Microsatellite mapping of the powdery mildew resistance gene Pm5e in common wheat (Triticum aestivum L.)

QTL Mapping of Adult Plant Resistance to Powdery Mildew in Chinese Wheat Landrace Baidatou

Wheat powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is one of the most devastating diseases affecting wheat throughout the world. Breeding and growing resistant wheat cultivars is one of the most economic and effective methods to control the disease, and as such, identifying and mapping the new and effective resistance genes is critical. Baidatou, a Chinese wheat landrace, shows excellent field resistance to powdery mildew. To identify the resistance gene(s) in Baidatou, 170 F7:8 recombinant inbred lines (RILs) derived from the cross Mingxian 169/Baidatou were evaluated for powdery mildew response at the adult-plant stage in the experimental fields in Yangling (YL) of Shaanxi Province and Tianshui (TS) in Gansu Province in 2019, 2020, and 2021. The relative area under disease progress curve (rAUDPC) of Mingxian 169/Baidatou F7:8 RILs indicated that the resistance of Baidatou to powdery mildew was controlled by quantitative trait loci (QTLs). Based on bulk segregation analysis combined with the 660K single nucleotide polymorphism (SNP) array and genotyping by target sequencing (16K SNP) of the entire RIL population, two QTLs, QPmbdt.nwafu-2AS and QPmbdt.nwafu-3AS, were identified, and these accounted for up to 44.5% of the phenotypic variation. One of the QTLs was located on the 3.32 cM genetic interval on wheat chromosome 2AS between the kompetitive allele-specific PCR markers AX-111012288 and AX_174233809, and another was located on the 9.6 cM genetic interval on chromosome 3AS between the SNP markers 3A_684044820 and 3A_686681822. These markers could be useful for successful breeding of powdery mildew resistance in wheat.

Characterization of the powdery mildew resistance locus in wheat breeding line Jimai 809 and its breeding application

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a severe disease that affects the yield and quality of wheat. Popularization of resistant cultivars in production is the preferred strategy to control this disease. In the present study, the Chinese wheat breeding line Jimai 809 showed excellent agronomic performance and high resistance to powdery mildew at the whole growth stage. To dissect the genetic basis for this resistance, Jimai 809 was crossed with the susceptible wheat cultivar Junda 159 to produce segregation populations. Genetic analysis showed that a single dominant gene, temporarily designated PmJM809, conferred the resistance to different Bgt isolates. PmJM809 was then mapped on the chromosome arm 2BL and flanked by the markers CISSR02g-1 and CIT02g-13 with genetic distances 0.4 and 0.8 cM, respectively, corresponding to a physical interval of 704.12-708.24 Mb. PmJM809 differed from the reported Pm genes on chromosome arm 2BL in origin, resistance spectrum, physical position and/or genetic diversity of the mapping interval, also suggesting PmJM809 was located on a complex interval with multiple resistance genes. To analyze and screen the candidate gene(s) of PmJM809, six genes related to disease resistance in the candidate interval were evaluated their expression patterns using an additional set of wheat samples and time-course analysis post-inoculation of the Bgt isolate E09. As a result, four genes were speculated as the key candidate or regulatory genes. Considering its comprehensive agronomic traits and resistance findings, PmJM809 was expected to be a valuable gene resource in wheat disease resistance breeding. To efficiently transfer PmJM809 into different genetic backgrounds, 13 of 19 closely linked markers were confirmed to be suitable for marker-assisted selection. Using these markers, a series of wheat breeding lines with harmonious disease resistance and agronomic performance were selected from the crosses of Jimai 809 and several susceptible cultivars.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01467-8.

Fighting wheat powdery mildew: from genes to fields

KEY MESSAGE

Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.

Characterization and identification of the powdery mildew resistance gene in wheat breeding line ShiCG15-009

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious fungal disease that critically threatens the yield and quality of wheat. Utilization of host resistance is the most effective and economical method to control this disease. In our study, a wheat breeding line ShiCG15-009, released from Hebei Province, was highly resistant to powdery mildew at all stages. To dissect its genetic basis, ShiCG15-009 was crossed with the susceptible cultivar Yannong 21 to produce F₁, F₂ and F_2:3 progenies. After genetic analysis, a single dominant gene, tentatively designated PmCG15-009, was proved to confer resistance to Bgt isolate E09. Further molecular markers analysis showed that PmCG15-009 was located on chromosome 2BL and flanked by markers XCINAU130 and XCINAU143 with the genetic distances 0.2 and 0.4 cM, respectively, corresponding to a physic interval of 705.14-723.48 Mb referred to the Chinese Spring reference genome sequence v2.1. PmCG15-009 was most likely a new gene differed from the documented Pm genes on chromosome 2BL since its different origin, genetic diversity, and physical position. To analyze and identify the candidate genes, six genes associated with disease resistance in the candidate interval were confirmed to be associated with PmCG15-009 via qRT-PCR analysis using the parents ShiCG15-009 and Yannong 21 and time-course analysis post-inoculation with Bgt isolate E09. To accelerate the transfer of PmCG15-009 using marker-assisted selection (MAS), 18 closely or co-segregated markers were evaluated and confirmed to be suitable for tracing PmCG15-009, when it was transferred into different wheat cultivars.

Identification of a Wheat Powdery Mildew Dominant Resistance Gene in the Pm5 Locus for High-Throughput Marker-Assisted Selection

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), poses a severe threat to wheat yield and quality worldwide. Rapid identification and the accurate transference of effective resistance genes are important to the development of resistant cultivars and the sustainable control of this disease. In the present study, the wheat line AL11 exhibited high levels of resistance to powdery mildew at both the seedling and adult plant stages. Genetic analysis of the AL11 × 'Shixin 733' mapping population revealed that its resistance was controlled by a single dominant gene, tentatively designated PmAL11. Using bulked segregant RNA-Seq and molecular marker analysis, PmAL11 was mapped to the Pm5 locus on chromosome 7B where it cosegregated with the functional marker Pm5e-KASP. Sequence alignment analysis revealed that the Pm5e-homologous sequence in AL11 was identical to the reported recessive gene Pm5e in wheat landrace 'Fuzhuang 30'. It appears that PmAL11 was most probably Pm5e, but it was mediated by a dominant inheritance pattern, so it should provide a valuable resistance resource for both genetic study and wheat breeding. To efficiently use and trace PmAL11 in breeding, a new kompetitive allele-specific PCR marker AL11-K2488 that cosegregated with this gene was developed and confirmed to be applicable in the different wheat backgrounds, thus promoting its use in the marker-assisted selection of PmAL11.

The Pm5e Gene Has No Negative Effect on Wheat Agronomic Performance: Evidence From Newly Established Near-Isogenic Lines

Wheat genotypes resistant to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) provide a sustainable means for disease control. We developed a pair of near-isogenic lines H962R and H962S with contrasting reactions to powdery mildew from a residue heterozygous line. H962R was resistant to 127 out of the 136 Bgt isolates collected from the major wheat-producing regions of China and showed a similar virulence/avirulence pattern as Fuzhuang 30, Xiaobaidong, and Hongquanmang carrying resistance allele of Pm5e, but H962S was resistant to none of them. A dominant gene was responsible for the powdery mildew resistance of H962R as revealed by the genetic analysis using segregating populations derived from a cross between H962R and H962S. Molecular marker analysis detected a resistance locus, designated PmH962, on a genetic interval of the chromosome arm 7BL where Pm5e resides. This locus was co-segregated with the functional marker of Pm5e. The PCR-based sequence alignment of Pm5e demonstrated that H962R had an identical sequence as Fuzhuang 30 (haplotype HapGA), and H962S possessed the same sequence as the powdery mildew susceptible cultivar Kenong 199. The genomic compositions of lines H962R and H962S were highly comparable as evidenced by only a small percentage of SNP variations detected by the 16K Genotyping by Target Sequencing (GBTS) SNP array and the 90K Illumina iSelect Wheat SNP array. The two lines performed similarly in the yield-related and plant growth traits investigated, except for greater kernel weight in H962R than in H962S. This indicates that Pm5e has no deleterious effect and can be served as an excellent disease resistance gene in wheat breeding.

Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat

Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.

Characterization of PmDGM Conferring Powdery Mildew Resistance in Chinese Wheat Landrace Duanganmang

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is a devastating disease that threatens yield and quality. Host resistance is considered the most effective and preferred means to control this disease. Wheat landrace Duanganmang (DGM) showed high resistance or near immunity to Blumeria graminis f. sp. tritici mixture from Henan Province, China. DGM was crossed with highly susceptible Chinese wheat landrace Huixianhong (HXH) and cultivar 'Shimai 15' (SM15) to produce genetic populations. The resistance of DGM to Blumeria graminis f. sp. tritici isolate E09 was shown to be controlled by a single dominant Mendelian factor, tentatively designated PmDGM. Marker analysis and 55K single nucleotide polymorphism (SNP) array scanning showed that this gene was positioned in the Pm5 interval (2.4 cM or 1.61 Mb) flanked by Xhenu099 and Xmp1158 in the Chinese Spring reference genome. Homology-based cloning and sequence analysis demonstrated that DGM has the identical NLR gene (Pm5e) and RXL gene reported in Fuzhuang 30 (FZ30), conferring and modifying powdery mildew resistance, respectively. However, based on the different reaction patterns to the Blumeria graminis f. sp. tritici isolate B15 between DGM and FZ30, the authors speculate that DGM may have two tightly linked genes that could not be separated in the current mapping population, one of which is PmDGM and the other being Pm5e. Hence, this study provides a valuable resistance resource for improvement of powdery mildew resistance.

Deciphering the genetic diversity and population structure of Turkish bread wheat germplasm using iPBS-retrotransposons markers

BACKGROUND

Research activities aiming to investigate the genetic diversity are very crucial because they provide information for the breeding and germplasm conservation activities. Wheat is one of the most important cereal crops globally by feeding more than a third of the human population around the world.

METHODS AND RESULTS

During present investigation, a total of 74 Turkish bread wheat accessions (54 landraces and 20 cultivars) were used as plant material and iPBS-retrotransposons marker system was used for the molecular characterization. 13 polymorphic primers used for molecular characterization resulted a total of 152 bands. Range of calculated diversity indices like polymorphism information content (0.11-0.702), effective numbers of alleles (1.026-1.526), Shannon's information index (0.101-0.247) and gene diversity (0.098-0.443) confirmed higher genetic variations in studied germplasm. Bread wheat landraces reflected higher genetic variations compared to commercial cultivars. Analysis of molecular variance resulted that higher (98%) genetic variations are present within populations. The model-based structure algorithm separated 74 bread wheat accessions in to two populations. Diversity indices based on structure evaluated population's revealed population B as a more diverse population. The principal coordinate analysis and neighbor-joining analysis separated 74 bread wheat accessions according to their collection points. Genetic distance for 74 Turkish bread wheat accessions explored Bingol and Asure accessions as genetically diverse that can be used as parents for breeding activities.

CONCLUSIONS

The extensive diversity of bread wheat in Turkish germplasm might be used as genetic resource for the exhaustive wheat breeding program. For instance, accessions Bingol and Asure were found genetically diverse and can be used as parents for future breeding activities.

Identification and validation of a novel locus, Qpm-3BL, for adult plant resistance to powdery mildew in wheat using multilocus GWAS

BACKGROUND

Powdery mildew (PM), one of the major diseases in wheat, severely damages yield and quality, and the most economical and effective way to address this issue is to breed disease-resistant cultivars. Accordingly, 371 landraces and 266 released cultivars in Henan Province were genotyped by a 660 K microarray and phenotyped for adult plant resistance (APR) to PM from 2017 to 2020, and these datasets were used to conduct multilocus genome-wide association studies (GWASs).

RESULTS

Thirty-six varieties showed stable APR in all the environments, and eleven quantitative trait nucleotides (QTNs) were found by multiple methods across multiple environments and best linear unbiased prediction (BLUP) values to be significantly associated with APR. Among these stable QTNs, four were previously reported, three were newly discovered in this study, and the others need to be further investigated. The major and newly discovered QTN, Qpm-3BL, was located at chr03BL_AX-109,052,670, while another newly discovered QTN, Qpm-1BL, was located between chr01BL_AX-108,771,002 and chr01BL_AX-110,117,322. Five and eight landraces were identified to be resistant based on Qpm-1BL (haplotype TC) and Qpm-3BL (allele T), respectively. To validate Qpm-3BL, a new kompetitive allele-specific PCR (KASP) marker was developed to scan 155 F₂ individuals, and the average resistance score supported the value of Qpm-3BL in marker-assisted breeding. Near Qpm-3BL, PmBMYD was identified by KEGG, gene expression and comparative genomics analyses to be a candidate. Its resistance mechanism may involve gene tandem repeats.

CONCLUSIONS

This study reveals a previously unknown gene for PM resistance that is available for marker-assisted breeding.

A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat

Powdery mildew poses severe threats to wheat production. The most sustainable way to control this disease is through planting resistant cultivars. We report the map-based cloning of the powdery mildew resistance allele Pm5e from a Chinese wheat landrace. We applied a two-step bulked segregant RNA sequencing (BSR-Seq) approach in developing tightly linked or co-segregating markers to Pm5e. The first BSR-Seq used phenotypically contrasting bulks of recombinant inbred lines (RILs) to identify Pm5e-linked markers. The second BSR-Seq utilized bulks of genetic recombinants screened from a fine-mapping population to precisely quantify the associated genomic variation in the mapping interval, and identified the Pm5e candidate genes. The function of Pm5e was validated by transgenic assay, loss-of-function mutants and haplotype association analysis. Pm5e encodes a nucleotide-binding domain leucine-rich-repeat-containing (NLR) protein. A rare nonsynonymous single nucleotide variant (SNV) within the C-terminal leucine rich repeat (LRR) domain is responsible for the gain of powdery mildew resistance function of Pm5e, an allele endemic to wheat landraces of Shaanxi province of China. Results from this study demonstrate the value of landraces in discovering useful genes for modern wheat breeding. The key SNV associated with powdery mildew resistance will be useful for marker-assisted selection of Pm5e in wheat breeding programs.

Mapping Powdery Mildew Resistance Gene pmYBL on Chromosome 7B of Chinese Wheat (Triticum aestivum L.) Landrace Youbailan

Chinese wheat landrace Youbailan has excellent resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. In the present study, genetic analysis indicated that a recessive gene, tentatively designated pmYBL, was responsible for the powdery mildew resistance of Youbailan. pmYBL was located in the 695-to-715-Mb genomic region of chromosome 7BL, with 19 gene-linked single-nucleotide polymorphism (SNP) markers. It was flanked by SNP1-12 and SNP1-2 with genetic distances of 0.6 and 1.8 centimorgans, respectively. The disease reaction patterns of Youbailan and four cultivars (lines) carrying the powdery mildew (Pm) genes located on chromosome arm 7BL indicated that pmYBL may be allelic or closely linked to these genes. All of the SNP markers linked to pmYBL were diagnostic, indicating that these markers will be useful for pyramiding pmYBL using marker-assisted selection.

