Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat

Introgression of an adult-plant powdery mildew resistance gene Pm4VL from Dasypyrum villosum chromosome 4V into bread wheat

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) seriously threatens wheat production worldwide. It is imperative to identify novel resistance genes from wheat and its wild relatives to control this disease by host resistance. Dasypyrum villosum (2n = 2x = 14, VV) is a relative of wheat and harbors novel genes for resistance against multi-fungal diseases. In the present study, we developed a complete set of new wheat-D. villosum disomic introgression lines through genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH) and molecular markers analysis, including four disomic substitution lines (2n=42) containing respectively chromosomes 1V#6, 2V#6, 3V#6, and 6V#6, and four disomic addition lines (2n=44) containing respectively chromosomes 4V#6, 5V#6, 6V#6 and 7V#6. These lines were subsequently evaluated for their responses to a mixture Bgt isolates at both seedling and adult-plant stages. Results showed that introgression lines containing chromosomes 3V#6, 5V#6, and 6V#6 exhibited resistance at both seedling and adult-plant stages, whereas the chromosome 4V#6 disomic addition line NAU4V#6-1 exhibited a high level of adult plant resistance to powdery mildew. Moreover, two translocation lines were further developed from the progenies of NAU4V#6-1 and the Ph1b mutation line NAU0686-ph1b. They were T4DL·4V#6S whole-arm translocation line NAU4V#6-2 and T7DL·7DS-4V#6L small-fragment translocation line NAU4V#6-3. Powdery mildew tests of the two lines confirmed the presence of an adult-plant powdery mildew resistance gene, Pm4VL, located on the terminal segment of chromosome arm 4V#6L (FL 0.6-1.00). In comparison with the recurrent parent NAU0686 plants, the T7DL·7DS-4V#6L translocation line NAU4V#6-3 showed no obvious negative effect on yield-related traits, providing a new germplasm in breeding for resistance.

Conversion of superior bread wheat genotype HD3209 carrying Lr19/Sr25 into CMS line for development of rust-resistant wheat hybrids

Hybrid development is one of the most promising strategies for boosting crop yields. Parental lines used to create hybrids must have good per se performance and disease resistance for developing superior hybrids. Indian wheat line HD3209 was developed by introducing the rust resistance genes Lr19/Sr25 into the background of popular wheat variety HD2932. The wheat line HD3209 carrying Lr19/Sr25 has been successfully and rapidly converted to the CMS line A-HD3209, with 96.01% background genome recovery, based on selection for agro-morphological traits, rust resistance, pollen sterility, and foreground and background analyses utilizing SSR markers. The converted CMS line A-HD3209 was completely sterile and nearly identical to the recurrent parent HD3209. Based on high per se performance and rust resistance, the study concludes that the derived CMS line A-HD3209 is promising and can be employed successfully in hybrid development.

Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study

BACKGROUND

Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers.

RESULTS

In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill.

CONCLUSION

In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.

Multiplex PCR assay for the simultaneous identification of race specific and non-specific leaf resistance genes in wheat (Triticum aestivum L.)

Race-nonspecific resistance is a key to sustainable management of pathogens in bread wheat (Triticum aestivum L.) breeding. It is more durable compared to race-specific immunity, conferred by the major genes (R), which are often overcome by pathogens. The accumulation of the genes, which provide the resistance to a specific race of a pathogen, together with the introduction of race-non-specific resistance genes is the most effective strategy aimed at preventing the breakdown of genetically conditioned immunity. PCR markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). Multiplexing assays provide increased throughput, reduced reaction cost, and conservation of limited sample material, which are beneficial for breeding purposes. Here, we described the process of customizing multiplex PCR assay for the simultaneous identification of the major leaf rust resistance genes Lr19, Lr24, Lr26, and Lr38, as well as the slow rusting, race-nonspecific resistance genes: Lr34 and Lr68, in thirteen combinations. The adaptation of PCR markers for multiplex assays relied on: (1) selection of primers with an appropriate length; (2) selection of common annealing/extension temperature for given primers; and (3) PCR mixture modifications consisting of increased concentration of primers for the scanty band signals or decreased concentration of primers for the strong bands. These multiplex PCR protocols can be integrated into a marker-assisted selection of the leaf rust-resistant wheat genotypes.

