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

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.

Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein

Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.

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.

Thinopyrum intermedium TiAP1 interacts with a chitin deacetylase from Blumeria graminis f. sp. tritici and increases the resistance to Bgt in wheat

The biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is a crucial factor causing reduction in global wheat production. Wild wheat relatives, for example Thinopyrum intermedium, is one of the wild-used parents in wheat disease-resistant breeding. From T. intermedium line, we identified the aspartic protease gene, TiAP1, which is involved in resistance against Bgt. TiAP1 is a secreted protein that accumulates in large amounts at the infection sites of Bgt and extends to the intercellular space. Yeast two-hybrid, luciferase complementation imaging and bimolecular florescent complimentary analysis showed that TiAP1 interacted with the chitin deacetylase (BgtCDA1) of Bgt. The yeast expression, purification and in vitro test confirmed the chitin deacetylase activity of BgtCDA1. The bombardment and VIGS-mediated host-induced gene silencing showed that BgtCDA1 promotes the invasion of Bgt. Transcriptome analysis showed the cell wall xylan metabolism, lignin biosynthesis-related and defence genes involved in the signal transduction were up-regulated in the transgenic TiAP1 wheat induced by Bgt. The TiAP1 in wheat may inactivate the deacetylation function of BgtCDA1, cause chitin oligomers expose to wheat chitin receptor, then trigger the wheat immune response to inhibit the growth and penetration of Bgt, and thereby enhance the resistance of wheat to pathogens.

Genome-edited powdery mildew resistance in wheat without growth penalties

Disruption of susceptibility (S) genes in crops is an attractive breeding strategy for conferring disease resistance^1,2. However, S genes are implicated in many essential biological functions and deletion of these genes typically results in undesired pleiotropic effects¹. Loss-of-function mutations in one such S gene, Mildew resistance locus O (MLO), confers durable and broad-spectrum resistance to powdery mildew in various plant species^2,3. However, mlo-associated resistance is also accompanied by growth penalties and yield losses^3,4, thereby limiting its widespread use in agriculture. Here we describe Tamlo-R32, a mutant with a 304-kilobase pair targeted deletion in the MLO-B1 locus of wheat that retains crop growth and yields while conferring robust powdery mildew resistance. We show that this deletion results in an altered local chromatin landscape, leading to the ectopic activation of Tonoplast monosaccharide transporter 3 (TaTMT3B), and that this activation alleviates growth and yield penalties associated with MLO disruption. Notably, the function of TMT3 is conserved in other plant species such as Arabidopsis thaliana. Moreover, precision genome editing facilitates the rapid introduction of this mlo resistance allele (Tamlo-R32) into elite wheat varieties. This work demonstrates the ability to stack genetic changes to rescue growth defects caused by recessive alleles, which is critical for developing high-yielding crop varieties with robust and durable disease resistance.

Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.

Tandem Protein Kinases Emerge as New Regulators of Plant Immunity

Plant-pathogen interactions result in disease development in a susceptible host. Plants actively resist pathogens via a complex immune system comprising both surface-localized receptors that sense the extracellular space as well as intracellular receptors recognizing pathogen effectors. To date, the majority of cloned resistance genes encode intracellular nucleotide-binding leucine-rich repeat receptor proteins. Recent discoveries have revealed tandem kinase proteins (TKPs) as another important family of intracellular proteins involved in plant immune responses. Five TKP genes-barley Rpg1 and wheat WTK1 (Yr15), WTK2 (Sr60), WTK3 (Pm24), and WTK4-protect against devastating fungal diseases. Moreover, a large diversity and numerous putative TKPs exist across the plant kingdom. This review explores our current knowledge of TKPs and serves as a basis for future studies that aim to develop and exploit a deeper understanding of innate plant immunity receptor proteins.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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.

Importance of Landraces in Cereal Breeding for Stress Tolerance

The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.

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.

Phytoene synthase 1 (Psy-1) and lipoxygenase 1 (Lpx-1) Genes Influence on Semolina Yellowness in Wheat Mediterranean Germplasm

Phytoene synthase 1 (Psy1) and lipoxygenase 1 (Lpx-1) are key genes involved in the synthesis and catalysis of carotenoid pigments in durum wheat, regulating the increase and decrease in these compounds, respectively, resulting in the distinct yellow color of semolina and pasta. Here, we reported new haplotype variants and/or allele combinations of these two genes significantly affecting yellow pigment content in grain and semolina through their effect on carotenoid pigments. To reach the purpose of this work, three complementary approaches were undertaken: the identification of QTLs associated to carotenoid content on a recombinant inbred line (RIL) population, the characterization of a Mediterranean panel of accessions for Psy1 and Lpx-1 genes, and monitoring the expression of Psy1 and Lpx-1 genes during grain filling on two genotypes with contrasting yellow pigments. Our data suggest that Psy1 plays a major role during grain development, contributing to semolina yellowness, and Lpx-1 appears to be more predominant at post-harvest stages and during pasta making.