Fine-Mapping of the Powdery Mildew Resistance Gene mlxbd in the Common Wheat Landrace Xiaobaidong

Powdery mildew, which is caused by Blumeria graminis f. sp. tritici (Bgt), is a disease of wheat worldwide. Xiaobaidong is a Chinese wheat landrace, which still maintains good resistance against powdery mildew. To obtain more genetic markers closely linked to the powdery mildew resistance gene mlxbd and narrow the candidate region for its isolation, new simple sequence repeats and cross intron-spanning markers were designed based on the genome sequence of Triticum aestivum cultivar Chinese Spring chromosome 7BL. The flanking markers 7BLSSR49 and WGGC5746 were found to be tightly linked to mlxbd at genetic distances of 0.4 cM and 0.3 cM, respectively. The resistance locus was mapped to a 63.40 kb and 0.29 Mb region of the Chinese Spring genome and Zavitan genome, respectively. The linked markers of mlxbd could be used as diagnostic markers for mlxbd. The linked molecular markers and delineated genomic region in the sequenced Chinese Spring genome will assist the future map-based cloning of mlxbd.

Identification of a Recessive Gene PmQ Conferring Resistance to Powdery Mildew in Wheat Landrace Qingxinmai Using BSR-Seq Analysis

Wheat powdery mildew is caused by Blumeria graminis f. sp. tritici (Bgt), a biotrophic fungal species. It is very important to mine new powdery mildew (Pm) resistance genes for developing resistant wheat cultivars to reduce the deleterious effects of the disease. This study was carried out to characterize the Pm gene in Qingxinmai, a winter wheat landrace from Xinjiang, China. Qingxinmai is resistant to many Bgt isolates collected from different wheat fields in China. F₁, F₂, and F_2:3 generations of the cross between Qingxinmai and powdery mildew susceptible line 041133 were developed. It was confirmed that a single recessive gene, PmQ, conferred the seedling resistance to a Bgt isolate in Qingxinmai. Bulked segregant analysis-RNA-Seq (BSR-Seq) was performed on the bulked homozygous resistant and susceptible F_2:3 families, which detected 57 single nucleotide polymorphism (SNP) variants that were enriched in a 40 Mb genomic interval on chromosome arm 2BL. Based on the flanking sequences of the candidate SNPs extracted from the Chinese Spring reference genome, 485 simple sequence repeat (SSR) markers were designed. Six polymorphic SSR markers, together with nine markers that were anchored on chromosome arm 2BL, were used to construct a genetic linkage map for PmQ. This gene was placed in a 1.4 cM genetic interval between markers Xicsq405 and WGGBH913 corresponding to 4.9 Mb physical region in the Chinese Spring reference genome. PmQ differed from most of the other Pm genes identified on chromosome arm 2BL based on its position and/or origin. However, this gene and Pm63 from an Iranian common wheat landrace were located in a similar genomic region, so they may be allelic.

Identification of a New Powdery Mildew Resistance Gene pmDHT at or Closely Linked to the Pm5 Locus in the Chinese Wheat Landrace Dahongtou

Chinese wheat landrace Dahongtou was resistant to 35 of 38 tested Chinese isolates of Blumeria graminis f. sp. tritici at the seedling stage. Genetic analysis of the F₂ populations and their derived F_2:3 families of crosses of Dahongtou with the susceptible varieties Mingxian 169 and Huixianhong indicated that the resistance of Dahongtou to B. graminis f. sp. tritici isolate E09 was conferred by a single recessive gene, tentatively designated as pmDHT. The gene was mapped to chromosome arm 7BL and flanked by markers Xwmc526/XBE443877 and Xgwm611/Xwmc511 at genetic distances of 0.8 and 0.3 cM, respectively. The chromosomal position of pmDHT was similar to the multi-allelic Pm5 locus on 7BL. Allelism tests with crosses of Dahongtou with Fuzhuang 30 (Pm5e) and Xiaobaidong (mlxbd) indicated that pmDHT was allelic to both Pm5e and mlxbd. However, pmDHT showed a different pattern of resistance to the 38 B. graminis f. sp. tritici isolates compared with wheat lines with Pm5a, Pm5b, Pm5e, mlxbd, and PmHYM and also differed from PmSGA. Thus, pmDHT was identified most likely as a new allele or at least a closely linked gene of the Pm5 locus. This gene can be transferred into susceptible wheat cultivars/lines and pyramided with other resistance genes through marker-assisted selection to improve powdery mildew resistance.

Molecular Mapping of a Recessive Powdery Mildew Resistance Gene in Wheat Cultivar Tian Xuan 45 Using Bulked Segregant Analysis with Polymorphic Single Nucleotide Polymorphism Relative Ratio Distribution

Powdery mildew is a destructive foliar disease of wheat worldwide. Wheat cultivar Tian Xuan 45 exhibits resistance to the highly virulent isolate HY5. Genetic analysis of the F₂ and F_2:3 populations of a cultivar Ming Xian 169/Tian Xuan 45 cross revealed that the resistance to HY5 was controlled by a single recessive gene, temporarily designated as PmTx45. A Manhattan plot with the relative frequency distribution of single nucleotide polymorphisms (SNPs) was used to rapidly narrow down the possible chromosomal regions of the associated genes. This microarray-based bulked segregant analysis (BSA) largely improved traditional analytical methods. PmTx45 was located in chromosomal bin 4BL5-0.86-1.00 and was flanked by SNP marker AX-110673642 and intron length polymorphism (ILP) marker ILP-4B01G269900 with genetic distances of 3.0 and 2.6 cM, respectively. Molecular detection in a panel of wheat cultivars using the markers linked to PmTx45 showed that the presence of PmTx45 in commercial wheat cultivars was rare. Resistance spectrum and chromosomal position analyses indicated that PmTx45 may be a novel recessive gene with moderate powdery mildew resistance. This new microarray-based BSA method is feasible and effective and has the potential application for mapping genes in wheat in marker-assisted breeding.

Characterization of Pm63, a powdery mildew resistance gene in Iranian landrace PI 628024

A new powdery mildew resistance gene conferring a wide spectrum of resistance to Bgt isolates in the USA, Pm63 , was identified in Iranian wheat landrace PI 628024 and mapped to the terminal region of the long arm of chromosome 2B. Powdery mildew is a globally important wheat disease causing severe yield losses, and host resistance is the preferred strategy for managing this disease. The objective of this study was to characterize a powdery mildew resistance gene in Iranian landrace PI 628024, which exhibited a wide spectrum of resistance to representative Blumeria graminis f. sp. tritici (Bgt) isolates collected from different regions of the USA. An F₂ population and F_2:3 lines derived from the cross PI 628024 × CItr 11349 were used in this study, and genetic analysis indicated that a single dominant gene, designated Pm63, conferred resistance to Bgt isolate OKS(14)-B-3-1. Linkage analysis located Pm63 to an interval of about 13.1 Mb on the long arm of chromosome 2B, spanning 710.3-723.4 Mb in the Chinese Spring reference sequence. Bin mapping assigned Pm63 to the terminal bin 2BL6-0.89-1.0, 1.1 cM proximal to STS marker Xbcd135-2 and 0.6 cM distal to SSR marker Xstars419. Allelism tests indicated that Pm63 is a new powdery mildew resistance gene, which differs from other genes in the terminal bin by origin, genomic location, and responses to a set of 16 representative US Bgt isolates. Pm63 can be widely used to enhance powdery mildew resistance in the Great Plains, western, and southeastern regions of the USA.

Development of SNP, KASP, and SSR Markers by BSR-Seq Technology for Saturation of Genetic Linkage Map and Efficient Detection of Wheat Powdery Mildew Resistance Gene Pm61

The gene Pm61 that confers powdery mildew resistance has been previously identified on chromosome arm 4AL in Chinese wheat landrace Xuxusanyuehuang (XXSYH). To facilitate the use of Pm61 in breeding practices, the bulked segregant analysis-RNA-Seq (BSR-Seq) analysis, in combination with the information on the Chinese Spring reference genome sequence, was performed in the F_2:3 mapping population of XXSYH × Zhongzuo 9504. Two single nucleotide polymorphism (SNP), two Kompetitive Allele Specific PCR (KASP), and six simple sequence repeat (SSR) markers, together with previously identified polymorphic markers, saturated the genetic linkage map for Pm61, especially in the proximal side of the target gene that was short of gene-linked markers. In the newly established genetic linkage map, Pm61 was located in a 0.71 cM genetic interval and can be detected in a high throughput scale by the KASP markers Xicsk8 and Xicsk13 or by the standard PCR-based markers Xicscx497 and Xicsx538. The newly saturated genetic linkage map will be useful in molecular marker assisted-selection of Pm61 in breeding for disease resistant cultivar and in its map-based cloning.