Transcriptome analysis of Lr19-virulent mutants provides clues for the AvrLr19 of Puccinia triticina

Introduction

Wheat leaf rust caused by Puccinia triticina (Pt) remains one of the most destructive diseases of common wheat worldwide. Understanding the pathogenicity mechanisms of Pt is important to control wheat leaf rust.

Methods

The urediniospores of Pt race PHNT (wheat leaf rust resistance gene Lr19-avirulent isolate) were mutagenized with ethyl methanesulfonate (EMS), and two Lr19-virulent mutants named M1 and M2 were isolated. RNA sequencing was performed on samples collected from wheat cultivars Chinese Spring and TcLr19 infected with wild-type (WT) PHNT, M1, and M2 isolates at 14 days post-inoculation (dpi), respectively. Screening AvrLr19 candidates by quantitative reverse transcription PCR (qPCR) and Agrobacterium-mediated transient assays in Nicotiana benthamiana.

Results

560 genes with single nucleotide polymorphisms (SNPs) and insertions or deletions (Indels) from non-differentially expressed genes were identified. Among them, 10 secreted proteins were screened based on their fragments per kilobase of exon model per million mapped reads (FPKM) values in the database. qPCR results showed that the expression profiles of 7 secreted proteins including PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, and PTTG_03570 among 10 secreted proteins in mutants were significantly different with that in wild-type isolate after infection wheat TcLr19 and might be related to the recognition between Lr19 and AvrLr19. In addition, a total of 216 differentially expressed genes (DEGs) were obtained from three different sample comparisons including M1-vs-WT, M2-vs-WT, and M1-vs-M2. Among 216 DEGs, 15 were predicted to be secreted proteins. One secreted protein named PTTG_04779 could inhibit programmed progress of cell death (PCD) induced by apoptosis-controlling genes B-cell lymphoma-2 associated X protein (BAX) on Nicotiana benthamiana, indicating that it might play a virulence function in plant. Taken together, total 8 secreted proteins, PTTG_04779, PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, PTTG_03570 are identified as AvrLr19 candidates.

Discussion

Our results showed that a large number of genes participate in the interaction between Pt and TcLr19, which will provide valuable resources for the identification of AvrLr19 candidates and pathogenesis-related genes.

Diversity of new Russian bread wheat cultivars according to leaf rust resistance genes

Background. Cultivation of resistant cultivars is an effective method of wheat protection against leaf rust. The purpose of this work was to characterize the juvenile leaf rust resistance of bread wheat cultivars listed in the State Register for Selection Achievements in 2021 and identify their Lr genes using molecular markers.

Materials and methods. The material included 18 cultivars of winter bread wheat and nine spring ones. Juvenile resistance in the seedling phase was assessed with two test clones (kLr9 и kLr19) and the Krasnodar population of Puccinia triticina Erikss. Molecular markers were used to identify 18 Lr genes.

Results and discussion. A high level of resistance (score 0 or 0;) was shown by cvs. ‘Khamdan’, ‘Sharm’ and ‘Omskaya 44’; moderate resistance (score 2, 2+) by ‘Albidum 2030’. Reactions of ‘Polina’, ‘Rossyp’, ‘Status’, ‘Balkysh’ and ‘Bogema’ were variable. The studied cultivars did not contain juvenile genes Lr9, Lr24, Lr25, Lr28, Lr29, Lr39, Lr47 or Lr66 and adult plant resistance genes Lr21 and Lr35. Markers of identifiable genes were not detected in cv. ‘Sharm’, highly resistant to leaf rust. ‘Khamdan’ had an ineffective Lr10 gene and a partial resistance gene Lr34, which offered no protection in the seedling stage. These cultivars seem to contain additional resistance genes. A high level of resistance to leaf rust in ‘Omskaya 44’ is provided by a combination of the Lr19, Lr26, Lr1 and Lr3 genes. In ‘Nemchinovskaya 85’, the partially effective adult plant resistance gene Lr37 was identified. In other tested cultivars, Lr1, Lr3, Lr10, Lr26 and Lr34 were widely represented. 

