Genome-wide association mapping of leaf rust and stripe rust resistance in wheat accessions using the 90K SNP array

Genetic Dissection of Triple Rust Resistance (Leaf, Yellow, and Stem Rust) in Kenyan Wheat Cultivar, "Kasuku"

Climate change is driving the spread of transboundary wheat diseases, necessitating the development of resilient wheat varieties for sustainable agriculture. Wheat rusts, including leaf rust (LR), yellow rust (YR), and stem rust (SR), remain among the most economically significant diseases, causing substantial yield losses worldwide. Enhancing genetic diversity by identifying and deploying rust resistance genes is crucial for durable resistance in wheat breeding programs. This study aimed to identify quantitative trait loci (QTL) associated with rust resistance in the CIMMYT wheat line Kasuku, released in Kenya in 2018. A recombinant inbred line (RIL) population (181 lines) derived from Kasuku (triple rust-resistant) and Apav#1 (triple rust-susceptible) was evaluated under artificial LR and YR epidemics in Mexico and YR and SR in Kenya. QTL mapping using genotyping-by-sequencing (DArTSeq) and phenotypic data identified four major loci: QLrYrSr.cim-1BL (Lr46/Yr29/Sr58) on 1BL, conferring resistance to LR, YR, and SR; QLrYr.cim-2AS (Yr17/Lr37) on 2AS, providing LR and YR resistance; QLrYr.cim-3AL on 3AL; and QLrYrSr.cim-6AL on 6AL, representing novel loci associated with multiple rust resistances. Additionally, minor QTL were also identified: for LR (QLr.cim-2DS on 2DS, QLr.cim-6DS on 6DS), for YR (QYrKen.cim-3DS on 3DS, QYrKen.cim-6BS on 6BS), and for SR (QSr.cim-2BS on 2BS, QSr.cim-5AL on 5AL, QSr.cim-6AS on 6AS). RILs carrying these QTL combinations exhibited significant reductions in rust severity. Flanking markers for these loci are being used to develop Kompetitive Allele-Specific PCR (KASP) markers for fine mapping and marker-assisted selection (MAS). These findings contribute to the strategic deployment of rust resistance genes in wheat breeding programs, facilitating durable resistance to multiple rust pathogens.

Genome-wide association mapping for the identification of stripe rust resistance loci in US hard winter wheat

KEY MESSAGE

The GWAS and testing with Yr gene linked markers identified 109 loci including 40 novel loci for all-stage and adult plant stage resistance to stripe rust in 459 US contemporary hard winter wheat genotypes. Stripe rust is a destructive wheat disease, caused by Puccinia striiformis f. sp. tritici (Pst). To identify sources of stripe rust resistance in US contemporary hard winter wheat, a panel of 459 Great Plains wheat genotypes was evaluated at the seedling stage against five US Pst races and at the adult plant stage in field environments in Oklahoma, Kansas, and Washington. The results showed that 7-14% of the genotypes were resistant to Pst races at the seedling stage, whereas 32-78% of genotypes were resistant at the adult plant stage across field environments, indicating the presence of adult plant resistance. Sixteen genotypes displayed a broad spectrum of resistance to all five Pst races and across all field environments. The panel was further genotyped using 9858 single-nucleotide polymorphisms (SNPs) generated from multiplex restriction amplicon sequencing (MRASeq) and the functional DNA markers linked to the known stripe rust resistance (Yr) genes Yr5, Yr15, Yr17, Yr18, Yr29, Yr36, Yr40, Yr46, and QYr.tamu-2B. A genome-wide association study (GWAS) was performed using genotypic and phenotypic data, which identified 110 SNPs and the functional markers linked to Yr15 and Yr17 to be significantly associated with stripe rust response. In addition, Yr5, Yr15, Yr17, Yr18, Yr29, and QYr.tamu-2B were detected by their functional DNA markers in the panel. This study identified 40 novel loci associated with stripe rust resistance in genomic regions not previously characterized by known Yr genes. These findings offer significant opportunities to diversify and enhance stripe rust resistance in hard winter wheat.

Do different wheat ploidy levels respond differently against stripe rust infection: Interplay between reactive oxygen species (ROS) and the antioxidant defense system?