Dissection of Pleiotropic QTL Regions Controlling Wheat Spike Characteristics Under Different Nitrogen Treatments Using Traditional and Conditional QTL Mapping

Optimal spike characteristics are critical in improving the sink capacity and yield potential of wheat even in harsh environments. However, the genetic basis of their response to nitrogen deficiency is still unclear. In this study, quantitative trait loci (QTL) for six spike-related traits, including heading date (HD), spike length (SL), spikelet number (SN), spike compactness (SC), fertile spikelet number (FSN), and sterile spikelet number (SSN), were detected under two different nitrogen (N) supplies, based on a high-density genetic linkage map constructed by PCR markers, DArTs, and Affymetrix Wheat 660 K SNP chips. A total of 157 traditional QTLand 54 conditional loci were detected by inclusive composite interval mapping, among which three completely low N-stress induced QTL for SN and FSN (qSn-1A.1, qFsn-1B, and qFsn-7D) were found to maintain the desired spikelet fertility and kernel numbers even under N deficiency through pyramiding elite alleles. Twenty-eight stable QTL showing significant differencet in QTL detection model were found and seven genomic regions (R2D, R4A, R4B, R5A, R7A, R7B, and R7D) clustered by these stable QTL were highlighted. Among them, the effect of R4B on controlling spike characteristics might be contributed from Rht-B1. R7A harboring three major stable QTL (qSn-7A.2, qSc-7A, and qFsn-7A.3) might be one of the valuable candidate regions for further genetic improvement. In addition, the R7A was found to show syntenic with R7B, indicating the possibly exsting homoeologous candidate genes in both regions. The SNP markers involved with the above highlighted regions will eventually facilitate positional cloning or marker-assisted selection for the optimal spike characteristics under various N input conditions.

Pm223899, a new recessive powdery mildew resistance gene identified in Afghanistan landrace PI 223899

A new recessive powdery mildew resistance gene, Pm223899, was identified in Afghanistan wheat landrace PI 223899 and mapped to an interval of about 831 Kb in the terminal region of the short arm of chromosome 1A. Wheat powdery mildew, a globally important disease caused by the biotrophic fungus Blumeria graminis f.sp. tritici (Bgt), has occurred with increased frequency and severity in recent years, and some widely deployed resistance genes have lost effectiveness. PI 223899 is an Afghanistan landrace exhibiting high resistance to Bgt isolates collected from the Great Plains. An F₂ population and F_2:3 lines derived from a cross between PI 223899 and OK1059060-126135-3 were evaluated for response to Bgt isolate OKS(14)-B-3-1, and the bulked segregant analysis (BSA) approach was used to map the powdery mildew resistance gene. Genetic analysis indicated that a recessive gene, designated Pm223899, conferred powdery mildew resistance in PI 223899. Linkage analysis placed Pm223899 to an interval of about 831 Kb in the terminal region of chromosome 1AS, spanning 4,504,697-5,336,062 bp of the Chinese Spring reference sequence. Eight genes were predicted in this genomic region, including TraesCS1AG008300 encoding a putative disease resistance protein RGA4. Pm223899 was flanked proximally by a SSR marker STARS333 (1.4 cM) and distally by the Pm3 locus (0.3 cM). One F₂ recombinant was identified between Pm3 and Pm223899 using a Pm3b-specific marker, indicating that Pm223899 is most likely a new gene, rather than an allele of the Pm3 locus. Pm223389 confers a high level of resistance to Bgt isolates collected from Pennsylvania, Oklahoma, Nebraska, and Montana. Therefore, Pm223389 can be used to enhance powdery mildew resistance in these states. Pm3b-1 and STARS333 have the potential to tag Pm223389 in wheat breeding.

Fine mapping of powdery mildew resistance gene Pm4e in bread wheat (Triticum aestivum L.)

Fine mapping of wheat powdery mildew-resistance gene Pm4e to a 0.19 cM interval with sequence-based markers provides the foundation for map-based cloning and marker-assisted selection with breeder-friendly markers. Powdery mildew caused by Blumeria graminis f. sp. tritici is a wheat foliar disease that poses a serious threat to global wheat production. Pm4 is a resistance gene locus that has played a key role in controlling this disease in wheat production and a few resistance alleles of this locus have been identified. We have previously mapped the Pm4e allele to a 6.7 cM interval on chromosome 2AL. In this study, Pm4e was delimited to a 0.19 cM interval flanked by Xwgrc763 and Xwgrc865, through employment of a larger segregating population, derived from the cross of resistant parent D29 with susceptible parent Yangmai 158 (Y158), and enrichment of the genetic interval with markers developed on Chinese Spring (C.S.) survey sequence. In this interval, Pm4e co-segregated with a few markers, some of which were either D29-dominant or Y158-dominant, implying great sequence variation in the interval between D29 and Y158. Most of these co-segregation markers could not differentiate the Pm4 alleles from each other. Survey of 55 wheat cultivars with four co-dominant markers showed that the Pm4e-co-segregating loci always co-exist. Annotation of the Pm4e interval-corresponding C.S. sequence revealed more than a dozen resistance gene analogs clustered in a 2.4 Mb region, although C.S. is susceptible to the Pm4e-avirulent isolate Bgt2. This study has established the foundation for map-based cloning of Pm4e. Moreover, some of the co-dominant markers developed in this study could help in marker-assisted transfer of Pm4e into elite cultivars.

Pm61: a recessive gene for resistance to powdery mildew in wheat landrace Xuxusanyuehuang identified by comparative genomics analysis

A single recessive powdery mildew resistance gene Pm61 from wheat landrace Xuxusanyuehuang was mapped within a 0.46-cM genetic interval spanning a 1.3-Mb interval of the genomic region of chromosome arm 4AL. Epidemics of powdery mildew incited by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) have caused significant yield reductions in many wheat (Triticum aestivum)-producing regions. Identification of powdery mildew resistance genes is required for sustainable improvement of wheat for disease resistance. Chinese wheat landrace Xuxusanyuehuang was resistant to several Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F₁, F₂, and F_2:3 populations produced by crossing Xuxusanyuehuang to susceptible cultivar Mingxian 169 revealed that the resistance of Xuxusanyuehuang was controlled by a single recessive gene. Bulked segregant analysis and simple sequence repeat (SSR) mapping placed the gene on chromosome bin 4AL-4-0.80-1.00. Comparative genomics analysis was performed to detect the collinear genomic regions of Brachypodium distachyon, rice, sorghum, Aegilops tauschii, T. urartu, and T. turgidum ssp. dicoccoides. Based on the use of 454 contig sequences and the International Wheat Genome Sequence Consortium survey sequence of Chinese Spring wheat, four EST-SSR and seven SSR markers were linked to the gene. An F₅ recombinant inbred line population derived from Xuxusanyuehuang × Mingxian 169 cross was used to develop the genetic linkage map. The gene was localized in a 0.46-cM genetic interval between Xgwm160 and Xicsx79 corresponding to 1.3-Mb interval of the genomic region in wheat genome. This is a new locus for powdery mildew resistance on chromosome arm 4AL and is designated Pm61.