Evaluation of the resistance to Chinese predominant races of Puccinia triticina and analysis of effective leaf rust resistance genes in wheat accessions from the U.S. National Plant Germplasm System

Puccinia triticina, which is the causative agent of wheat leaf rust, is widely spread in China and most other wheat-planting countries around the globe. Cultivating resistant wheat cultivars is the most economical, effective, and environmentally friendly method for controlling leaf rust-caused yield damage. Exploring the source of resistance is very important in wheat resistance breeding programs. In order to explore more effective resistance sources for wheat leaf rust, the resistance of 112 wheat accessions introduced from the U.S. National Plant Germplasm System were identified using a mixture of pathogenic isolates of THTT, THTS, PHTT, THJT and THJS which are the most predominant races in China. As a result, all of these accessions showed high resistance at seedling stage, of which, ninety-nine accessions exhibited resistance at adult plant stage. Eleven molecular markers of eight effective leaf rust resistance genes in China were used to screen the 112 accessions. Seven effective leaf rust resistance genes Lr9, Lr19, Lr24, Lr28, Lr29, Lr38 and Lr45 were detected, except Lr47. Twenty-three accessions had only one of those seven effective leaf rust resistance gene. Eleven accessions carried Lr24+Lr38, and 7 accessions carried Lr9+Lr24+Lr38, Lr24+Lr38+Lr45, Lr24+Lr29+Lr38 and Lr19+Lr38+Lr45 respectively. The remaining seventy-one accessions had none of those eight effective leaf rust resistance genes. This study will provide theoretical guidance for rational utilization of these introduted wheat accessions directly or for breeding the resistant wheat cultivars.

An Update on Resistance Genes and Their Use in the Development of Leaf Rust Resistant Cultivars in Wheat

Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.

Identification of Resistant Germplasm and Detection of Genes for Resistance to Powdery Mildew and Leaf Rust from 2,978 Wheat Accessions

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici and Puccinia triticina, respectively, are widespread diseases of wheat worldwide. The use of resistant cultivars is considered the most economical, environment-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 wheat accessions (22.1%) were highly resistant to a widely prevalent B. graminis f. sp. tritici isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of B. graminis f. sp. tritici isolates at the adult plant stage. Meanwhile, 63 accessions (2.1%) were highly resistant to leaf rust at the adult plant stage, of which 54 were resistant to a predominant and highly virulent P. triticina race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven powdery mildew genes (Pm genes; Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and 10 Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, whereas Pm24 was not detected. In addition, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant to leaf rust, four leaf rust genes (Lr genes; Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions singly or in combination, whereas six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

The Emergence of New Aggressive Leaf Rust Races with the Potential to Supplant the Resistance of Wheat Cultivars

Simple Summary

The pathogen that causes wheat leaf rust, Puccinia triticina, possesses numerous aggressive races that can erode the resistant genes in its host. This study presents the recognition of the new physiological races of P. triticina, their distribution, and their resistance genes in wheat cultivars, which are critical for directing and improving wheat breeding programs for resistance to leaf rust. Winds often transport the pathogen’s initial inoculum from one country to another. Our findings trigger an alert to the whole world about developing races capable of supplanting leaf rust resistance.

Abstract

Characterization of the genetic structure and the physiological races of Puccinia triticina is a growing necessity to apply host genetic resistance against wheat leaf rust as a successful control strategy. Herein, we collected and identified about 130 isolates of P. triticina from 16 Egyptian commercial wheat cultivars grown at different locations, over two seasons (2019/2020 and 2020/2021). The 130 isolates of P. triticina were segregated into 17 different physiological races. TTTST and TTTKS were the most common virulent races, whereas TTTST and MTTGT were the most frequent races. The races were classified into three groups, based on their distinct DNA band sizes (150 bp, 200 bp, and 300 bp) after RAPD analysis. The new wheat cultivars (Sakha-94, Sakha-95, and Shandweel-1) infected with the most virulent race (TTTST), Gemmeiza-12, and Misr-3 were resistant to all physiological races. The resistance of these cultivars was mostly due to the presence of Lr19- and Lr28-resistant genes. Our results serve as a warning about emerging aggressive races capable of supplanting resistance to leaf rust, and help in the understanding of the pathotype–cultivar–location association and its role in the susceptibility/resistance of new wheat cultivars to P. triticina.

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.

