A genetic analysis of adult plant resistance to stripe rust in the wheat cultivar Kariega

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Single-nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost effective, flexible, and user-friendly. In this study, a new GenoBaits WheatSNP16K (GBW16K) GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies. The GBW16K array contains 14 868 target SNP regions that are evenly distributed across the wheat genome, and 37 669 SNPs in these regions can be identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions is 0.270, which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci (QTLs). A genetic linkage map, constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco"S" and the Chinese landrace Mingxian169, enables the identification of Yr27, Yr30, and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco"S" and of Yr18 from Mingxian169. QYr.nwafu-2BL.4 is different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis, micro-collinearity, gene annotation, RNA sequencing, and SNP data. This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.

Genome-wide mapping of quantitative trait loci conferring resistance to stripe rust in spring wheat line PI 660072

KEY MESSAGE

Two major QTL for resistance to stripe rust were mapped on chromosome 2BL and 4BL in spring wheat PI 660072, and their KASP markers were developed. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Identifying resistance genes is crucial for developing resistant cultivars to control the disease. Spring wheat PI 660072 (Triticum aestivum) has been identified to possess both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust. To elucidate the genetic basis of the resistance in PI 660072, a mapping population consisting of 211 F5-F7 recombinant-inbred lines (RILs) was developed from a cross of PI 660072 with susceptible spring wheat Avocet S. The mapping population was phenotyped for stripe rust responses across five field environments from 2020 to 2022 and genotyped using the 15 K SNP (single nucleotide polymorphism) array to map stripe rust resistance loci. The mapping population was also tested at the seedling stage with predominant Chinese Pst races CYR31, CYR32, CYR34 and PST-YX1-3-1 in the greenhouse. Stripe rust resistance genes were identified using the quantitative trait locus (QTL) mapping approach. Two QTL were identified with QYrPI660072.swust-2BL mapped on the long arm of chromosome 2B for ASR and QYrPI660072.swust-4BL on the long arm of chromosome 4B for APR. To facilitate marker-assisted selection breeding, Kompetitive allele specific PCR (KASP) markers, KASP-1269 for QYrPI660072.swust-2BL and KASP-3209 for QYrPI660072.swust-4BL, were developed. These markers could be used to introgress the effective resistance QTL into new wheat cultivars.

Genome-wide QTL mapping for stripe rust resistance in spring wheat line PI 660122 using the Wheat 15K SNP array

Introduction

Stripe rust is a global disease of wheat. Identification of new resistance genes is key to developing and growing resistant varieties for control of the disease. Wheat line PI 660122 has exhibited a high level of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 239 recombinant inbred lines (RILs) was developed from a cross between PI 660122 and an elite Chinese cultivar Zhengmai 9023.

Methods

The RIL population was phenotyped for stripe rust response in three field environments and genotyped with the Wheat 15K single-nucleotide polymorphism (SNP) array.

Results

A total of nine quantitative trait loci (QTLs) for stripe rust resistance were mapped to chromosomes 1B (one QTL), 2B (one QTL), 4B (two QTLs), 4D (two QTLs), 6A (one QTL), 6D (one QTL), and 7D (one QTL), of which seven QTLs were stable and designated as QYrPI660122.swust-4BS, QYrPI660122.swust-4BL, QYrPI660122.swust-4DS, QYrPI660122.swust-4DL, QYrZM9023.swust-6AS, QYrZM9023.swust-6DS, and QYrPI660122.swust-7DS. QYrPI660122.swust-4DS was a major all-stage resistance QTL explaining the highest percentage (10.67%-20.97%) of the total phenotypic variation and was mapped to a 12.15-cM interval flanked by SNP markers AX-110046962 and AX-111093894 on chromosome 4DS.

Discussion

The QTL and their linked SNP markers in this study can be used in wheat breeding to improve resistance to stripe rust. In addition, 26 lines were selected based on stripe rust resistance and agronomic traits in the field for further selection and release of new cultivars.

Genome-Wide QTL Mapping for Stripe Rust Resistance in Winter Wheat Pindong 34 Using a 90K SNP Array

Winter wheat cultivar Pindong 34 has both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust, which is caused by Puccinia striiformis f. sp. tritici (Pst). To map the quantitative trait loci (QTL) for stripe rust resistance, an F_6-10 recombinant inbred line (RIL) population from a cross of Mingxian 169 × Pingdong 34 was phenotyped for stripe rust response over multiple years in fields under natural infection conditions and with selected Pst races under controlled greenhouse conditions, and genotyping was performed with a 90K single nucleotide polymorphism (SNP) array chip. Inclusive composite interval mapping (ICIM) identified 12 APR resistance QTLs and 3 ASR resistance QTLs. Among the 12 APR resistance QTLs, QYrpd.swust-1BL (explaining 9.24-13.33% of the phenotypic variation), QYrpd.swust-3AL.1 (11.41-14.80%), QYrpd.swust-3AL.2 (11.55-16.10%), QYrpd.swust-6BL (9.39-12.78%), QYrpd.swust-6DL (9.52-16.36%), QYrpd.swust-7AL (9.09-17.0%), and QYrpd.swust-7DL (8.87-11.38%) were more abundant than in the five tested environments and QYrpd.swust-1AS (11.05-12.72%), QYrpd.swust-1DL (9.81-13.05%), QYrpd.swust-2BL.1 (9.69-10.57%), QYrpd.swust-2BL.2 (10.36-12.97%), and QYrpd.swust-2BL.3 (9.54-13.15%) were significant in some of the tests. The three ASR resistance QTLs QYrpd.swust-2AS (9.69-13.58%), QYrpd.swust-2BL.4 (9.49-12.07%), and QYrpd.swust-7AS (16.16%) were detected based on the reactions in the seedlings tested with the CYR34 Pst race. Among the 15 QTLs detected in Pindong 34, the ASR resistance gene QYrpd.swust-7AS mapped on the short arm of chromosome 7A was likely similar to the previously reported QTL Yr61 in the region. The QTLs identified in the present study and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.

Genetic Analysis of Adult Plant Resistance to Stripe Rust in Common Wheat Cultivar "Pascal"

Wheat stripe rust is an important foliar disease that affects the wheat yield globally. Breeding for resistant wheat varieties is one of the most economically and environmentally effective ways to control this disease. The common wheat (Triticum aestivum L.) cultivar "Pascal" exhibited susceptibility to stripe rust at the seedling stage but it showed high resistance to stripe rust at the adult plant stage over 20 years in Gansu, a hotspot of the disease in northwestern China. To understand the genetic mechanism of stripe rust resistance in this cultivar, a 55K SNP array was used to analyze the two parents and the 220 recombinant inbred lines (RILs) derived from the cross of "Huixianhong" × "Pascal." We detected three new stripe rust adult plant resistance (APR) quantitative trait locus (QTL) contributed by Pascal, viz. QYr.gaas-1AL, QYr.gaas-3DL, and QYr.gaas-5AS, using the inclusive composite interval mapping method. They were flanked by SNP markers AX-111218361-AX-110577861, AX-111460455-AX-108798599, and AX-111523523-AX-110028503, respectively, and explained the phenotypic variation ranging from 11.0 to 23.1%. Bulked segregant exome capture sequencing (BSE-Seq) was used for fine mapping of QYr.gaas-1AL and selection of candidate genes, TraesCS1A02G313700, TraesCS1A02G313800, and TraesCS1A02G314900 for QYr.gaas-1AL. KASP markers BSE-1A-12 and HXPA-3D for QYr.gaas-1AL and QYr.gaas-3DL were developed for breeders to develop durable stripe rust-resistant wheat varieties.