Characterization of Pm59, a novel powdery mildew resistance gene in Afghanistan wheat landrace PI 181356

A new powdery mildew resistance gene, designated Pm59, was identified in Afghanistan wheat landrace PI 181356, and mapped in the terminal region of the long arm of chromosome 7A. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important foliar disease of wheat worldwide. In the Great Plains of the USA, Bgt isolates virulent to widely used powdery mildew resistance genes, such as Pm3a, were previously identified. The objectives of this study were to characterize the powdery mildew resistance gene in Afghanistan landrace PI 181356, which exhibited high resistance to Bgt isolates collected in southern Great Plains, and identify molecular markers for marker-assisted selection. An F₂ population and F_2:3 lines derived from a cross between PI 181356 and OK1059060-126135-3 were used in this study. Genetic analysis indicated that PI 181356 carries a single dominant gene, designated Pm59, in the terminal region of the long arm of chromosome 7A. Pm59 was mapped to an interval between sequence tag site (STS) markers Xmag1759 and Xmag1714 with genetic distances of 0.4 cM distal to Xmag1759 and 5.7 cM proximal to Xmag1714. Physical mapping suggested that Pm59 is in the distal bin 7AL 0.99-1.00. Pm59 is a novel powdery mildew resistance gene, and confers resistance to Bgt isolates collected from the Great Plains and the state of Montana. Therefore, Pm59 can be used to breed powdery mildew-resistant cultivars in these regions. Xmag1759 is ideal for marker-assisted selection of Pm59 in wheat breeding.

Characterization of a new Pm2 allele associated with broad-spectrum powdery mildew resistance in wheat line Subtil

Wheat powdery mildew is a severe disease affecting yield and quality. Host resistance was proved to be effective and environment-friendly. Wheat line Subtil is an elite germplasm resource resistant to 28 of 30 tested Bgt isolates. Genetic analysis showed that the powdery mildew resistance in Subtil was conferred by a single dominant gene, temporarily designated PmSub. Using bulked segregant analysis, PmSub was mapped to chromosome arm 5DS, and flanked by the markers Bwm16 and Cfd81/Bwm21 at 5.0 and 0.9 cM, respectively. Allelism tests further confirmed PmSub was allelic with documented Pm2 alleles. Then, homologous sequences of Pm2a related sequence was cloned from Subtil and Chinese Spring. It was completely identical to the reported Pm2a sequence, but significantly different from that of Chinese Spring. A marker SWGI067 was developed based on the sequence divergence of homologous sequence in Subtil and Chinese Spring. SWGI067 was closely linked to PmSub, indicating that the gene PmSub itself was different from the cloned Pm2a related sequence. Meanwhile, Subtil produced significantly different reaction pattern compared with other genotypes with Pm genes at or near Pm2 locus. Therefore, PmSub was most likely a new allele of Pm2. PmSub has opportunities for marker-assisted selecting for high-efficiency wheat improvement.

Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538

The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs.

Characterization of a Segregation Distortion Locus with Powdery Mildew Resistance in a Wheat-Thinopyrum intermedium Introgression Line WE99

Exploitation of host resistance is important for controlling powdery mildew of wheat (Triticum aestivum L.). In this study, a wheat-Thinopyrum intermedium introgression line, designated WE99, conferred seedling resistance to 47 of 49 Blumeria graminis f. sp. tritici isolates. Genetic analysis demonstrated that the resistance segregation deviated significantly from a single gene Mendelian ratio. However, marker analysis indicated that only a single recessive resistance gene, temporarily designated PmWE99, conferred powdery mildew resistance (Pm). PmWE99 was mapped to chromosome arm 2BS and linked to the three simple-sequence repeat markers Gwm148, Gwm271, and Barc55. Using race spectrum analysis, PmWE99 was shown to be significantly different from the documented genes Pm42 and MlIW170 located on chromosome arm 2BS and, thus, appeared to be a new Pm gene. Examination of the genotype frequencies in the F_2:3 families showed that a genetic variation in the PmWE99 interval that favored the transmission of the WE99 allele could be the cause of the deviated segregation. Further investigation revealed that the abnormal segregation only occurred at the PmWE99 interval and was not common at other loci in this population. Identification of PmWE99 will increase the diversity of the Pm genes for wheat improvement.

Characterization of a New Pm2 Allele Conferring Powdery Mildew Resistance in the Wheat Germplasm Line FG-1

Powdery mildew has a negative impact on wheat production. Novel host resistance increases the diversity of resistance genes and helps to control the disease. In this study, wheat line FG-1 imported from France showed a high level of powdery mildew resistance at both the seedling and adult stages. An F2 population and F2:3 families from the cross FG-1 × Mingxian 169 both fit Mendelian ratios for a single dominant resistance gene when tested against multiple avirulent Blumeria tritici f. sp. tritici (Bgt) races. This gene was temporarily designated PmFG. PmFG was mapped on the multi-allelic Pm2 locus of chromosome 5DS using seven SSR, 10 single nucleotide polymorphism (SNP)-derived and two SCAR markers with the flanking markers Xbwm21/Xcfd81/Xscar112 (distal) and Xbwm25 (proximal) at 0.3 and 0.5 cM being the closest. Marker SCAR203 co-segregated with PmFG. Allelism tests between PmFG and documented Pm2 alleles confirmed that PmFG was allelic with Pm2. Line FG-1 produced a significantly different reaction pattern compared to other lines with genes at or near Pm2 when tested against 49 Bgt isolates. The PmFG-linked marker alleles detected by the SNP-derived markers revealed significant variation between FG-1 and other lines with genes at or near Pm2. It was concluded that PmFG is a new allele at the Pm2 locus. Data from seven closely linked markers tested on 31 wheat cultivars indicated opportunities for marker-assisted pyramiding of this gene with other genes for powdery mildew resistance and additional traits.

Molecular tagging of a new broad-spectrum powdery mildew resistance allele Pm2c in Chinese wheat landrace Niaomai

A new broad-spectrum powdery mildew resistance allele Pm2c was identified and mapped in Chinese wheat landrace Niaomai. Chinese wheat landrace Niaomai showed resistance to 27 of 28 Chinese Blumeria graminis f. sp tritici (Bgt) races. Genetic analysis of an F2 population and its derived F2:3 families from the cross Niaomai × Mingxian 169 and backcross population, Niaomai/2*Mingxian 169, indicated that the resistance of Niaomai to Bgt races was conferred by a single dominant resistance gene, temporarily designated PmNM. Molecular tagging showed that PmNM was located on chromosome 5DS and flanked by SSR markers Xcfd81 and Xcfd78 with the genetic distances of 0.1/0.4 cM and 4.9/7.5 cM, respectively. Niaomai showed a different array of responses compared to lines with Pm2a, Pm2b, PmD57-5D, PmLX66, PmX3986-2 and Pm48 genes, sharing the same Xcfd81 allele but differing from Xcfd78 allele for Pm2a and Pm2b lines. Allelism tests based on crosses of Niaomai with Ulka/8*Cc and KM2939 showed that PmNM is allelic to Pm2a and Pm2b. We concluded that PmNM is a new allele of Pm2, re-designated Pm2c. Pm2c could be transferred into wheat cultivars by marker-assisted selection to improve the powdery mildew resistance of breeding cultivars/lines.

PmLX66 and PmW14: New Alleles of Pm2 for Resistance to Powdery Mildew in the Chinese Winter Wheat Cultivars Liangxing 66 and Wennong 14

Wheat powdery mildew (caused by Blumeria graminis f. sp. tritici) can be effectively managed by growing resistant cultivars. 'Liangxing 66' and 'Wennong 14' are the current winter wheat cultivars grown in northern China where powdery mildew is epidemic. Both cultivars have been demonstrated to carry single dominant genes for resistance to powdery mildew, tentatively designated PmLX66 and PmW14, on chromosome 5DS and share common linked markers with Pm2. Allelism tests were performed using a total of 15,657 plants of F₂ segregating populations to determine the relationship between PmLX66, PmW14, and Pm2. All progeny from the crosses Liangxing 66 × 'Ulka/8*Chancellor' (Ulka/8*Cc), Wennong 14 × Ulka/8*Cc, and Liangxing 66 × Wennong 14 were resistant when tested with B. graminis f. sp. tritici isolate E20, indicating that PmLX66 and PmW14 are allelic to Pm2 and to each other. Liangxing 66 was resistant to 76.7% of the 60 B. graminis f. sp. tritici isolates from northern China, a slightly smaller proportion than Ulka/8*Cc (78.3%). However, Wennong 14 (85.0%) was more resistant against this set of B. graminis f. sp. tritici isolates than Ulka/8*Cc and Liangxing 66. Liangxing 66 and Wennong 14 differed from Ulka/8*Cc in respect to a number of B. graminis f. sp. tritici isolates. Based on these findings, PmLX66 and PmW14 are new alleles at the Pm2 locus.