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) is the most damaging wheat disease, causing substantial losses in global wheat production and productivity. Our study aimed to unravel the complex reciprocity between reactive oxygen species and the antioxidant defense system as a source of resistance against stripe rust in diploid, tetraploid and hexaploid wheat genotypes. The significant genetic variability for stripe rust in the materials under study was evident as the genotypes showed contrasting responses during both the adult and seedling stages. Our thorough perspective on the biochemical responses of wheat genotypes to stripe rust infection revealed distinct patterns in oxidative damage, antioxidant enzymes and photosynthetic pigments. Principal component analysis revealed inverse correlations between antioxidants and ROS, underscoring their key function in maintaining the cellular redox balance and protecting plants against oxidative damage. Diploid (Ae. tauschii) wild wheat exhibited a better biochemical defense system and greater resistance to stripe rust than the tetraploid (T. durum) and hexaploid (Triticum aestivum) wheat genotypes. The antioxidant enzyme activity of durum wheat was moderate compared to diploid and hexaploid wheat genotypes. The hexaploid wheat genotypes exhibited increased ROS production, reduced antioxidant enzyme activity and decreased photosynthetic pigment levels. This study enhances understanding of the antioxidant defense system across different wheat ploidies facing stripe rust, serving as a valuable strategy for improving crop disease resistance. This study validated the biochemical response of stripe rust-resistant and susceptible candidate genotypes, which will be used to develop genetic resources for discovering stripe rust resistance genes in wheat.

Unraveling genetic mysteries: A comprehensive review of GWAS and DNA insights in animal and plant pathosystems

DNA serves as the carrier of genetic information, with sequence variations playing a pivotal role in defining hereditary traits. Genome-Wide Association Studies (GWAS) facilitate the investigation of the links between genetic variations and phenotypes, significantly influencing biological research, particularly in animal and plant pathology. By identifying genetic markers associated with specific traits or diseases, GWAS enhances our understanding of host-pathogen interactions and improves disease-resistant breeding strategies. It has been vital in revealing the genetic basis of disease resistance, pinpointing key genes and DNA loci, which enrich genetic resources for breeding programs and deepen our knowledge of disease resistance mechanisms at the DNA level. Additionally, GWAS contributes to pathogen population genetics, facilitating a thorough exploration of pathogen virulence. Integrating GWAS with marker-assisted selection enhances breeding efficiency and precision in selecting for disease-resistant traits. While previous research has largely focused on host genetics, the genetic variation of pathogens is equally significant. Notably, reports integrating animal and plant pathosystems are still lacking. Given the importance of these systems, this review summarizes key advancements in this field, addresses current challenges, and proposes future directions, thereby offering a vital reference for ongoing research.

Broad-spectrum resistance to fungal foliar diseases in wheat: recent efforts and achievements

Wheat (Triticum spp.) is one of the most important cereal crops in the world. Several diseases affect wheat production and can cause 20-80% yield loss annually. Out of these diseases, stripe rust, also known as yellow rust (Puccinia striiformis f. sp. tritici), stem rust (Puccinia graminis f. sp. tritici), leaf rust (Puccinia recondita), and powdery mildew (Blumeria graminis f. sp. tritici) are the most important fungal diseases that infect the foliar part of the plant. Many efforts were made to improve wheat resistance to these diseases. Due to the continuous advancement in sequencing methods and genomic tools, genome-wide association study has become available worldwide. This analysis enabled wheat breeders to detect genomic regions controlling the resistance in specific countries. In this review, molecular markers significantly associated with the resistance of the mentioned foliar diseases in the last five years were reviewed. Common markers that control broad-spectrum resistance in different countries were identified. Furthermore, common genes controlling the resistance of more than one of these foliar diseases were identified. The importance of these genes, their functional annotation, and the potential for gene enrichment are discussed. This review will be valuable to wheat breeders in producing genotypes with broad-spectrum resistance by applying genomic selection for the target common markers and associated genes.