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future.

Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust (Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population

Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.

Genome-wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces

Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding programs an association mapping (AM) panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the AM panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers across 19 chromosomes with significant SNP-trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study do not correspond to previously reported Yr genes or QTL, suggesting new genomic regions for stripe rust resistance.

Accomplishments in wheat rust research in South Africa

Rust diseases, although seasonal, have been severe constraints in wheat production in South Africa for almost 300 years. Rust research gained momentum with the institution of annual surveys in the 1980s, followed by race identification, an understanding of rust epidemiology, and eventually a focused collaboration amongst pathologists, breeders and geneticists. Diversity in South African populations of Puccinia triticina, P. graminis f. sp. tritici and P. striiformis f. sp. tritici has been described and isolates are available to accurately phenotype wheat germplasm and study pathogen populations at national, regional and global levels. Sources of resistance have been, and still are, methodically analysed and molecular marker systems were developed to incorporate, stack and verify complex resistance gene combinations in breeding lines and cultivars. Vigilance, capacity, new technologies, collaboration and sustained funding are critical for maintaining and improving the current research impetus for future management of these important diseases.

Genome-Wide Mapping of Adult Plant Resistance to Leaf Rust and Stripe Rust in CIMMYT Wheat Line Arableu#1

Leaf (brown) rust (LR) and stripe (yellow) rust (YR), caused by Puccinia triticina and P. striiformis f. sp. tritici, respectively, significantly reduce wheat production worldwide. Disease-resistant wheat varieties offer farmers one of the most effective ways to manage these diseases. The common wheat (Triticum aestivum L.) Arableu#1, developed by the International Maize and Wheat Improvement Center and released as Deka in Ethiopia, shows susceptibility to both LR and YR at the seedling stage but a high level of adult plant resistance (APR) to the diseases in the field. We used 142 F₅ recombinant inbred lines (RILs) derived from Apav#1 × Arableu#1 to identify quantitative trait loci (QTLs) for APR to LR and YR. A total of 4,298 genotyping-by-sequencing markers were used to construct a genetic linkage map. The study identified four LR resistance QTLs and six YR resistance QTLs in the population. Among these, QLr.cim-1BL.1/QYr.cim-1BL.1 was located in the same location as Lr46/Yr29, a known pleiotropic resistance gene. QLr.cim-1BL.2 and QYr.cim-1BL.2 were also located on wheat chromosome 1BL at 37 cM from Lr46/Yr29 and may represent a new segment for pleiotropic resistance to both rusts. QLr.cim-7BL is likely Lr68 given its association with the tightly linked molecular marker cs7BLNLRR. In addition, QLr.cim-3DS, QYr.cim-2AL, QYr.cim-4BL, QYr.cim-5AL, and QYr.cim-7DS are probably new resistance loci based on comparisons with published QTLs for resistance to LR and YR. Our results showed the diversity of minor resistance QTLs in Arableu#1 and their role in conferring near-immune levels of APR to both LR and YR, when combined with the pleiotropic APR gene Lr46/Yr29.

Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China

Wheat stripe rust can cause considerable yield losses, and genetic resistance is the most effective approach for controlling the disease. To identify the genomic regions responsible for Puccinia striiformis f. sp. tritici (Pst) resistance in a set of winter wheat strains mainly from southwestern China, and to identify DNA markers in these regions, we carried out a genome-wide association study (GWAS) of 120 China winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90K wheat SNP arrays. In total, 16 SNP loci were significantly associated with wheat stripe rust in field and greenhouse trials. Of these, three distinctive SNPs on chromosomes 1B, 4A, and 6A were identified at a site in Mianyang in 2014, where the most prevalent wheat stripe rust races since 2009 have been V26 (G22-9, G22-14). This suggests that the three SNP loci were linked to the new quantitative trait loci (QTL)/genes resistant to the V26 races. Germplasm with immunity to Pst is a good source of stripe rust resistance for breeding, and after further validation, SNPs closely linked to resistance QTLs/genes could be converted into user-friendly markers and facilitate marker-assisted selection to improve wheat stripe rust resistance.

Genetic architecture of wheat stripe rust resistance revealed by combining QTL mapping using SNP-based genetic maps and bulked segregant analysis

A major stripe rust resistance QTL was mapped to a 0.4 centimorgan (cM) genetic region on the long arm of chromosome 7B, using combined genome-wide linkage mapping and bulk segregant analysis. The German winter wheat cv. Centrum has displayed high levels of adult plant stripe rust resistance (APR) in field environments for many years. Here, we used the combined genome-wide linkage mapping and pool-extreme genotyping to characterize the APR resistance. One hundred and fifty-one F_2:7 recombinant inbred lines derived from a cross between susceptible landrace Mingxian 169 and Centrum were evaluated for stripe rust resistance in multiple environments and genotyped by the wheat 35K single nucleotide polymorphism (SNP) array. Three stable quantitative trait loci (QTL) were identified using QTL analysis across five field environments. To saturate the major QTL, the wheat 660K SNP array was also used to genotype bulked extremes. A major QTL named QYrcen.nwafu-7BL from Centrum was mapped in a 0.4 cM genetic interval flanking by AX-94556751 and AX-110366788 across a 2 Mb physical genomic region, explaining 19.39-42.81% of the total phenotypic variation. It is likely a previously uncharacterized QTL based on pedigree analysis, reaction response, genotyping data and map comparison. The SNP markers closely linked with QYrcen.nwafu-7BL were converted to KASP markers and validated in a subset of 120 wheat lines. A 211 F₂ breeding population from a cross of an elite cultivar Xinong 979 with Centrum were developed for marker-based selection. Three selected lines with desirable agronomic traits and the positive alleles of both KASP markers showed acceptable resistance which should be used as resistance donors in wheat breeding programs. The other QTL QYrcen.nwafu-1AL and QYrcen.nwafu-4AL with additive effects could enhance the level of resistance conferred by QYrcen.nwafu-7BL.

Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces (Triticum aestivum L.) From the Yellow and Huai River Valleys

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker-trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.

Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi-Environmental Analysis

Cassava, Manihot esculenta Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to two Xam strains (Xam318 and Xam681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response to Xam revealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance to Xam explaining between 15.8 and 22.1% of phenotypic variance, were detected and localized on a high resolution SNP-based genetic map of cassava. Four of them show stability among the two evaluated seasons. Genotype by environment analysis detected three QTL by environment interactions and the broad sense heritability for Xam318 and Xam681 were 20 and 53%, respectively. DNA sequence analysis of the QTL intervals revealed 29 candidate defense-related genes (CDRGs), and two of them contain domains related to plant immunity proteins, such as NB-ARC-LRR and WRKY.

Genome wide association mapping of stripe rust resistance in Afghan wheat landraces

Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R²≈0.16 at 0cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R² decayed below 0.2 at 0.3cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.

Development of a Greenhouse Screening Method for Adult Plant Response in Wheat to Stem Rust

Screening for adult plant resistance in wheat to stem rust, caused by Puccinia graminis f. sp. tritici, is generally conducted in field plots. Although such evaluations are successful if managed properly, field ratings are time consuming, expensive, weather dependent, and open to inoculum of unwanted races or other confounding diseases. The objective of this study was to develop a dependable system of screening the response of adult plants to stem rust under greenhouse conditions. A comparison of inoculation methods and incubation environments showed that plants inoculated with urediniospores suspended in water, followed by a 24 h dew period in a plastic chamber constructed in a greenhouse, gave the most consistent results. Measurements of response type, stem rust severity, and frequency in follow-up experiments indicated that the most reliable infection was obtained when plants sprayed with 1.25 mg urediniospores per ml water were incubated in the plastic chamber. Using the optimized protocol, a Kariega × Avocet S doubled haploid population was inoculated with two P. graminis f. sp. tritici races. Depending on the race, composite interval mapping showed flag leaf infection type to be significantly influenced by regions on chromosomes 6A, 6D, and 7D. Stem rust severity and reaction type mapped to chromosomes 6D and/or 6A. The Lr34/Yr18/Sr57 gene derived from Kariega on chromosome 7D affected the rust response on flag leaves but not on stems of greenhouse-grown plants. This study showed that phenotyping and genetic analysis of especially major effect stem rust resistance in adult wheat plants is possible and reproducible under controlled conditions in a greenhouse.

Genome-Wide Linkage Mapping of QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Population Linmai 2 × Zhong 892

Stripe rust is one of the most devastating diseases of wheat (Triticum aestivum) worldwide. Adult-plant resistance (APR) is an efficient approach to provide long-term protection of wheat from the disease. The Chinese winter wheat cultivar Zhong 892 has a moderate level of APR to stripe rust in the field. To determine the inheritance of the APR resistance in this cultivar, 273 F6 recombinant inbred lines (RILs) were developed from a cross between Linmai 2 and Zhong 892. The RILs were evaluated for maximum disease severity (MDS) in two sites during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for five environments. Illumina 90k SNP (single nucleotide polymorphism) chips were used to genotype the RILs and their parents. Composite interval mapping (CIM) detected eight QTL, namely QYr.caas-2AL, QYr.caas-2BL.3, QYr.caas-3AS, QYr.caas-3BS, QYr.caas-5DL, QYr.caas-6AL, QYr.caas-7AL and QYr.caas-7DS.1, respectively. All except QYr.caas-2BL.3 resistance alleles were contributed by Zhong 892. QYr.caas-3AS and QYr.caas-3BS conferred stable resistance to stripe rust in all environments, explaining 6.2-17.4% and 5.0-11.5% of the phenotypic variances, respectively. The genome scan of SNP sequences tightly linked to QTL for APR against annotated proteins in wheat and related cereals genomes identified two candidate genes (autophagy-related gene and disease resistance gene RGA1), significantly associated with stripe rust resistance. These QTL and their closely linked SNP markers, in combination with kompetitive allele specific PCR (KASP) technology, are potentially useful for improving stripe rust resistances in wheat breeding.

Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm

Identified DArT and SNP markers including a first reported QTL on 3AS, validated large effect APR on 3BS. The different genes can be used to incorporate stripe resistance in cultivated varieties. Stripe rust [yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst)] is a serious disease in wheat (Triticum aestivum). This study employed genome-wide association mapping (GWAM) to identify markers linked to stripe rust resistance genes using Diversity Arrays Technology (DArT(®)) and single-nucleotide polymorphism (SNP) Infinium 9K assays in 200 ICARDA wheat genotypes, phenotyped for seedling and adult plant resistance in two sites over two growing seasons in Syria. Only 25.8 % of the genotypes showed resistance at seedling stage while about 33 and 44 % showed moderate resistance and resistance response, respectively. Mixed-linear model adjusted for false discovery rate at p < 0.05 identified 12 DArT and 29 SNP markers on chromosome arms 3AS, 3AL, 1AL, 2AL, 2BS, 2BL, 3BS, 3BL, 5BL, 6AL, and 7DS significantly linked to Pst resistance genes. Of these, the locus on 3AS has not been previously reported to confer resistance to stripe rust in wheat. The QTL on 3AS, 3AL, 1AL, 2AL, and 2BS were effective at seedling and adult plant growth stages while those on 3BS, 3BL, 5BL, 6AL and 7DS were effective at adult plant stage. The 3BS QTL was validated in Cham-6 × Cham-8 recombinant inbred line population; composite interval analysis identified a stripe resistance QTL flanked by the DArT marker, wPt-798970, contributed by Cham-6 parent which accounted for 31.2 % of the phenotypic variation. The DArT marker "wPt-798970" lies 1.6 cM away from the 3BS QTL detected within GWAM. Epistatic interactions were also investigated; only the QTL on 1AL, 3AS and 6AL exhibited interactions with other loci. These results suggest that GWAM can be an effective approach for identifying and improving resistance to stripe rust in wheat.

Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.)

Potential novel and known QTL for race-specific all-stage and adult plant resistance to stripe rust were identified by genome-wide association mapping in the US PNW winter wheat accessions. Stripe rust (Puccinia striiformis F. sp. tritici; also known as yellow rust) is a globally devastating disease of wheat (Triticum aestivum L.) and a major threat to wheat production in the US Pacific Northwest (PNW), therefore both adult plant and all-stage resistance have been introduced into the winter wheat breeding programs in the PNW. The goal of this study was to identify quantitative trait loci (QTL) and molecular markers for these resistances through genome-wide association (GWAS) mapping in winter wheat accessions adapted to the PNW. Stripe rust response for adult plants was evaluated in naturally occurring epidemics in a total of nine environments in Washington State, USA. Seedling response was evaluated with three races under artificial inoculation in the greenhouse. The panel was genotyped with the 9K Illumina Wheat single nucleotide polymorphism (SNP) array and additional markers linked to previously reported genes and QTL for stripe rust resistance. The population was grouped into three sub-populations. Markers linked to Yr17 and previously reported QTL for stripe rust resistance were identified on chromosomes 1B, 2A, and 2B. Potentially novel QTL associated with race-specific seedling response were identified on chromosomes 1B and 1D. Potentially novel QTL associated with adult plant response were located on chromosomes 2A, 2B, 3B, 4A, and 4B. Stripe rust was reduced when multiple alleles for resistance were present. The resistant allele frequencies were different among sub-populations in the panel. This information provides breeders with germplasm and closely linked markers for stripe rust resistance to facilitate the transfer of multiple loci for durable stripe rust resistance into wheat breeding lines and cultivars.