Identification of Wheat Leaf Rust Resistance Genes in Chinese Wheat Cultivars and the Improved Germplasms

Leaf rust is an important wheat disease that is a significant hindrance for wheat production in most areas of the world. Breeding resistant cultivars can effectively and economically control the disease. In the present study, a wheat collection consisting of 100 cultivars from China and 18 improved germplasms from global landrace donors together with 36 known single Lr gene lines were tested with 20 strains of Puccinia triticina Eriks. in the seedling stage to postulate the Lr gene in the cultivars and germplasms. In addition, 12 diagnostic molecular markers specific to 10 Lr genes were used to detect the presence of the Lr genes in the wheat collection. Resistance to leaf rust of these cultivars at the adult plant stage was tested in fields under natural infection during the 2016 to 2018 cropping seasons in Baoding, Hebei Province. The gene postulation combined with molecular marker detection showed that six Lr genes (Lr1, Lr26, Lr33, Lr34, Lr45, and Lr46) were identified in 44 wheat accessions, including 37 cultivars and seven improved germplasms. Among the 44 wheat accessions postulated with Lr genes, Lr1 was present in four accessions, Lr26 in 12 accessions, Lr33 in two accessions, Lr34 in 14 accessions, Lr45 in three accessions, and Lr46 in 16 accessions. In the collection of 118 cultivars/germplasms, 34 wheat lines displayed adult-plant resistance carrying Lr34, Lr46, and/or underdetermined genes. Therefore, a high level of leaf rust resistance can be achieved through the combination of all-stage resistance and adult-plant resistance genes together in wheat cultivars.

A novel leaf rust resistance gene introgressed from Aegilops markgrafii maps on chromosome arm 2AS of wheat

A novel leaf rust resistance gene, LrM, introgressed from Aegilops markgrafii and mapped on chromosome 2AS using SSR- and SNP-based PCR markers will aid in broadening the genetic base of rust resistance in wheat. A new leaf rust resistance gene tentatively named LrM was introgressed from the diploid non-progenitor species Ae. markgrafii (2n = 2x = 14, genome CC) into common wheat using the nulli-5B mechanism. The introgression line ER9-700 showed a high degree of resistance against a wide spectrum of Puccinia triticina pathotypes. Genetic analysis was performed using the F₁, F₂, F_2:3 and BC₁F₁ generations derived from the cross ER9-700/Agra Local. The results showed a single dominant gene for leaf rust resistance. The resistance gene LrM was mapped on chromosome arm 2AS using SSR- and SNP-based PCR markers. Preliminary mapping with SSR markers in the F_2:3 population from the cross ER9-700/Agra Local identified two SSR markers flanking the LrM. SNPs were identified in the genomic region flanked by SSR markers, and SNP-based PCR markers were developed to construct the final map. Three SNP-based PCR markers co-segregated and mapped closest to the resistance gene at a distance of 2 cM. The gene LrM was distinguished from all the other genes designated and mapped on chromosome arm 2AS by molecular markers and rust reaction. All five markers used in the mapping amplified identical alleles in the donor Ae. markgrafii accession and introgression line ER9-700. The chromosomal location and rust reaction suggest that LrM is a novel leaf rust resistance gene that may be useful in broadening the genetic base of leaf rust resistance in wheat.

Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions

We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr, respectively. Single-trait genome-wide association studies (GWAS) revealed several environment-specific and multi-environment quantitative trait loci (QTL). Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B within a 4.4-cM region. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exist within the 3B cluster including the durable rust resistance gene Yr30. An Sr/Lr QTL on chromosome 3D was found mainly in the synthetic-derived germplasm from Annuello background which is known to carry the Agropyron elongatum 3D translocation involving the Sr24/Lr24 resistance locus. Interestingly, estimating the SNP effects using a BayesR method showed that the correlation among the highest 1% of QTL effects across environments (excluding GWAS QTL) had significant correlations, with average r values of 0.26, 0.16 and 0.55 for Lr, Sr and Yr, respectively. These results indicate the importance of small effect QTL in achieving durable rust resistance which can be captured using genomic selection.