Fine Mapping a Broad-Spectrum Powdery Mildew Resistance Gene in Chinese Landrace Datoumai, PmDTM, and Its Relationship with Pm24

Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a globally important wheat disease causing severe yield losses, and deployment of resistant varieties is the preferred choice for managing this disease. Chinese wheat landrace Datoumai was resistant to 22 of 23 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 derived from the cross Datoumai × Huixianhong revealed that the powdery mildew resistance of Datoumai is controlled by a single dominant gene, temporarily designated as PmDTM. Bulked segregant analysis and simple sequence repeat mapping with 200 F₂ plants showed that PmDTM was located in the same genetic region as Pm24 on chromosome 1DS. To fine map PmDTM, 12 critical recombinants were identified from 1,192 F₂ plants and delimited PmDTM to a 0.5-cM Xhnu58800 to Xhnu59000 interval covering 180.5 Kb (38,728,125 to 38,908,656 bp) on chromosome 1DS, and only one highly confident gene, TraesCS1D02G058900, was annotated within this region. TraesCS1D02G058900 encodes a receptor-like serine/threonine-protein kinase (STK), and a 6-bp deletion in exon 5 may confer the resistance to powdery mildew. Allele frequency analysis indicated that the STK allele with 6-bp deletion was only present in three landraces (Datoumai, Chiyacao [Pm24], and Hulutou) and was absent in all of the 353 Chinese modern cultivars and 147 foreign cultivars. These results demonstrate that PmDTM is mapped to the same locus as Pm24 and can be widely used to enhance powdery mildew resistance in wheat growing regions worldwide.

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.

A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive diseases that pose a great threat to wheat production. Wheat landraces represent a rich source of powdery mildew resistance. Here, we report the map-based cloning of powdery mildew resistance gene Pm24 from Chinese wheat landrace Hulutou. It encodes a tandem kinase protein (TKP) with putative kinase-pseudokinase domains, designated WHEAT TANDEM KINASE 3 (WTK3). The resistance function of Pm24 was validated by transgenic assay, independent mutants, and allelic association analyses. Haplotype analysis revealed that a rare 6-bp natural deletion of lysine-glycine codons, endemic to wheat landraces of Shaanxi Province, China, in the kinase I domain (Kin I) of WTK3 is critical for the resistance function. Transgenic assay of WTK3 chimeric variants revealed that only the specific two amino acid deletion, rather than any of the single or more amino acid deletions, in the Kin I of WTK3 is responsible for gaining the resistance function of WTK3 against the Bgt fungus.

Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

Powdery mildew is one of the most widespread diseases of wheat. The development and deployment of resistant varieties are one of the most economical and effective methods to manage this disease. Our previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred a high level of resistance to powdery mildew of wheat. In this study, resistance spectrum of TA7733 was assayed by using 15 Blumeria graminis f. sp. tritici (Bgt) isolates prevalent in different regions of China. The result indicated that TA7733 was highly resistant to all tested Bgt isolates and the gene(s) on chromosome 2Mb conferred broad-spectrum resistance to powdery mildew. In order to characterize mechanism of powdery mildew resistance by identifying candidates R-genes derived from Ae. biuncialis chromosome 2Mb and develop 2Mb-specific molecular markers, we performed RNA-seq analysis on TA7733 and CS. In total we identified 7,278 unigenes that showed specific expression in TA7733 pre and post Bgt-infection when compared to CS. Of these 7,278 unigenes, 295 were annotated as putative resistance (R) genes. Comparatively analysis of R-gene sequences from TA7733 and CS and integration CS Ref Seq v1.0 were used to develop R-gene specific primers. Of 295 R-genes we identified 53 R-genes were specific to 2Mb and could be involved in powdery mildew resistance. Functional annotation of majority of the 53 R-genes encoded nucleotide binding leucine rich repeat (NLR) protein. The broad-spectrum resistance to powdery mildew in TA7733 and availability of 2Mb-derived putative candidate R-gene specific molecular markers identified in this study will lay foundations for transferring powdery mildew resistance from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination. Our study also provides useful candidates for further isolation and cloning of powdery mildew resistance gene(s) from Ae. biuncialis chromosome 2Mb.