Yr60, a Gene Conferring Moderate Resistance to Stripe Rust in Wheat

Stripe rust, caused by Puccinia striiformis f. sp. tritici W., is a devastating disease of wheat worldwide. A new stripe rust resistance gene with moderate seedling and adult plant resistance was mapped using an F₅ recombinant inbred line (RIL) population developed from the cross of the resistant parent 'Almop' with the susceptible parent 'Avocet'. The parents and RILs were phenotyped for seedling stripe rust response variation in a greenhouse and in field trials at Toluca, Mexico for 2 years. Almop showed moderate levels of resistance at both seedling and adult plant stages compared with the highly susceptible response of Avocet. The distribution of homozygous resistant, homozygous susceptible, and segregating RILs conformed to segregation at a single locus. Seedlings and adult plant responses were correlated, indicating that the same gene conferred resistance at both stages. A bulk segregant analysis approach with widely distributed simple sequence repeat (SSR) markers mapped the resistance gene to the distal region of the long arm of chromosome 4A. The SSR marker wmc776 cosegregated with this gene, whereas markers wmc219 and wmc313 were tightly linked and both located at 0.6 centimorgans. The resistance locus was designated Yr60.

New Races of Puccinia striiformis Found in Europe Reveal Race Specificity of Long-Term Effective Adult Plant Resistance in Wheat

Resistance to Puccinia striiformis was examined in nine wheat recombinant inbred lines (RILs) from a cross between 'Camp Rémy' (resistant parent) and 'Récital' (susceptible parent) using an isolate of a strain common to the northwestern European population before 2011 (old) and two additional isolates, one representing an aggressive and high-temperature-adapted strain (PstS2) and another representing a virulence phenotype new to Europe since 2011 (new). The RILs carried different combinations of quantitative trait loci (QTL) for resistance to P. striiformis. Under greenhouse conditions, the three isolates gave highly contrasting results for infection type, latent period, lesion length, and diseased leaf area. The PstS2 isolate revealed Yr genes and QTL which conferred complete resistance in adult plants. Six QTL had additive effects against the old isolate whereas the effects of these QTL were significantly lower for the new isolate. Furthermore, the new isolate revealed previously undetected resistance in the susceptible parent. Disease severity under field conditions agreed with greenhouse results, except for Camp Rémy being fully resistant to the new isolate and for two RILs being susceptible in the field. These results stress the need of maintaining high genetic diversity for disease resistance in wheat and of using pathogen isolates of diverse origin in studies of host resistance genetics.

Quantitative trait loci of stripe rust resistance in wheat

Over thirty publications during the last 10 years have identified more than 140 QTLs for stripe rust resistance in wheat. It is likely that many of these QTLs are identical genes that have been spread through plant breeding into diverse backgrounds through phenotypic selection under stripe rust epidemics. Allelism testing can be used to differentiate genes in similar locations but in different genetic backgrounds; however, this is problematic for QTL studies where multiple loci segregate from any one parent. This review utilizes consensus maps to illustrate important genomic regions that have had effects against stripe rust in wheat, and although this methodology cannot distinguish alleles from closely linked genes, it does highlight the extent of genetic diversity for this trait and identifies the most valuable loci and the parents possessing them for utilization in breeding programs. With the advent of cheaper, high throughput genotyping technologies, it is envisioned that there will be many more publications in the near future describing ever more QTLs. This review sets the scene for the coming influx of data and will quickly enable researchers to identify new loci in their given populations.

QTL analysis of the spring wheat "Chapio" identifies stable stripe rust resistance despite inter-continental genotype × environment interactions

Chapio is a spring wheat developed by CIMMYT in Mexico by a breeding program that focused on multigenic resistances to leaf rust and stripe rust. A population consisting of 277 recombinant inbred lines (RILs) was developed by crossing Chapio with Avocet. The RILs were genotyped with DArT markers (137 randomly selected RILs) and bulked segregant analysis conducted to supplement the map with informative SSR markers. The final map consisted of 264 markers. Phenotyping against stripe rust was conducted for three seasons in Toluca, Mexico and at three sites over two seasons (total of four environments) in Sichuan Province, China. Significant loci across the two inter-continental regions included Lr34/Yr18 on 7DS, Sr2/Yr30 on 3BS, and a QTL on 3D. There were significant genotype × environment interactions with resistance gene Yr31 on 2BS being effective in most of the Toluca environments; however, a late incursion of a virulent pathotype in 2009 rendered this gene ineffective. This locus also had no effect in China. Conversely, a 5BL locus was only effective in the Chinese environments. There were also complex additive interactions. In the Mexican environments, Yr31 suppressed the additive effect of Yr30 and the 3D locus, but not of Lr34/Yr18, while in China, the 3D and 5BL loci were generally not additive with each other, but were additive when combined with other loci. These results indicate the importance of maintaining diverse, multi-genic resistances as Chapio had stable inter-continental resistance despite the fact that there were QTLs that were not effective in either one or the other region.

Stripe rust resistance genes in the UK winter wheat cultivar Claire

Stripe rust resistance in the winter wheat cultivar Claire had remained effective in the UK and Europe since its release in 1999 and consequently has been used extensively in wheat breeding programs. However, in 2012, reports indicated that this valuable resistance may now have been compromised. To characterise stripe rust resistance in Claire and determine which genes may still confer effective resistance a cross was made between Claire and the stripe rust susceptible cultivar Lemhi. A genetic linkage map, constructed using SSR, AFLP, DArT and NBS-AFLP markers had a total map length of 1,730 cM. To improve the definition of two quantitative trait loci (QTL) identified on the long arm of chromosome 2D further markers were developed from wheat EST. Stripe rust resistance was evaluated on adult plants under field and glasshouse conditions by measuring the extent of fungal growth and sporulation, percentage infection (Pi) and the necrotic/chlorotic responses of the plant to infection, infection type (IT). Four QTL contributing to stripe rust adult plant resistance (APR) were identified in Claire, QYr.niab-2D.1, QYr.niab-2D.2, QYr.niab-2B and QYr.niab-7B. For Pi QYr.niab-2D.1 explained up to 25.4 % of the phenotypic variation, QYr.niab-2D.2 up to 28.7 %, QYr.niab-2B up to 21.7 % and QYr.niab-7B up to 13.0 %. For IT the percentages of phenotypic variation explained were 23.4, 31.8, 17.2 and 12.6 %, respectively. In addition to the four QTL conferring APR in Claire, a race-specific, seedling expressed resistance gene was identified on chromosome 3B.

