicated segregation of two stem rust seedling genes (?2 test P value of 0.00002). Both parents were also tested for the known APR genes Lr34/Yr18/Sr57, Lr46/Yr29/Sr58, Lr67/Yr46/Sr55 and Sr2/Yr30 using molecular markers and results indicate that APAV#1 does not carry any known APR genes, while Copio might have Lr46 and Sr2. This population was tested in four field environments (US, Pakistan, Mexico, and Kenya) for leaf, stem and yellow rusts during 2015-16 and 2016-17. Disease severity distributions of all three rusts for the RILs across all environments were continuous, suggestive of quantitative and polygenic resistance.
We are using genotyping by sequencing (GBS) as a genotyping platform and anticipate having preliminary mapping results available by spring 2018.
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.
Seed & Plant Improvement Institute (SPII), AREEO, Karaj, Iran
Ramin Roohparvar, Safarali Safavi, Gholamhossein Ahmadi
In recent years, wheat stem rust, caused by Puccinia graminis f.sp. tritici, has been reconsidered in Iran due to its prevalence and the emergence of the dangerous Ug99 race. This study was conducted to understand pathogenic variation in the population of P. graminis f.sp. tritici, detection of effective genes, and identification of resistance in Iranian commercial wheat cultivars or advanced lines, by planting stem rust trap nurseries under natural disease infection in several regions of Iran during the 2016-2017 cropping season. The trap nursery in each location included 48 wheat lines each carrying a single gene of stem rust (Sr) resistance, seven lines each carrying Sr multigenes, eight additional lines to confirm four Sr genes, 149 commercial wheat cultivars or advanced lines from Iran, plus several susceptible checks. The percentage leaf area affected (disease severity) and infection type were recorded at adult plant stage when disease was well developed on flag leaves of susceptible checks. Results showed presence of virulence for several Sr genes in one or more locations. However, the single genes of Sr13, Sr23, Sr24, and two complex genes of Sr7a+Sr6+Sr12 and Sr6+Sr24+Sr36+Sr1RS-Am were still effective against stem rust in all locations. The results of evaluations of commercial wheat cultivars or advanced lines showed that approximately 16% the genotypes tested including wheat cultivars Gonbad, Shiroudi, Chamran-2, Baharan, Dena, Karkheh, and Arya were resistant in all locations.
Northwest A&F University
Dejun Han, Jia Guo, Manuel Spannagl, Jianhui Wu, Aizhong Cao, Peidu Chen, IWGSC, Lili Huang, Jun Guo, Klaus Mayer, Zhensheng, Kang
Wheat cultivation in many regions faces threats by devastating fungal infections. However, wheat cultivar 92R137 shows resistance to Puccinia striiformis infection. To isolate the stripe rust resistance gene Yr26, an integrated transcriptomic and comparative genomics approach was undertaken. Near-isogenic lines of wheat (carrying Yr26 or not) infected with two Puccinia striiformis f. sp. tritici (Pst) (Virulence or avirulence to Yr26) were analysed in a dual detailed time series RNA-seq study. The emerging IWGSC refseq v1.0 genome assembly sequence serves as a valuable template and was also used for comparative genomics studies of the gene candidate region with the genome sequences of close relatives and wheat progenitors. Using bulked segregant analysis (BSA) to identify polymorphic SNPs between parent and resistant DNA (R-bulk) and susceptible DNA (S-bulk), flanking markers for Yr26 were identified. These two markers were mapped to the Chinese spring reference genome sequence, spanning a region of about 250 kb. The synteny analysis of this candidate region in CS chr1B with chr1A, chr1D, Wild Emmer Wheat (Td_chr1A and Td_chr1B) and Barley (chr1H) identified three candidate Yr26 genes. To detect gene candidates a dual time series RNA-seq analysis was performed. Genes differently expressed between rust susceptible (NIL-S) host lines and rust resistant (NIL-R) lines, carrying the Yr26 candidate gene were analysed. Both lines were inoculated with Pst carrying different avirulence factors (Pst-CYR32 and Pst-V26), compatible or incompatible with the corresponding wheat lines. Differential gene expression analysis (DEG) between compatible and incompatible interaction revealed DEGs in the wheat genome and in the Pst genome. From a network analysis of both wheat and Pst genes, we inferred connected co-expressed modules. Resulting modules showed particular enrichments for disease resistance, defense response to fungus and cell wall components.
Plant Pathology Research Institute
Atef Shahin, Mohamed Abu Zaid
Resistance genes Sr2, Sr22, Sr24, Sr25 and Sr26 confer adult plant resistance to Pgt race TTKSK (=Ug99). Ten Egyptian wheat varieties and four bread wheat entries from CIMMYT were screened with five DNA markers to determine the presence of these genes, and were evaluated for stem rust response at Sakha and Sids during the successive growing seasons of 2015/16 and 2016/17. Varieties Giza 171, Sakha 94, Gemmeiza 11, and CIMMYT lines 6043, 6091, 6107 and 6197 were resistant with severities ranging from TrR to 5MR/MS. Sr2 was present in all entries; Sr24 was present in one local Egyptian cultivar (Misr2); Sr25 was present in Misr 1, Misr 2, Gemmeiza 9, Gemmeiza 11, and lines 6091 and 6197; and Sr26 was present in line 6197.