Genetic and physical mapping of powdery mildew resistance gene MlHLT in Chinese wheat landrace Hulutou

A powdery mildew resistance gene MlHLT derived from a Chinese wheat landrace maps within a 3.6 centimorgan (cM) genetic interval spanning a 13.4 megabase (Mb) physical genomic region on chromosome 1DS. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is a devastating disease that can cause severe yield losses. Chinese wheat landrace Hulutou confers nearly immune resistance against prevailing Bgt isolate E09 in Beijing. Genetic analysis indicate that the powdery mildew resistance of Hulutou is controlled by a single dominant gene, provisionally designated MlHLT. Bulked segregant analysis(BSA) and simple sequence repeat (SSR) mapping showed that MlHLT is located on chromosome arm 1DS between markers Xgwm337 and Xcfd83/Xcfd72. By applying comparative genomics analysis, collinearity genomic regions of the MlHLT locus on Aegilops tauschii chromosome 1DS were identified in Brachypodium distachyon chromosome 2, rice chromosome 5 and sorghum chromosome 9, respectively. Three new polymorphic markers were developed using the draft genome sequences and the extended single nucleotide polymorphism (SNP) marker sequences of Ae. tauschii accession AL8/78, as well as the Triticum aestivum cv. Chinese Spring 454 contig sequences and the International Wheat Genome Sequencing Consortium (IWGSC) survey sequences. MlHLT mapped into a 3.6 cM genetic interval spanning 13.4 Mb physical genomic region containing seven contigs (ctg220, ctg4623, ctg1063, ctg5929, ctg3163, ctg699 and ctg1065) on 1DS that has synteny with a 369.8 kb genomic region in Brachypodium, a 380.8 kb genomic region in rice and a 298.4 kb genomic region in sorghum. The genetic and physical maps of MlHLT provide framework for map-based cloning and marker-assisted selection (MAS) of the powdery mildew resistance gene MlHLT in Hulutou.

Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat

Host resistance is the most economical, effective and ecologically sustainable method of controlling diseases in crop plants. In bread wheat, despite the high number of resistance loci that have been cataloged to date, only few have been cloned, underlying the need for genomics-guided investigations capable of providing a prompt and acute knowledge on the identity of effective resistance genes that can be used in breeding programs. Proteins with a nucleotide-binding site (NBS) encoded by the major plant disease resistance (R) genes play an important role in the responses of plants to various pathogens. In this study, a comprehensive analysis of NBS-encoding genes within the whole wheat genome was performed, and the genome scale characterization of this gene family was established. From the recently published wheat genome sequence, we used a data mining and automatic prediction pipeline to identify 580 complete ORF candidate NBS-encoding genes and 1,099 partial-ORF ones. Among complete gene models, 464 were longer than 200 aa, among them 436 had less than 70 % of sequence identity to each other. This gene models set was deeply characterized. (1) First, we have analyzed domain architecture and identified, in addition to typical domain combinations, the presence of particular domains like signal peptides, zinc fingers, kinases, heavy-metal-associated and WRKY DNA-binding domains. (2) Functional and expression annotation via homology searches in protein and transcript databases, based on sufficient criteria, enabled identifying similar proteins for 60 % of the studied gene models and expression evidence for 13 % of them. (3) Shared orthologous groups were defined using NBS-domain proteins of rice and Brachypodium distachyon. (4) Finally, alignment of the 436 NBS-containing gene models to the full set of scaffolds from the IWGSC's wheat chromosome survey sequence enabled high-stringence anchoring to chromosome arms. The distribution of the R genes was found balanced on the three wheat sub-genomes. In contrast, at chromosome scale, 50 % of members of this gene family were localized on 6 of the 21 wheat chromosomes and ~22 % of them were localized on homeologous group 7. The results of this study provide a detailed analysis of the largest family of plant disease resistance genes in allohexaploid wheat. Some structural traits reported had not been previously identified and the genome-derived data were confronted with those stored in databases outlining the functional specialization of members of this family. The large reservoir of NBS-type genes presented and discussed will, firstly, form an important framework for marker-assisted improvement of resistance in wheat, and, secondly, open up new perspectives for a better understanding of the evolution dynamics of this gene family in grass species and in polyploid systems.

Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.)

We have previously reported Xgwm382 as a diagnostic marker for disease resistance against yellow rust in Izgi2001 x ES14 F2 population. Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and Xgwm311, in the same population, we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1-21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of Xgwm382 and Xgwm311 on chromosome 2AL in our plant material.

Transgenic Expression of the Functional Fragment Hpa110-42 of the Harpin Protein Hpa1 Imparts Enhanced Resistance to Powdery Mildew in Wheat

Powdery mildew, one of devastating diseases of wheat worldwide, is caused by Erysiphe graminis f. sp. tritici, a fungal species with constant population changes, which often poses challenges in disease management with host resistance. Transgenic approaches that utilize broad-spectrum resistance may limit changes of pathogen populations and contribute to effective control of the disease. The harpin protein Hpa1, produced by the rice bacterial blight pathogen, can induce resistance to bacterial blight and blast in rice. The fragment comprising residues 10 through 42 of Hpa1, Hpa1_10-42, is reportedly three- to eightfold more effective than the full-length protein. This study evaluated the transgenic expression of the Hpa1_10-42 gene for resistance to powdery mildew in wheat caused by E. graminis f. sp. tritici. Nine Hpa1_10-42 transgenic wheat lines were generated. The genomic integration of Hpa1_10-42 was confirmed, and expression of the transgene was detected at different levels in the individual transgenic lines. Following inoculation with the E. graminis f. sp. tritici isolate Egt15 in the greenhouse, five transgenic lines had significantly higher levels of resistance to powdery mildew compared with nontransformed plants. Thus, transgenic expression of Hpa1_10-42 conferred resistance to one isolate of E. graminis f. sp. tritici in wheat in the greenhouse.

Identification and phylogenetic analysis of a CC-NBS-LRR encoding gene assigned on chromosome 7B of wheat

Hexaploid wheat displays limited genetic variation. As a direct A and B genome donor of hexaploid wheat, tetraploid wheat represents an important gene pool for cultivated bread wheat. Many disease resistant genes express conserved domains of the nucleotide-binding site and leucine-rich repeats (NBS-LRR). In this study, we isolated a CC-NBS-LRR gene locating on chromosome 7B from durum wheat variety Italy 363, and designated it TdRGA-7Ba. Its open reading frame was 4014 bp, encoding a 1337 amino acid protein with a complete NBS domain and 18 LRR repeats, sharing 44.7% identity with the PM3B protein. TdRGA-7Ba expression was continuously seen at low levels and was highest in leaves. TdRGA-7Ba has another allele TdRGA-7Bb with a 4 bp deletion at position +1892 in other cultivars of tetraploid wheat. In Ae. speltoides, as a B genome progenitor, both TdRGA-7Ba and TdRGA-7Bb were detected. In all six species of hexaploid wheats (AABBDD), only TdRGA-7Bb existed. Phylogenic analysis showed that all TdRGA-7Bb type genes were grouped in one sub-branch. We speculate that TdRGA-7Bb was derived from a TdRGA-7Ba mutation, and it happened in Ae. speltoides. Both types of TdRGA-7B participated in tetraploid wheat formation. However, only the TdRGA-7Bb was retained in hexaploid wheat.