Genetic Analysis of Adult Plant Resistance to Yellow Rust and Leaf Rust in Common Spring Wheat Quaiu 3

Identifying and utilizing rust resistance genes in wheat has been hampered by the continuous and rapid emergence of new pathogen races. A major focus of many wheat breeding programs is achieving durable adult plant resistance (APR) to yellow (stripe) rust (YR) and leaf (brown) rust (LR), caused by Puccinia striiformis and P. triticina, respectively. This study aimed to determine the genetic basis of resistance to YR and LR in the common spring wheat 'Quaiu 3'. To that end, we evaluated 198 F₅ recombinant inbred lines (RILs), derived from a cross of susceptible 'Avocet-YrA' with Quaiu 3, for APR to LR and YR in artificially inoculated field trials conducted in Mexico during the 2009 and 2010 growing seasons. High narrow-sense heritability (h²) estimates, ranging between 0.91 and 0.95, were obtained for both LR and YR disease severities for both years. The quantitative and qualitative approaches used to estimate gene numbers showed that, in addition to known resistance genes, there are at least two to three APR genes associated with LR and YR resistance in the RIL population. The moderately effective race-specific resistance gene Lr42 and the pleiotropic slow-rusting APR gene Lr46/Yr29 were found to interact with additional unidentified APR genes. The unidentified APR genes should be of particular interest for further characterization through molecular mapping, and for utilization by wheat breeding programs.

QTL mapping of adult-plant resistance to stripe rust in a population derived from common wheat cultivars Naxos and Shanghai 3/Catbird

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a severe foliar disease of common wheat (Triticum aestivum L.) worldwide. Use of adult-plant resistance (APR) is an efficient approach to provide long-term protection of crops from the disease. The German spring wheat cultivar Naxos showed a high level of APR to stripe rust in the field. To identify the APR genes in this cultivar, a mapping population of 166 recombinant inbred lines (RILs) was developed from a cross between Naxos and Shanghai 3/Catbird (SHA3/CBRD), a moderately susceptible line developed by CIMMYT. The RILs were evaluated for maximum disease severity (MDS) in Sichuan and Gansu in the 2009-2010 and 2010-2011 cropping seasons. Composite interval mapping (CIM) identified four QTL, QYr.caas-1BL.1RS, QYr.caas-1DS, QYr.caas-5BL.3 and QYr.caas-7BL.1, conferring stable resistance to stripe rust across all environments, each explaining 1.9-27.6, 2.1-5.8, 2.5-7.8 and 3.7-9.1 % of the phenotypic variance, respectively. QYr.caas-1DS flanked by molecular markers XUgwm353-Xgdm33b was likely a new QTL for APR to stripe rust. Because the interval between flanking markers for each QTL was less than 6.5 cM, these QTL and their closely linked markers are potentially useful for improving resistance to stripe rust in wheat breeding.

Identification of adult plant resistance to stripe rust in the wheat cultivar Cappelle-Desprez

Following the appearance of stripe rust in South Africa in 1996, efforts have been made to identify new sources of durable resistance. The French cultivar Cappelle-Desprez has long been considered a source of durable, adult plant resistance (APR) to stripe rust. As Cappelle-Desprez contains the seedling resistance genes Yr3a and Yr4a, wheat lines were developed from which Yr3a and Yr4a had been removed, while selecting for Cappelle-Desprez derived APR effective against South African pathotypes of the stripe rust fungus, Puccinia striiformis f. sp. tritici. Line Yr16DH70, adapted to South African wheat growing conditions, was selected and crossed to the stripe rust susceptible cultivar Palmiet to develop a segregating recombinant inbred line mapping population. A major effect QTL, QYr.ufs-2A was identified on the short arm of chromosome 2A derived from Cappelle-Desprez, along with three QTL of smaller effect, QYr.ufs-2D, QYr.ufs-5B and QYr.ufs-6D. QYr.ufs-2D was located within a region on the short arm of chromosome 2D believed to be the location of the stripe rust resistance gene Yr16. An additional minor effect QTL, QYr.ufs-4B, was identified in the cv. Palmiet. An examination of individual RILs carrying single or combinations of each QTL indicated significant resistance effects when QYr.ufs-2A was combined with the three minor QTL from Cappelle-Desprez, and between QYr.ufs-2D and QYr.ufs-5B.

Characterization of a major QTL for adult plant resistance to stripe rust in US soft red winter wheat

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of soft red winter wheat in the eastern region of the USA. Pioneer 26R61 has provided effective resistance to stripe rust for 10 years. To elucidate the genetic basis of the resistance, a mapping population of 178 recombinant inbred lines (RILs) was developed using single-seed descent from a cross between Pioneer 26R61 and the susceptible cultivar AGS 2000. A genetic map with 895 markers covering all 21 chromosomes was used for QTL analysis. One major QTL was detected, explaining up to 56.0% of the mean phenotypic variation, flanked by markers Xbarc124 and Xgwm359, and assigned to the distal 22% of the short arm of wheat chromosome 2A. Evidence showed that it was different from Yr17 derived from Ae. ventricosa, the only formally named Yr gene in 2AS, and the QTL was temporarily designated as YrR61. In addition, a minor QTL, QYr.uga-6AS, probably conditioned high-temperature adult plant resistance. The QTL explained 6-7% of the trait variation. Preliminary test of the flanking markers for YrR61, in two cultivars and two promising breeding lines with Pioneer 26R61 in their pedigree, indicated that YrR61 was present in these cultivars and lines, and these markers could therefore be used in marker-assisted selection.

The genetic characterisation of stripe rust resistance in the German wheat cultivar Alcedo

Stripe rust resistance in the German winter wheat cv. Alcedo has been described as durable, the resistance having remained effective when grown extensively in Germany and Eastern Europe between 1975 and 1989. Genetic characterisation of field resistance in a cross between Alcedo and the stripe rust susceptible UK winter wheat cv. Brigadier identified two major QTL in Alcedo located on the long arms of chromosomes 2D (QPst.jic-2D) and 4B (QPst.jic-4B). Stripe rust resistance was evaluated by measuring the extent of fungal growth, percentage infection (Pi) and the necrotic/chlorotic response of the plant to infection, infection type (IT). Both QPst.jic-2D and QPst.jic-4B contributed significantly to the reduction in stripe rust infection (Pi), with QPst.jic-2D explaining up to 36.20% and QPst.jic-4B 28.90% of the phenotypic variation measured for Pi. Both QTL were identified by the IT phenotypic scores, with QPst.jic-2D in particular being associated with a strong necrotic phenotype (low IT), QPst.jic-2D explaining up to 53.10% of IT phenotypic variation and QPst.jic-4B 22.30%. In addition, two small effect QTL for field stripe rust resistance were identified in Brigadier, QPst.jic-1B on the long arm of chromosome 1B and QPst.jic-5A on the short arm of chromosome 5A. The influence of QPst.jic-1B was primarily seen with the Pi phenotype, contributing up to 13.10% of the explained phenotypic variation. QPst.jic-5A was only detected using an approximate multiple-QTL model and selecting markers linked to the major effect QTL, QPst.jic-2D and QPst.jic-4B as co-factors. Seedling stripe rust resistance was also mapped in the cross, which confirmed the location of Yr17 from Brigadier to the short arm of chromosome 2A. A seedling expressed QTL was also located in Alcedo that mapped to the same location as the field stripe rust resistance QPst.jic-2D.