Study of Androgenic Plant Families of Alloplasmic Introgression Lines (H. vulgare) -T. aestivum and the Use of Sister DH Lines in Breeding

One of the limitations in obtaining the genetic diversity of doubled haploid (DH) lines via anther culture is the development of families of regenerants, and each family represents a clone. This work examines the results of studying this phenomenon in anther culture of alloplasmic (H. vulgare)–T. aestivum and euplasmic lines with 1RS.1BL and 7DL-7Ai translocations and hybrids between them. Parameters of androgenesis such as the number of embryo-like structures, the total number of regenerants, and the number of green regenerants per 100 anthers varied depending on the genotype. In all genotypes from embryo-like structures, predominant development of families of plantlets rather than single plantlets was found. The source of family plantlets was polyembryos. About 75% of families consisted of regenerants at the same fertility level. On average, 37.74%4% of the R0 plants were fertile. The sister DH lines of three hybrid combinations were formed from seeds of R1 plants (2n = 42) with high fertility and in the presence of wheat–alien translocations. After four years of breeding trials, the sister DH lines of three families with fungal disease resistance increased yield, and some parameters of grain quality exceeding the controls were identified as promising for breeding.

Marker-assisted pyramiding of Thinopyrum-derived leaf rust resistance genes Lr19 and Lr24 in bread wheat variety HD2733

This study was undertaken to pyramid two effective leaf rust resistance genes (Lr19 and Lr24) derived from Thinopyrum (syn. Agropyron), in the susceptible, but agronomically superior wheat cultivar HD2733 using marker-assisted selection. In the year 2001, HD2733 was released for irrigated timely sown conditions of the north eastern plains zone (NEPZ) of India became susceptible to leaf rust, a major disease of the region. Background selection helped in developing near-isogenic lines (NILs) of HD2733 with Lr19 and Lr24 with 97.27 and 98.94%, respectively, of genomic similarity with the parent cultivar, after two backcrossing and one generation of selfing.NILs were intercrossed to combine the genes Lr19 and Lr24. The combination of these two genes in the cultivar HD2733 is expected to provide durable leaf rust resistance in farmers' fields.

Molecular charactarization of wheat advanced lines for leaf rust resistant genes using SSR markers

A total of fifty seven wheat advanced lines were screened to detect the existence of leaf rust resistant genes (Lr9, Lr13, Lr19, Lr24, Lr26, Lr28, Lr32, Lr34, Lr35, Lr36, Lr37, Lr39 and Lr46) using thirteen SSR markers. Only four markers for Lr13, Lr32, Lr34 and Lr35 produced separate, reproducible bands which indicated the positive linkage of leaf rust resistance with these SSR markers. The highest frequency was observed for Lr32 (100%), as it was detected in all fifty seven lines, followed by Lr34 (89.4%) in 51 lines, Lr35 (87.7%) in 50 lines and Lr13 (31.5%) in 18 lines respectively. All the four resistant genes were identified in fifteen lines which is only 26% of the studied population. These results indicate that there are limited number of variant genes for leaf rust resistance in the studied wheat advanced lines. Therefore, strategies for arraying these genes to lengthen infection resistance are advised to eliminate wheat rust diseases. In addition, more reliable and capable markers are essential to be settled for marker assisted selection of these and other genes.

Identification of Leaf Rust Resistance Genes in Chinese Common Wheat Cultivars

Puccinia triticina Eriks. (Pt), the causal agent of wheat (Triticum aestivum L.) leaf rust, is the most widespread disease of common wheat worldwide. In the present study, 83 wheat cultivars from three provinces of China and 36 tester lines with known leaf rust resistance (Lr) genes were inoculated in the greenhouse with 18 Pt pathotypes to identify seedling effective Lr genes. Field tests were also performed to characterize slow leaf rusting responses at the adult plant growth stage in Baoding and Zhoukou in the 2014-15 and 2015-16 cropping seasons. Twelve Lr genes, viz. Lr1, Lr26, Lr3ka, Lr11, Lr10, Lr2b, Lr13, Lr21, Lr34, Lr37, Lr44, and Lr46 either singly or in combination were identified in 41 cultivars. Known Lr genes were not detected in the remaining 42 cultivars. The most commonly identified resistance genes were Lr26 (20 cultivars), Lr46 (18 cultivars), and Lr1 (eight cultivars). Less frequently detected genes included Lr13, Lr34, and Lr37 (each present in four cultivars), Lr10 (three cultivars), and Lr3ka and Lr44 (each in two cultivars). Evidence for the presence of genes Lr11, Lr2b, and Lr21 (each in one cultivar) was also obtained. Seventeen cultivars were found to have slow rusting resistance in both field growing seasons.

Recent trends and perspectives of molecular markers against fungal diseases in wheat

Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40-60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases.