Identification of the gene Pm47 on chromosome 7BS conferring resistance to powdery mildew in the Chinese wheat landrace Hongyanglazi

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease that causes substantial yield losses in wheat (Triticum aestivum) in China and other parts of the world. This foliar disease can be effectively managed by host resistance. The Chinese landrace Hongyanglazi from Shaanxi province is highly resistant to many Bgt isolates at the seedling stage. Genetic analysis using an F2:3 population derived from a cross between Hongyanglazi and susceptible cultivar Zhongzuo 9504 indicated that Hongyanglazi carried a single recessive gene (tentatively designated PmHYLZ) conferring its resistance to Bgt isolate E09. PmHYLZ was flanked by EST marker BE606897 and microsatellite marker Xgwm46 on chromosome 7BS at genetic distances of 1.7 and 3.6 cM, respectively. This gene differed from Pm40, also located on 7BS, by origin, linked markers, and reactions to 13 Bgt isolates. Based on these findings, PmHYLZ was permanently designated as Pm47.

PmX: a recessive powdery mildew resistance gene at the Pm4 locus identified in wheat landrace Xiaohongpi

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most devastating foliar diseases of wheat and imposes a constant challenge on wheat breeders. Xiaohongpi, a Chinese landrace of wheat (Triticum aestivum L.), shows resistance to powdery mildew during the entire growth stage in the field and under controlled conditions. The F1 plants from cross of the powdery mildew susceptible cultivar Yangmai158 with Xiaohongpi were susceptible to isolate Bgt19, the locally most prevalent Bgt isolate. In the derived F2 population and F3 progenies, the resistance segregation deviated significantly from the one-gene Mendelian ratio. However, marker analysis indicated that only one recessive gene conferred the resistance, which co-segregated with Xsts-bcd1231 that showed co-segregation with Pm4a in different studies. Allelism test indicated that this recessive resistance gene, designated as pmX, is either allelic or tightly linked to Pm4a. The pmX gene was different from Pm4 alleles in resistance spectrum. Examination of the genotype frequencies at pmX and the linked marker loci in the F2 population showed that a genetic variation favoring the transmission of Xiaohongpi alleles could be the cause of deviated segregation. Mapping of the pmX-linked markers using Chinese Spring deletion lines indicated that it resides in the 0.85-1.00 bin of chromosome 2AL.

Molecular mapping of a powdery mildew resistance gene in common wheat landrace Baihulu and its allelism with Pm24

Powdery mildew is one of the most devastating diseases of wheat in areas with cool and maritime climates. Chinese wheat landrace Baihulu confers a high level of resistance against a wide range of Blumeria graminis DC f. sp. tritici (Bgt) races, especially those currently prevailing in Shaanxi. The objectives of this study were to determine the chromosome bin location of the mlbhl gene from Baihulu and its allelism with Pm24. To investigate the inheritance of powdery mildew resistance and detect adjacent molecular markers, we constructed a segregating population of 301 F(2) plants and corresponding F(2:3) families derived from Baihulu/Shaanyou 225. Genetic analysis revealed that a single dominant gene was responsible for seedling stage powdery mildew resistance in Baihulu. A genetic map comprising Xgwm106, Xgwm337, Xgwm1675, Xgwm603, Xgwm789, Xbarc229, Xgpw4503, Xcfd72, Xcfd83, Xcfd59, Xcfd19, and mlbhl spanned 28.2 cM on chromosome 1D. Xgwm603/Xgwm789 and Xbarc229 were flanking markers tightly linked to mlbhl at genetic distances of 1.5 and 1.0 cM, respectively. The mlbhl locus was located in chromosome bin 1DS 0.59-1.00 delimited by the SSR markers Xgwm337 and Xbarc229. When tested with a differential array of 23 Bgt isolates Baihulu displayed a response pattern that was clearly distinguishable from that of Chiyacao and varieties or lines possessing documented Pm genes. Allelism analysis indicated that mlbhl is a new gene, either allelic or closely linked with Pm24. The new gene was designated Pm24b.

High-density genetic and physical bin mapping of wheat chromosome 1D reveals that the powdery mildew resistance gene Pm24 is located in a highly recombinogenic region

Genetic maps of wheat chromosome 1D consisting of 57 microsatellite marker loci were constructed using Chinese Spring (CS) × Chiyacao F(2) and the International Triticeae Mapping Initiative (ITMI) recombinant inbred lines (RILs) mapping populations. Marker order was consistent, but genetic distances of neighboring markers were different in two populations. Physical bin map of 57 microsatellite marker loci was generated by means of 10 CS 1D deletion lines. The physical bin mapping indicated that microsatellite marker loci were not randomly distributed on chromosome 1D. Nineteen of the 24 (79.2%) microsatellite markers were mapped in the distal 30% genomic region of 1DS, whereas 25 of the 33 (75.8%) markers were assigned to the distal 59% region of 1DL. The powdery mildew resistance gene Pm24, originating from the Chinese wheat landrace Chiyacao, was previously mapped in the vicinity of the centromere on the short arm of chromosome 1D. A high density genetic map of chromosome 1D was constructed, consisting of 36 markers and Pm24, with a total map length of 292.7 cM. Twelve marker loci were found to be closely linked to Pm24. Pm24 was flanked by Xgwm789 (Xgwm603) and Xbarc229 with genetic distances of 2.4 and 3.6 cM, respectively, whereas a microsatellite marker Xgwm1291 co-segregated with Pm24. The microsatellite marker Xgwm1291 was assigned to the bin 1DS5-0.70-1.00 of the chromosome arm 1DS. It could be concluded that Pm24 is located in the '1S0.8 gene-rich region', a highly recombinogenic region of wheat. The results presented here would provide a start point for the map-based cloning of Pm24.

A universal core genetic map for rice

To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (<500 individuals). We chose anchors that were evenly distributed across the rice chromosomes, with spacing between 2 and 3.5 Mbp (except in the telomeric regions, where spacing was 1.5 Mbp). Anchor selection was performed using in silico tools and data: the O. sativa cv. Nipponbare rice genome sequence, the CHARM tool, information from the Gramene database and the OrygenesDB database. Sixteen AA-genome accessions of the Oryza genus were used to evaluate polymorphisms for the selected markers, including accessions from O. sativa, O. glaberrima, O. barthii, O. rufipogon, O. glumaepatula and O. meridionalis. High levels of polymorphism were found for the tested O. sativa x O. glaberrima or O. sativa x wild rice combinations. We developed Paddy Map, a simple database that is helpful in selecting optimal sets of polymorphic SSRs for any cross that involves the previously mentioned species. Validation of the UCGM was done by using it to develop three interspecific genetic maps and by comparing genetic SSR locations with their physical positions on the rice pseudomolecules. In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation.