Lr34 multi-pathogen resistance ABC transporter: molecular analysis of homoeologous and orthologous genes in hexaploid wheat and other grass species

The Triticum aestivum (bread wheat) disease resistance gene Lr34 confers durable, race non-specific protection against three fungal pathogens, and has been a highly relevant gene for wheat breeding since the green revolution. Lr34, located on chromosome 7D, encodes an ATP-binding cassette (ABC) transporter. Both wheat cultivars with and without Lr34-based resistance encode a putatively functional protein that differ by only two amino acid polymorphisms. In this study, we focused on the identification and characterization of homoeologous and orthologous Lr34 genes in hexaploid wheat and other grasses. In hexaploid wheat we found an expressed and putatively functional Lr34 homoeolog located on chromosome 4A, designated Lr34-B. Another homoeologous Lr34 copy, located on chromosome 7A, was disrupted by the insertion of repetitive elements. Protein sequences of LR34-B and LR34 were 97% identical. Orthologous Lr34 genes were detected in the genomes of Oryza sativa (rice) and Sorghum bicolor (sorghum). Zea mays (maize), Brachypodium distachyon and Hordeum vulgare (barley) lacked Lr34 orthologs, indicating independent deletion of this particular ABC transporter. Lr34 was part of a gene-rich island on the wheat D genome. We found gene colinearity on the homoeologous A and B genomes of hexaploid wheat, but little microcolinearity in other grasses. The homoeologous LR34-B protein and the orthologs from rice and sorghum have the susceptible haplotype for the two critical polymorphisms distinguishing the LR34 proteins from susceptible and resistant wheat cultivars. We conclude that the particular Lr34-haplotype found in resistant wheat cultivars is unique. It probably resulted from functional gene diversification that occurred after the polyploidization event that was at the origin of cultivated bread wheat.

Identification of genomic regions controlling adult-plant stripe rust resistance in Chinese landrace Pingyuan 50 through bulked segregant analysis

ABSTRACT Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars with adult-plant resistance (APR) is an effective approach for the control of the disease. In this study, 540 simple sequence repeat markers were screened to map quantitative trait loci (QTL) for APR to stripe rust in a doubled haploid (DH) population of 137 lines derived from the cross Pingyuan 50 x Mingxian 169. The DH lines were planted in randomized complete blocks with three replicates in Gansu and Sichuan provinces during the 2005-06, 2006-07, and 2007-08 cropping seasons, providing data for four environments. Artificial inoculations were carried out in Gansu and Sichuan with the prevalent Chinese race CYR32. Broad-sense heritability of resistance to stripe rust for maximum disease severity was 0.91, based on the mean value averaged across four environments. Inclusive composite interval mapping detected three QTL for APR to stripe rust on chromosomes 2BS, 5AL, and 6BS, designated QYr.caas-2BS, QYr.caas-5AL, and QYr.caas-6BS, respectively, separately explaining from 4.5 to 19.9% of the phenotypic variation. QYr.caas-5AL, different from QTL previously reported, was flanked by microsatellite markers Xwmc410 and Xbarc261, and accounted for 5.0 to 19.9% of phenotypic variance. Molecular markers closely linked to the QTL could be used in marker-assisted selection for APR to stripe rust in wheat breeding programs.

QTL mapping for adult-plant resistance to stripe rust in Italian common wheat cultivars Libellula and Strampelli

Italian common wheat cultivars Libellula and Strampelli, grown for over three decades in Gansu province of China, have shown effective resistance to stripe rust. To elucidate the genetic basis of the resistance, F(3) populations were developed from crosses between the two cultivars and susceptible Chinese wheat cultivar Huixianhong. The F(3) lines were evaluated for disease severity in Beijing, Gansu and Sichuan from 2005 to 2008. Joint- and single-environment analyses by composite interval mapping identified five quantitative trait loci (QTLs) in Libellula for reduced stripe rust severity, designated QYr.caas-2DS, QYr.caas-4BL, QYr.caas-5BL.1, QYr.caas-5BL.2 and QYr.caas-7DS, and explained 8.1-12.4, 3.6-5.1, 3.4-8.6, 2.6 and 14.6-35.0%, respectively, of the phenotypic variance across four environments. Six interactions between different pairs of QTLs explained 3.2-7.1% of the phenotypic variance. The QTLs QYr.caas-4BL, QYr.caas-5BL.1 and QYr.caas-7DS were also detected in Strampelli, explaining 4.5, 2.9-5.5 and 17.1-39.1% of phenotypic variance, respectively, across five environments. Three interactions between different pairs of QTLs accounted for 6.1-35.0% of the phenotypic variance. The QTL QYr.caas-7DS flanked by markers csLV34 and Xgwm295 showed the largest effect for resistance to stripe rust. Sequence analyses confirmed that the lines with the QYr.caas-7DS allele for resistance carried the resistance allele of the Yr18/Lr34 gene. Our results indicated that the adult-plant resistance gene Yr18 and several minor genes confer effective durable resistance to stripe rust in Libellula and Strampelli.

Characterization of genetic components involved in durable resistance to stripe rust in the bread wheat 'Renan'

Stripe rust, caused by Puccinia striiformis f. tritici, is one of the most widespread and destructive wheat diseases in areas where cool temperatures prevail. The wheat cv. Renan, carrying the specific gene Yr17, has shown effective resistance for a long time, even though some pathotypes overcame the Yr17 gene. The objectives of this study were to locate and map genetic loci associated with adult-plant resistance (APR) to stripe rust in a recombinant inbred line population derived from a cross between Renan (resistant) and Récital (susceptible). Field assays were performed for 4 years (1995, 1996, 2005, and 2006) to score disease-progress data and identify APR quantitative trait loci (QTLs). Three QTLs, QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B, with resistance alleles derived from Renan were detected in 1995 to 1996 with the 237E141 pathotype, which is avirulent against genotypes carrying Yr17. These QTLs were stable and explained a major part of the phenotypic variation seen in 2005 to 2006, when the 237E141 V17 pathotype was used. Each of these QTLs contributed approximately 4 to 15% of the phenotypic variance and was effective at different adult plant stages. Interactions were observed between some markers of the Yr17 gene and three Renan QTLs: QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B. Resistance based on the combination of different APR types should provide durable resistance to P. striiformis.