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.

Latent Infection of Powdery Mildew on Volunteer Wheat in Sichuan Province, China

Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici, is one of the most destructive wheat diseases in China, especially in Sichuan Province. Successfully oversummered B. graminis f. sp. tritici can become a primary infection source for wheat seedlings in the fall. Determining the latent infection level of B. graminis f. sp. tritici in volunteer wheat and the oversummering areas of B. graminis f. sp. tritici is important for estimating potential B. graminis f. sp. tritici epidemics. In this study, we clarified the critical role of volunteer wheat in the B. graminis f. sp. tritici oversummering cycle and determined whether latent B. graminis f. sp. tritici infection was present in volunteer wheat by using real-time polymerase chain reaction (real-time PCR). The results indicated that volunteer wheat was mostly found in the northeast and middle regions of Sichuan, where lower temperatures and higher precipitation are common. A total of 13.2% of samples showed symptoms of B. graminis f. sp. tritici (spores) in the field, and 36.8% of samples were found to carry the B. graminis f. sp. tritici pathogen, even though no symptoms were observed. Volunteer wheat with B. graminis f. sp. tritici infection symptoms was found at an altitude of 536 m but volunteer wheat latently infected by B. graminis f. sp. tritici was identified at the lowest altitude of 323 m. Crop shade (e.g., corn and lima bean) provided suitable conditions for the survival of volunteer wheat in the summer. In addition, volunteer wheat played a key role in the B. graminis f. sp. tritici oversummering cycle. Moreover, B. graminis f. sp. tritici could oversummer by infecting generations of volunteer wheat in the summer, thereby becoming the primary infection source for autumn-sown wheat. The results showed that the latent infection of wheat diseases could be rapidly quantified by real-time PCR. Here, the primary disease center of autumn-sown wheat in Ya'an and Wenjiang were detected accurately based on this method. This study provides solid evidence for identifying the disease center, which offers guidance for wheat disease control and management.

Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence

A high-resolution genetic linkage map was constructed using the comparative genomics analysis approach and the wheat reference genome, which placed wheat powdery mildew resistance gene Pm52 in a 0.21-cM genetic interval on chromosome arm 2BL. The gene Pm52 confers resistance to powdery mildew and has been previously mapped on chromosome arm 2BL in winter wheat cultivar Liangxing 99. Because of its effectiveness against the disease, this study was initiated to finely map Pm52 using the comparative genomics analysis approach and the wheat reference genomic sequence. Based on the EST sequences that were located in the chromosome region flanking Pm52, four EST-SSR markers were developed, and another nine SSR markers were developed using the comparative genomics technology. These thirteen markers were integrated into a genetic linkage map using an F_2:3 subpopulation of the Liangxing 99 × Zhongzuo 9504 cross. Pm52 was mapped within a 3.2-cM genetic interval in the subpopulation that corresponded to a ~40-Mb genomic interval on chromosome arm 2BL of the Chinese Spring reference genome. The Pm52-flanking markers Xicsl163 and Xicsl62 identified 344 recombinant individuals from 8820 F₂ plants. Nine SSR markers generated from the Chinese Spring genomic interval were incorporated into a high-resolution genetic linkage map, which placed Pm52 in a 0.21-cM genetic interval corresponding to 5.6-Mb genomic region. The constructed high-resolution genetic linkage map will facilitate the map-based cloning of Pm52 and its marker-assisted selection.

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.

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.

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.

Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses

A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F_5:6 and F_6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.

Marker-Assisted Development and Evaluation of Near-Isogenic Lines for Broad-Spectrum Powdery Mildew Resistance Gene Pm2b Introgressed into Different Genetic Backgrounds of Wheat