Monitoring Three Plasmopara halstedii Resistance Genes in Iranian Sunflower Inbred Lines

BACKGROUND

Downy mildew caused by Plasmopara halstedii is a devastating disease in sunflower worldwide. Several dominant resistance genes designated as Pl have been identified and linked molecular markers have been demonstrated. However, no information on theresistance genes is available forIranian lines.

OBJECTIVES

The presence of three map-based molecular markers previously proved to be linked to different resistance genes were evaluated in sunflower inbred lines.

MATERIALS AND METHODS

Using PCR-based and CAPS molecular markers, 26 sunflower inbred lines with different responses to P. halstedii race 100 were used to detect the presence of three resistance loci including Pl₁ , Pl₆ and Pl₁₃ within the lines.

RESULTS

Molecular marker linked to Pl₁₃ was present in some of the sunflower lines but was not correlated with the phenotypic reaction of the lines to race 100. Despite the use of three markers linked to Pl₆ , PCR failed to amplify any corresponding product. This data may suggest that none of the genotypes possessed Pl₆ locus. Pl₁ -linked cleaved amplified polymorphic sequences (CAPS) were present in several resistance lines and effectively differentiated susceptible and resistant sunflower lines.

CONCLUSIONS

Applicability of molecular markers in breeding programs revisited in disease management.

Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.)

Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7414) and a repulsion phase marker (IABTPPN7983) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7983, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7414 did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7414 (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F2 population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.

Study of rust resistance genes in wheat germplasm with DNA markers

Wheat is a vital dietary component for human health and widely consumed in the world. Wheat rusts are dangerous pathogens and contribute serious threat to its production. In present study, PCR-Based DNA Markers were employed to check the rust resistance genes among 20 wheat genotypes and 22 markers were amplified. NTSYS-pc 2.2 was used to calculate genetic diversity and Nei and Li's coefficients ranged from 0.55 to 0.95. Cluster analysis was obtained using UPGMA (Unweighted Pair Group Method of Arithmetic Average) algorithm. Maximum no. of genes (23) was amplified from TW-760010 genotype whereas minimum no of genes (14) were amplified from TW-76005 genotype. The data gained from present study open up new ways to produce new varieties by breeding rust resistant germplasm to avoid the economic and food loss and varieties with improved characteristics.

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.

Fine genetic mapping of greenbug aphid-resistance gene Gb3 in Aegilops tauschii

The greenbug, Schizaphis graminum (Rondani), is an important aphid pest of small grain crops especially wheat (Triticum aestivum L., 2n = 6x = 42, genomes AABBDD) in many parts of the world. The greenbug-resistance gene Gb3 originated from Aegilops tauschii Coss. (2n = 2x = 14, genome D(t)D(t)) has shown consistent and durable resistance against prevailing greenbug biotypes in wheat fields. We previously mapped Gb3 in a recombination-rich, telomeric bin of wheat chromosome arm 7DL. In this study, high-resolution genetic mapping was carried out using an F(2:3) segregating population derived from two Ae. tauschii accessions, the resistant PI 268210 (original donor of Gb3 in the hexaploid wheat germplasm line 'Largo') and susceptible AL8/78. Molecular markers were developed by exploring bin-mapped wheat RFLPs, SSRs, ESTs and the Ae. tauschii physical map (BAC contigs). Wheat EST and Ae. tauschii BAC end sequences located in the deletion bin 7DL3-0.82-1.00 were used to design STS (sequence tagged site) or CAPS (Cleaved Amplified Polymorphic Sequence) markers. Forty-five PCR-based markers were developed and mapped to the chromosomal region spanning the Gb3 locus. The greenbug-resistance gene Gb3 now was delimited in an interval of 1.1 cM by two molecular markers (HI067J6-R and HI009B3-R). This localized high-resolution genetic map with markers closely linked to Gb3 lays a solid foundation for map based cloning of Gb3 and marker-assisted selection of this gene in wheat breeding.