A novel homeobox-like gene associated with reaction to stripe rust and powdery mildew in common wheat

Stripe rust and powdery mildew, caused by Puccinia striiformis f. sp. tritici and Blumeria graminis f. sp. tritici, respectively, are severe diseases in wheat (Triticum aestivum) worldwide. In our study, differential amplification of a 201-bp cDNA fragment was obtained in a cDNA-amplified fragment length polymorphism (AFLP) analysis between near-isogenic lines Yr10NIL and Avocet S, inoculated with P. striiformis f. sp. tritici race CYR29. A full-length cDNA (1,357 bp) of a homeobox-like gene, TaHLRG (GenBank accession no. EU385606), was obtained in common wheat based on the sequence of GenBank accession AW448633 with high similarity to the above fragment. The genomic DNA sequence (2,396 bp) of TaHLRG contains three exons and two introns. TaHLRG appeared to be a novel homeobox-like gene, encoding a protein with a predicted 66-amino-acid homeobox domain. It was involved in race-specific responses to stripe rust in real-time quantitative polymerase chain reaction (PCR) analyses with Yr9NIL, Yr10NIL, and Avocet S. It was also associated with adult-plant resistance to stripe rust and powdery mildew based on the field trials of doubled haploid lines derived from the cross Bainong 64/Jingshuang 16 and two F(2:3) populations from the crosses Lumai 21/Jingshuang 16 and Strampelli/Huixianhong. A functional marker, THR1 was developed based on the sequence of TaHLRG and located on chromosome 6A using a set of Chinese Spring nulli-tetrasomic lines.

QTL identification and microphenotype characterisation of the developmentally regulated yellow rust resistance in the UK wheat cultivar Guardian

Yellow rust (causal agent: Puccinia striiformis f.sp. tritici) resistance in the UK wheat cultivar Guardian is developmentally regulated, resistance increasing as the plant matures. Yellow rust resistance was assessed under field conditions on plants after ear emergence to ensure maximum expression of resistance. Three quantitative trait loci (QTL) for yellow rust resistance were identified, being located on chromosomes 1B (QPst.jic-1B), 2D (QPst.jic-2D) and 4B (QPst.jic-4B). The largest resistance effect, QPst.jic-1B located to the same position on the long arm of chromosome 1B as the known durable source of yellow rust resistance, Yr29. Microscopic studies were carried out to determine what effect the resistance in Guardian had on the development of P. striiformis f.sp. tritici. While the adult plant resistance in Guardian did not prevent germinated urediniospores from establishing an effective infection site, the growth of hyphae within flag leaf tissue was significantly inhibited, slowing the development of microcolonies. 3,3-diaminabenzadine (DAB) and trypan blue staining indicated that this inhibition of hyphal growth was not associated with hydrogen peroxide accumulation or extensive plant cell death.

Quantitative trait loci for high-temperature adult-plant and slow-rusting resistance to Puccinia striiformis f. sp. tritici in wheat cultivars

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most damaging diseases of wheat (Triticum aestivum) globally. High-temperature adult-plant resistance (HTAPR) and slow-rusting have great potential for sustainable management of the disease. The wheat cultivars Luke and Aquileja have been previously reported to possess HTAPR and slow-rusting to stripe rust, respectively. Aquileja displayed less number of stripes per unit leaf area than Luke, while Luke showed lower infection type than Aquileja at adult-plant stages of growth under high-temperature conditions. The objectives of this study were to confirm the resistances and to map the resistance genes in Luke and Aquileja. Luke was crossed with Aquileja, and 326 of the F(2) plants were genotyped using 282 microsatellite primer pairs. These F(2) plants and their derived F(3) families were evaluated for resistance to stripe rust by inoculation in the fields and greenhouses of high- and low-temperatures. Infection type was recorded for both seedlings and adult plants, and stripe number was recorded for adult plants only. Two quantitative trait loci (QTL) were identified, on the short arm of chromosome 2B, to be significantly associated with infection type at adult-plant stages in the fields and in the high-temperature greenhouse. The locus distal to centromere, referred to as QYrlu.cau-2BS1, and the locus proximal to centromere, referred to as QYrlu.cau-2BS2, were separated by a genetic distance of about 23 cM. QYrlu.cau-2BS1 was flanked by the microsatellite markers Xwmc154 and Xgwm148, and QYrlu.cau-2BS2 was flanked by Xgwm148 and Xabrc167. QYrlu.cau-2BS1 and QYrlu.cau-2BS2 explained up to 36.6 and 41.5% of the phenotypic variation of infection type, respectively, and up to 78.1% collectively. No significant interaction between the two loci was detected. Another QTL, referred to as QYraq.cau-2BL, was detected on the long arm of chromosome 2B to be significantly associated with stripe number. QYraq.cau-2BL was flanked by the microsatellite markers Xwmc175 and Xwmc332, and it explained up to 61.5% of the phenotypic variation of stripe number. It is possible that these three QTL are previously unmapped loci for resistance to stripe rust.

Quantitative trait loci for slow-rusting resistance in wheat to leaf rust and stripe rust identified with multi-environment analysis

Rust diseases are a major cause of yield loss in wheat worldwide, and are often controlled through the incorporation of resistance genes using conventional phenotypic selection methods. Slow-rusting resistance genes are expressed quantitatively and are typically small in genetic effect thereby requiring multiple genes to provide adequate protection against pathogens. These effects are valuable and are generally considered to confer durable resistance. Therefore an understanding of the chromosomal locations of such genes and their biological effects are important in order to ensure they are suitably deployed in elite germplasm. Attila is an important wheat grown throughout the world and is used as a slow-rusting donor in international spring wheat breeding programs. This study identified chromosomal regions associated with leaf rust and stripe rust resistances in a cross between Attila and a susceptible parent, Avocet-S, evaluated over 3 years in the field. Genotypic variation for both rusts was large and repeatable with line-mean heritabilities of 94% for leaf rust resistance and 87% for stripe rust. Three loci, including Lr46/Yr29 on chromosome 1BL, were shown to provide resistance to leaf rust whereas six loci with small effects conferred stripe rust resistance, with a seventh locus having an effect only by epistasis. Disease scoring over three different years enabled inferences to be made relating to stripe rust pathogen strains that predominated in different years.