At present, most of released wheat cultivars or breeding lines in China are susceptible to powdery mildew (Pm) (caused by Blumeria graminis f. sp. tritici, Bgt), so there is an urgent need to rapidly transfer effective and broad-spectrum Pm resistance genes into elite cultivars/lines. Near-isogenic lines (NILs) with short target gene region are very important in molecular breeding and map-based cloning and can be developed by combining marker-assisted selection and conventional phenotypic identification. However, no Pm gene NILs were reported by using this method in the previous studies. A new broad-spectrum dominant resistance gene Pm2b, derived from the Chinese wheat breeding line KM2939, conferred high resistance to Pm at both the seedling and adult stages. In this study, with the aid of forward and background selection (FS and BS) using molecular markers, the Pm2b gene was introgressed into three elite susceptible commercial cultivars Shimai 15, Shixin 828, and Kenong 199 through the back-crossing procedure. With the appropriate backcrossing generations, selected population sizes and marker number for BS, the homozygous resistant BC3F2:3 NILs of Pm2b gene in the three genetic backgrounds with the highest recipient genome composition of about 99%, confirmed by simple sequence repeat markers and 660K single nucleotide polymorphic array, were developed and evaluated for the powdery mildew resistance and agronomic traits. The different resistance and similar or improved agronomic performance between Pm2b NILs and their corresponding recurrent parents indicated their potential value in the marker-assisted breeding of the Pm2b gene. Moreover, the development of four flanked diagnostic markers (CFD81, BWM25, BWM20, and BWM21) of the Pm2 gene can effectively assist the forward selection and accelerate the transfer and use of this resistance gene.

Mapping of novel powdery mildew resistance gene(s) from Agropyron cristatum chromosome 2P

A physical map of Agropyron cristatum 2P chromosome was constructed for the first time and the novel powdery mildew resistance gene(s) from chromosome 2P was(were) also mapped. Agropyron cristatum (L.) Gaertn. (2n = 28, PPPP), a wild relative of common wheat, is highly resistant to powdery mildew. Previous studies showed that wheat-A. cristatum 2P disomic addition line II-9-3 displayed high resistance to powdery mildew, and the resistance was attributable to A. cristatum chromosome 2P. To utilize and physically map the powdery mildew resistance gene(s), 15 wheat-A. cristatum 2P translocation lines and three A. cristatum 2P deletion lines with different chromosomal segment sizes, obtained from II-9-3 using ⁶⁰Co-γ ray irradiation, were characterized using cytogenetic and molecular marker analysis. A. cristatum 2P chromosomal segments in the translocations were translocated to different wheat chromosomes, including 1A, 4A, 5A, 6A, 7A, 1B, 2B, 3B, 7B, 3D, 4D, and 6D. A physical map of the 2P chromosome was constructed with 82 STS markers, consisting of nine bins with 34 markers on 2PS and eight bins with 48 markers on 2PL. The BC₁F₂ populations of seven wheat-A. cristatum 2P translocation lines (2PT-3, 2PT-4, 2PT-5, 2PT-6, 2PT-8, 2PT-9, and 2PT-10) were developed by self-pollination, tested with powdery mildew and genotyped with 2P-specific STS markers. From these results, the gene(s) conferring powdery mildew resistance was(were) located on 2PL bin FL 0.66-0.86 and 19 2P-specific markers were identified in this bin. Moreover, two new powdery mildew-resistant translocation lines (2PT-4 and 2PT-5) with small 2PL chromosome segments were obtained. The newly developed wheat lines with powdery mildew resistance and the closely linked molecular markers will be valuable for wheat disease breeding in the future.

A large-scale chromosome-specific SNP discovery guideline

Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted 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 mapping and marker development for the Triticum dicoccoides-derived stripe rust resistance gene YrSM139-1B in bread wheat cv. Shaanmai 139

KEY MESSAGE

YrSM139-1B maybe a new gene for effective resistance to stripe rust and useful flanking markers for marker-assisted selection were developed.

ABSTRACT

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important foliar disease of wheat. Two dominant stripe rust resistant genes YrSM139-1B and YrSM139-2D were pyramided in bread wheat cultivar Shaanmai 139; one from wild emmer and the other from Thinopyrum intermedium. Three near-isogenic F7:8 line pairs (contrasting RILs), N122-1013R/S, N122-185R/S, and N122-1812R/S, independently derived from different F2 plants and differing at the YrSM139-1B locus were generated from the cross Shaanmai 139 × Hu 901-19 through marker-assisted selection. A large F2:3 population from cross N122-1013R × N122-1013S tested for stripe rust response and subjected to analysis with markers in the 1BS10-0.5 bin region using SSR expressed sequence tags (EST) and site-specific sequence markers developed from the 90 K Illumina iSelect SNP array. Five EST-STS markers and four allele-specific PCR markers were mapped to the YrSM139-1B region. The 30.5 cM genetic map for YrSM139-1B consisted of nine markers, two of which were closer to YrSM139-1B than Xgwm273, which was used in producing the contrasting RIL pairs. Race response data and allelism tests showed that YrSM139-1B is different from Yr10, Yr15, and Yr24/26/CH42.