Identification of microsatellite markers linked to leaf rust resistance gene Lr25 in wheat

The leaf rust resistance gene Lr25, transferred from Secale cereale L. into wheat and located on chromosome 4B, imparts resistance to all pathotypes of leaf rust in South-East Asia. In an F(2)-derived F(3) population, created by crossing TcLr25 that carries the gene Lr25 for leaf rust resistance with leaf rust-susceptible parent Agra Local, three microsatellite markers located on the long arm of chromosome 4B were found to be linked to the Lr25 locus. The donor parent TcLr25 is a near-isogenic line derived from the variety Thatcher. The most virulent pathotype of leaf rust in the South-East Asian region, designated 77-5 (121R63-1), was used for challenging the population under artificially controlled conditions. The marker Xgwm251 behaved as a co-dominant marker placed 3.8 cM away from the Lr25 locus on 4BL. Two null allele markers, Xgwm538 and Xgwm6, in the same linkage group were located at a distance of 3.8 cM and 16.2 cM from the Lr25 locus, respectively. The genetic sequence of Xgwm251, Lr25, Xgwm538, and Xgwm6 covered a total length of 20 cM on 4BL. The markers were validated for their specificity to Lr25 resistance in a set of 43 wheat genetic stocks representing 43 other Lr genes.

Genetic and correlation analysis of silique-traits in Brassica napus L. by quantitative trait locus mapping

Rapeseed yield is directly and indirectly influenced by the silique-traits, such as silique length (SL), seeds per silique (SS), seed weight (SW), because the silique is an organ which produced yield and a major photosynthesis organ as well. In this study, a linkage map comprising 150 simple sequence repeat and 195 amplified fragment length polymorphism markers covering 1,759.6 cM was constructed in a doubled haploid population from a cross between two genotypes of 'HZ396' and 'Y106'. In field experiments across three seasons and two locations in China 140 doubled haploid lines and their corresponding parents were evaluated for silique-traits. In total, 26 quantitative trait loci (QTL) were detected, of which 15 were clustered and integrated into 5 pleiotropic unique QTL by meta-analysis. These unique QTL, which in a certain sense reflected the significant positive correlation between SS and SL and the significant negative correlation between SW and SS by the genomic location and effects of QTL detected, were mapped on linkage groups N7, N8 and N13. A trait-by-trait meta-analysis revealed 5, 2 and 3 consensus QTL for SL, SS and SW, respectively. Epistatic effects varied according to the specific traits performed. All the epistatic interactions showed significant additive by additive effects while no significant epistasis by environment effect was identified. These findings provided a better understanding of the genetic factors controlling silique-traits and gained insights into the gene networks affecting silique-traits at QTL level in rapeseed.

Comparison ofThinopyrum intermediumderivatives carrying barley yellow dwarf virus resistance in wheat

Resistance to both barley yellow dwarf virus (BYDV) and cereal yellow dwarf virus (CYDV) has been demonstrated in wheat genetic stocks with Thinopyrum intermedium chromatin. A number of resistance-bearing translocations have been reported on chromosome arm 7DL from two independent Th. intermedium sources; one source is the addition line L1 and the other is the spontaneous substitution line P29. Another source of resistance in wheat cytogenetic stocks is available as a 2Ai(2D) substitution line. We used a set of 38 molecular markers and the available deletion stocks to compare the size of the 7DL translocations more comprehensively than has been done previously. We also compared the efficacy of BYDV resistance of the various genetic stocks both before and after transfer to a common genetic background. TC14 was confirmed as carrying the smallest translocation, replacing about 20% of the distal end of 7DL. TC5 and TC10 had 90% of the chromosome arm replaced by Th. intermedium chromatin; the proximal 10% corresponded to wheat chromatin. YW642 appeared to have the whole 7DL replaced by Th. intermedium chromatin, as confirmed by the co-dominant marker cfd68 mapping on the bin nearest the centromere. Translocation line P961341 had bins 3, 7, and 8 replaced by Th. intermedium chromatin, making this the second smallest translocation with BYDV and CYDV resistance. The translocation sizes reported here differ from some of the previous estimates. The translocated Th. intermedium segments appeared to be bigger than the replaced wheat 7DL fragments. All the resistances derived from the L1 and P29 group 7 chromosomes and the 2Ai#2 chromosome were effective in reducing the number of infected plants and the mean virus titre, regardless of the background. Some evidence is discussed suggesting the long arm of the Th. intermedium group 7 chromosome 7Ai#1 carries two resistances, the distal Bdv2 and a proximal second gene.