Histopathology and PR-protein markers provide insight into adult plant resistance to stripe rust of wheat

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a serious disease of wheat. The spring wheat cultivar Kariega expresses complete adult plant resistance to stripe rust, whereas Avocet S is susceptible. In former studies, quantitative trait loci (QTL) analysis of doubled haploid lines derived from a Kariega x Avocet S cross revealed two major QTL (QYr.sgi-7D and QYr.sgi-2B.1) and two minor QTL (QYr.sgi-1A and QYr.sgi-4A.1) responsible for the adult resistance of Kariega in the field. Avocet S contains none of these QTL. In the present study, stripe rust development was compared, by means of fluorescence and confocal laser scanning microscopy, in flag leaves of Kariega, Avocet S and six doubled haploid (DH) lines, containing all four, none or one QTL. Depending on the QTL present, the infection types of the DH lines ranged from resistant to fully susceptible. No differences in fungal growth were observed during the first 5 days post inoculation (dpi), whereas the mean length of the fungal colonies started to differ at 6 dpi. Interestingly, MP 51 carrying QYr.sgi-7D responded with lignification to the fungal growth without restricting it, whereas MP 35 containing QYr.sgi-2B.1 did not show lignified host tissue, but fungal growth was restricted. RT PCR experiments with sequences of pathogenesis-related (PR) proteins resulted in a slightly stronger induction of PR 1, 2 and 5, known markers for the hypersensitive reaction, and peroxidases in MP 51, whereas a second band for chitinases was detected in MP 35 only.

Adult plant resistance-related gene expression in 'Camp Remy' wheat inoculated with Puccinia striiformis

The French wheat variety 'Camp Remy' (CR) possesses a durable, adult plant resistance to yellow rust (YR), caused by the pathogen Puccinia striiformis. Using cDNA-AFLP on different sets of heterogeneous inbred families (HIFs) derived from the cross CR x Récital, we compared gene expression profiles during one seedling and two adult developmental stages following inoculation with P. striiformis. Transcripts differentially expressed in response to YR infection were isolated and cloned. Sequence analysis of the resultant clones revealed several classes of putative genes, including those related to resistance/defence responses, transcription and signal transduction, and primary metabolism. The expression profiles of seven selected genes were obtained using real-time PCR in CR leaves at the same three stages of development. The results confirmed the stage-specific expression of the genes at one or two specific stages in response to P. striiformis infection and demonstrated that CR modifies the expression of some resistance/defence-related genes during its transition from the seedling to adult growth stages. These results provided the first clue to understand the molecular basis of quantitative trait loci for adult plant resistance to YR and connect it with durability.

Challenges for sustainable cereal rust control in South Africa

The cultivation of small grain cereals was introduced to South Africa by Dutch settlers in the 17th Century. According to historical records the first documented epidemic of wheat stem rust occurred in the south-western parts of the current Western Cape in 1726. Recurring stem and leaf rust epidemics were associated with expanding wheat production and became particularly severe in the winter-rainfall regions of the Western and Eastern Cape, as well as in the summer-rainfall regions of the Free State. The wheat stripe rust pathogen was first detected in South Africa in 1996. Due to susceptibility of cultivars at the time of this exotic introduction, stripe rust has caused significant losses in commercial wheat production over the past 10 years. Pathotype surveys of Puccinia graminis and P. triticina were initiated in the 1920s, but were discontinued until research on wheat stem rust was resumed in the 1960s. Recent evidence has shown that P. graminis f. sp. tritici continues to evolve. In addition, the annual number of wheat stem rust collections is increasing, emphasising the sustained threat of this damaging pathogen. A stem rust pathotype first detected in 2000, with newly acquired virulence for Sr8b and Sr38, currently constitutes more than 80% of all collections. Leaf and stem rust diseases also occur on barley, oat, triticale, and rye and are important production constraints in several regions. Some studies have described variability in these pathogens but long-term records of pathogenicity changes in barley and oat rust are not available. Cereal rust diseases have clearly played an important role in South African agriculture and many production regions remain favourable for rust development. Current expertise in cereal rusts covers most technologies necessary to study the respective host–pathogen systems. However, a general lack of capacity and fragmentation of research groups prevent a unified approach and remain a challenge for sustainable cereal rust control in South Africa. A national strategy for cereal rust control, with particular emphasis on pathogen and host resources, and breeding for resistance, is urgently needed.

High-temperature adult-plant (HTAP) stripe rust resistance gene Yr36 from Triticum turgidum ssp. dicoccoides is closely linked to the grain protein content locus Gpc-B1

Several new races of the stripe rust pathogen have become frequent throughout the wheat growing regions of the United States since 2000. These new races are virulent to most of the wheat seedling resistance genes limiting the resistance sources that can be used to combat this pathogen. High-temperature adult-plant (HTAP) stripe rust resistance has proven to be more durable than seedling resistance due to its non-race-specific nature, but its use is limited by the lack of mapping information. We report here the identification of a new HTAP resistance gene from Triticum turgidum ssp. dicoccoides (DIC) designated as Yr36. Lines carrying this gene were susceptible to almost all the stripe rust pathogen races tested at the seedling stage but showed adult-plant resistance to the prevalent races in California when tested at high diurnal temperatures. Isogenic lines for this gene were developed by six backcross generations. Field tests in two locations showed increased levels of field resistance to stripe rust and increased yields in isogenic lines carrying the Yr36 gene compared to those without the gene. Recombinant substitution lines of chromosome 6B from DIC in the isogenic background of durum cv. Langdon were used to map the Yr36 gene on the short arm of chromosome 6B completely linked to Xbarc101, and within a 2-cM interval defined by PCR-based markers Xucw71 and Xbarc136. Flanking locus Xucw71 is also closely linked to the grain protein content locus Gpc-B1 (0.3-cM). Marker-assisted selection strategies are presented to improve stripe rust resistance and simultaneously select for high or low Gpc-B1 alleles.

Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat

The incorporation of effective and durable disease resistance is an important breeding objective for wheat improvement. The leaf rust resistance gene Lr34 and stripe rust resistance gene Yr18 are effective at the adult plant stage and have provided moderate levels of durable resistance to leaf rust caused by Puccinia triticina Eriks. and to stripe rust caused by Puccinia striiformis Westend. f. sp. tritici. These genes have not been separated by recombination and map to chromosome 7DS in wheat. In a population of 110 F(7) lines derived from a Thatcher x Thatcher isogenic line with Lr34/Yr18, field resistance to leaf rust conferred by Lr34 and to stripe rust resistance conferred by Yr18 cosegregated with adult plant resistance to powdery mildew caused by Blumeria graminis (DC) EO Speer f. sp. tritici. Lr34 and Yr18 were previously shown to be associated with enhanced stem rust resistance and tolerance to barley yellow dwarf virus infection. This chromosomal region in wheat has now been linked with resistance to five different pathogens. The Lr34/Yr18 phenotypes and associated powdery mildew resistance were mapped to a single locus flanked by microsatellite loci Xgwm1220 and Xgwm295 on chromosome 7DS.