Identification and genetic mapping of pm42, a new recessive wheat powdery mildew resistance gene derived from wild emmer (Triticum turgidum var. dicoccoides)

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases worldwide in areas with cool or maritime climates. Wild emmer (Triticum turgidum var. dicoccoides) is an important potential donor of disease resistances and other traits for common wheat improvement. A powdery mildew resistance gene was transferred from wild emmer accession G-303-1M to susceptible common wheat by crossing and backcrossing, resulting in inbred line P63 (Yanda1817/G-303-1 M//3*Jing411, BC(2)F(6)). Genetic analysis of an F(2) population and the F(2:3) families developed from a cross of P63 and a susceptible common wheat line Xuezao showed that the powdery mildew resistance in P63 was controlled by a single recessive gene. Molecular markers and bulked segregant analysis were used to characterize and map the powdery mildew resistance gene. Nine genomic SSR markers (Xbarc7, Xbarc55, Xgwm148, Xgwm257, Xwmc35, Xwmc154, Xwmc257, Xwmc382, Xwmc477), five AFLP-derived SCAR markers (XcauG3, XcauG6, XcauG10, XcauG20, XcauG22), three EST-STS markers (BQ160080, BQ160588, BF146221) and one RFLP-derived STS marker (Xcau516) were linked to the resistance gene, designated pm42, in P63. pm42 was physically mapped on chromosome 2BS bin 0.75-0.84 using Chinese Spring nullisomic-tetrasomic, ditelosomic and deletion lines, and was estimated to be more than 30 cM proximal to Xcau516, a RFLP-derived STS marker that co-segregated with the wild emmer-derived Pm26 which should be physically located in 2BS distal bin 0.84-1.00. pm42 was highly effective against 18 of 21 differential Chinese isolates of B. graminis f. sp. tritici. The closely linked molecular markers will enable the rapid transfer of pm42 to wheat breeding populations thus adding to their genetic diversity.

Inheritance and mapping of powdery mildew resistance gene Pm43 introgressed from Thinopyrum intermedium into wheat

Powdery mildew resistance from Thinopyrum intermedium was introgressed into common wheat (Triticum aestivum L.). Genetic analysis of the F(1), F(2), F(3) and BC(1) populations from powdery mildew resistant line CH5025 revealed that resistance was controlled by a single dominant allele. The gene responsible for powdery mildew resistance was mapped by the linkage analysis of a segregating F(2) population. The resistance gene was linked to five co-dominant genomic SSR markers (Xcfd233, Xwmc41, Xbarc11, Xgwm539 and Xwmc175) and their most likely order was Xcfd233-Xwmc41-Pm43-Xbarc11-Xgwm539-Xwmc175 at 2.6, 2.3, 4.2, 3.5 and 7.0 cM, respectively. Using the Chinese Spring nullisomic-tetrasomic and ditelosomic lines, the polymorphic markers and the resistance gene were assigned to chromosome 2DL. As no powdery mildew resistance gene was previously assigned to chromosome 2DL, this new resistance gene was designated Pm43. Pm43, together with the identified closely linked markers, could be useful in marker-assisted selection for pyramiding powdery mildew resistance genes.

Pm23: a new allele of Pm4 located on chromosome 2AL in wheat

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the major diseases of common wheat (Triticum aestivum) worldwide. The powdery mildew resistance gene Pm23, identified in the common wheat Line 81-7241 and originally assigned to wheat chromosome 5A, was relocated on chromosome 2AL with the aid of molecular markers. Mapping of microsatellite markers in two wheat crosses segregating for Pm23 and Pm4b, respectively, in combination with the reported mapping of Pm4a, indicated that the three genes were all linked to the marker Xgwm356 with a distance of 3-5 cM. Allelism between Pm4b and Pm23 was then confirmed, when the progenies of a cross between VPM1 (Pm4b) and Line 81-7241, were shown to be all resistant to a B. graminis isolate avirulent to the both parents. Pm23 is therefore a new allele of the Pm4 locus, and was redesignated as Pm4c.

Identification and mapping of pm2026: a recessive powdery mildew resistance gene in an einkorn (Triticum monococcum L.) accession

Triticum monococcum accession TA2026 showed resistance to wheat powdery mildew. To identify the resistance gene and transfer it to common wheat, genetic analysis and molecular mapping were conducted using an F2 population and derived F3 families from the cross of TA2026xM389. The results indicated that TA2026 possessed a recessive powdery mildew resistance gene. This gene was mapped to the terminal portion of chromosome 5AmL and flanked by SSR marker loci Xcfd39 and Xgwm126. Eight RFLP markers previously mapped to the terminal chromosome 5AmL were converted into STS markers. Three loci, detected by MAG1491, MAG1493 and MAG1494, the STS markers derived from RFLP probes CDO1312, PSR164 and PSR1201, respectively, were linked to this resistance gene with Xmag1493 only 0.9 cM apart from it. In addition, the STS marker MAG2170 developed from the tentative consensus wheat cDNA encoding the Mlo-like protein identified a locus co-segregating with Xmag1493. This is the first recessive powdery mildew resistance gene identified on chromosome 5Am, and is temporarily designated pm2026. We have successfully transferred it to a tetraploid background, and this resistance stock will now be used as the bridge parent for its transfer to common wheat.

Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat

Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a PCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.

Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.)

Powdery mildew is a major fungal disease in wheat growing areas worldwide. A novel source of resistance to wheat powdery mildew present in the germplasm line NC97BGTD7 was genetically characterized as a monogenic trait in greenhouse and field trials using F(2) derived lines from a NC97BGTD7 X Saluda cross. Microsatellite markers were used to map and tag this resistance gene, now designated Pm34. Three co-dominant microsatellite markers linked to Pm34 were identified and their most likely order was established as: Xbarc177-5D, 5.4cM, Pm34, 2.6cM, Xbarc144-5D, 14cM, Xgwm272-5D. These microsatellite markers were previously mapped to the long arm of the 5D chromosome and their positions were confirmed using Chinese Spring nullitetrasomic Nulli5D-tetra5A and ditelosomic Dt5DL lines. Pm2, the only other known Pm gene on chromosome 5D, has been mapped to the short arm and its specificity is different from that of Pm34.

Microsatellite mapping of a Triticum urartu Tum. derived powdery mildew resistance gene transferred to common wheat (Triticum aestivum L.)

A powdery mildew resistance gene from Triticum urartu Tum. accession UR206 was successfully transferred into hexaploid wheat (Triticum aestivum L.) through crossing and backcrossing. The F1 plants, which had 28 chromosomes and an average of 5.32 bivalents and 17.36 univalents in meiotic pollen mother cells (PMC), were obtained through embryos rescued owing to shriveling of endosperm in hybrid seed of cross Chinese Spring (CS) x UR206. Hybrid seeds were produced through backcrossing F1 with common wheat parents. The derivative lines had normal chromosome numbers and powdery mildew resistance similar to the donor UR206, indicating that the powdery mildew resistance gene originating from T. urartu accession UR206 was successfully transferred and expressed in a hexaploid wheat background. Genetic analysis indicated that a single dominant gene controlled the powdery mildew resistance at the seedling stage. To map and tag the powdery mildew resistance gene, 143 F2 individuals derived from a cross UR206 x UR203 were used to construct a linkage map. The resistant gene was mapped on the chromosome 7AL based on the mapped microsatellite makers. The map spanned 52.1 cM and the order of these microsatellite loci agreed well with the established microsatellite map of chromosome arm 7AL. The resistance gene was flanked by the microsatellite loci Xwmc273 and Xpsp3003, with the genetic distances of 2.2 cM and 3.8 cM, respectively. On the basis of the origin and chromosomal location of the gene, it was temporarily designated PmU.

Development of wheat near-isogenic lines for powdery mildew resistance

Using three Chinese wheat cultivars, 'Bainong 3217', 'Beijing 837' and 'Laizhou 953', as recurrent parents, 33 near-isogenic lines (NILs) carrying 22 powdery mildew resistance genes (Pm1c, Pm2, Pm4b, Pm12, Pm13, Pm16, Pm20, Pm21, Pm23, and 13 undocumented genes) were developed. All NILs had no significant difference to their recurrent parents in the investigated traits of agronomic importance. The results of AFLP analysis indicated Jaccard's genetic similarity of the NILs with their recurrent parents varied from 0.96 to 0.98, and confirmed that the NILs had high genetic similarity with their recurrent parents. The resistance to powdery mildew was stably expressed by the relevant NILs. Eleven of the NILs were tested using molecular markers linked to the resistance genes Pm1c, Pm4b, Pm13, Pm21, PmP, PmE, PmPS5A, PmPS5B, PmY39, PmY150, and PmH, and they were all found to carry the targeted genes. The potential application of these NILs in gene discovery is discussed.