A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL

A recombinant inbred line (RIL) population and a set of advanced lines from multiple crosses were used to investigate the leaf rust (Puccinia triticina Eriks.) resistance carried by the durum wheat cultivar Creso and its derivatives (Colosseo and Plinio). One hundred seventy-six RILs from the cross Colosseo x Lloyd were tested under artificial rust inoculation in the field. The response at the seedling stage was also investigated. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult open field based-response was mapped on 7BL, with the favourable allele inherited from Colosseo. QLr.ubo-7B.2 showed R2 and LOD peak values for the area under disease progress curve (AUDPC) equal to 72.9% and 44.5, respectively. The presence and location of QLr.ubo-7B.2 was validated by a linkage disequilibrium-based test using two-year field data of 62 advanced lines from 21 crosses with Creso, Colosseo or Plinio as resistance donors. QLr.ubo-7B.2 maps in a gene-dense region (7BL10-0.78-1.00) carrying several genes/QTLs in wheat and barley for resistance to rusts and other fungal diseases.

AB-QTL analysis in winter wheat: II. Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population

The present study aimed to localize exotic quantitative trait locus (QTL) alleles for the improvement of leaf rust (P. triticina) resistance in an advanced backcross (AB) population, B22, which is derived from a cross between the winter wheat cultivar Batis (Triticum aestivum) and the synthetic wheat accession Syn022L. The latter was developed from hybridization of T. turgidum ssp. dicoccoides and T. tauschii. Altogether, 250 BC2F3 lines of B22 were assessed for seedling resistance against the leaf rust isolate 77WxR under controlled conditions. In addition, field resistance against leaf rust was evaluated by assessing symptom severity under natural infestation across multiple environments. Simultaneously, population B22 was genotyped with a total of 97 SSR markers, distributed over the wheat A, B and D genomes. The phenotype and genotype data were subjected to QTL analysis by applying a 3-factorial mixed model analysis of variance including the marker genotype as a fixed effect and the environments, the lines and the marker by environment interactions as random effects. The QTL analysis revealed six putative QTLs for seedling resistance and seven for field resistance. For seedling resistance, the effects of exotic QTL alleles improved resistance at all detected loci. The maximum decrease of disease symptoms (-46.3%) was associated with marker locus Xbarc149 on chromosome 1D. For field resistance, two loci had stable main effects across environments and five loci exhibited marker by environment interaction effects. The strongest effects were detected at marker locus Xbarc149 on chromosome 1D, at which the exotic allele decreased seedling symptoms by 46.3% and field symptoms by 43.6%, respectively. Some of the detected QTLs co-localized with known resistance genes, while others appear to be as novel resistance loci. Our findings indicate, that the exotic wheat accession Syn022L may be useful for the improvement of leaf rust resistance in cultivated wheat.

Trigenomic chromosomes by recombination of Thinopyrum intermedium and Th. ponticum translocations in wheat

Rusts and barley yellow dwarf virus (BYDV) are among the main diseases affecting wheat production world wide for which wild relatives have been the source of a number of translocations carrying resistance genes. Nevertheless, along with desirable traits, alien translocations often carry deleterious genes. We have generated recombinants in a bread wheat background between two alien translocations: TC5, ex-Thinopyrum (Th) intermedium, carrying BYDV resistance gene Bdv2; and T4m, ex-Th. ponticum, carrying rust resistance genes Lr19 and Sr25. Because both these translocations are on the wheat chromosome arm 7DL, homoeologous recombination was attempted in the double hemizygote (TC5/T4m) in a background homozygous for the ph1b mutation. The identification of recombinants was facilitated by the use of newly developed molecular markers for each of the alien genomes represented in the two translocations and by studying derived F(2), F(3) and doubled haploid populations. The occurrence of recombination was confirmed with molecular markers and bioassays on families of testcrosses between putative recombinants and bread wheat, and in F(2) populations derived from the testcrosses. As a consequence it has been possible to derive a genetic map of markers and resistance genes on these previously fixed alien linkage blocks. We have obtained fertile progeny carrying new tri-genomic recombinant chromosomes. Furthermore we have demonstrated that some of the recombinants carried resistance genes Lr19 and Bdv2 yet lacked the self-elimination trait associated with shortened T4 segments. We have also shown that the recombinant translocations are fixed and stable once removed from the influence of the ph1b. The molecular markers developed in this study will facilitate selection of individuals carrying recombinant Th. intermedium-Th. ponticum translocations (Pontin series) in breeding programs.