Bacterial N-Acyl Homoserine Lactone Priming Enhances Leaf-Rust Resistance in Winter Wheat and Some Genomic Regions Are Associated with Priming Efficiency

Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated adaptability of pathogen populations hamper achieving durable resistance in wheat. Emerging alternatives, such as microbial priming, may represent an effective measure to stimulate plant defense mechanisms and could serve as a means of controlling a broad range of pathogens. In this study, 175 wheat genotypes were inoculated with two bacterial strains: Ensifer meliloti strain expR+ch (producing N-acyl homoserine lactone (AHL)) or transformed E. meliloti carrying the lactonase gene attM (control). In total, 21 genotypes indicated higher resistance upon bacterial AHL priming. Subsequently, the phenotypic data of 175 genotypes combined with 9917 single-nucleotide polymorphisms (SNPs) in a genome-wide association study to identify quantitative trait loci (QTLs) and associated markers for relative infection under attM and expR+ch conditions and priming efficiency using the Genome Association and Prediction Integrated Tool (GAPIT). In total, 15 QTLs for relative infection under both conditions and priming efficiency were identified on chromosomes 1A, 1B, 2A, 3A, 3B, 3D, 6A, and 6B, which may represent targets for wheat breeding for priming and leaf-rust resistance.

Pleiotropic Quantitative Trait Loci (QTL) Mining for Regulating Wheat Processing Quality- and Yield-Related Traits

To investigate the genetic basis of processing quality- and yield-related traits in bread wheat (Triticum aestivum L., AABBDD), a systematic analysis of wheat processing quality- and yield-related traits based on genome-wide association studies (GWASs) of 285 regional test lines of wheat from Hebei province, China, was conducted. A total of 87 quantitative trait loci (QTL), including twenty-one for water absorption (WA), four for wet gluten content, eight for grain protein content, seventeen for dough stability time (DST), thirteen for extension area (EA), twelve for maximum resistance (MR), five for thousand-grain weight (TGW), one for grain length, and six for grain width were identified. These QTL harbored 188 significant single-nucleotide polymorphisms (SNPs). Twenty-five SNPs were simultaneously associated with multiple traits. Notably, the SNP AX-111015470 on chromosome 1A was associated with DST, EA, and MR. SNPs AX-111917292 and AX-109124553 on chromosome 5D were associated with wheat WA and TGW. Most processing quality-related QTL and seven grain yield-related QTL identified in this study were newly discovered. Among the surveyed accessions, 18 rare superior alleles were identified. This study identified significant QTL associated with quality-related and yield-related traits in wheat, and some of them showed pleiotropic effects. This study will facilitate molecular designs that seek to achieve synergistic improvements of wheat quality and yield.

Development and identification of a novel wheat-Thinopyrum ponticum disomic substitution line DS5Ag(5D) with new genes conferring resistance to powdery mildew and leaf rust

BACKGROUND

Powdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.) production. Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbExExStStStSt) contains genes that confer high levels of resistance to these diseases.

RESULTS

An elite wheat-Th. ponticum disomic substitution line, DS5Ag(5D), was developed in the Bainong Aikang 58 (AK58) background. The line was assessed using genomic in situ hybridization (GISH), oligo-nucleotide probe multiplex (ONPM) fluorescence in situ hybridization (FISH), and molecular markers. Twenty eight chromosome-specific molecular markers were identified for the alien chromosome, and 22 of them were co-dominant. Additionally, SNP markers from the wheat 660 K SNP chip were utilized to confirm chromosome identification and they provide molecular tools for tagging the chromosome in concern. The substitution line demonstrated high levels of resistance to powdery mildew throughout its growth period and to leaf rust at the adult stage. Based on the resistance evaluation of five F5 populations between the substitution lines and wheat genotypes with different levels of sensitivity to the two diseases. Results showed that the resistance genes located on 5Ag confered stable resistance against both diseases across different backgrounds. Resistance spectrum analysis combined with diagnostic marker detection of known resistance genes of Th. ponticum revealed that 5Ag contained two novel genes, Pm5Ag and Lr5Ag, which conferred resistance to powdery mildew and leaf rust, respectively.

CONCLUSIONS

In this study, a novel wheat-Th. ponticum disomic substitution line DS5Ag(5D) was successfully developed. The Th. ponticum chromosome 5Ag contain new resistance genes for powdery mildew and leaf rust. Chromosomic-specific molecular markers were generated and they can be used to track the 5Ag chromosome fragments. Consequently, this study provides new elite germplasm resources and molecular markers to facilitate the breeding of wheat varieties that is resistant to powdery mildew and leaf rust.

Genetic basis of an elite wheat cultivar Guinong 29 with harmonious improvement between multiple diseases resistance and other comprehensive traits

Fungal diseases, such as powdery mildew and rusts, significantly affect the quality and yield of wheat. Pyramiding diverse types of resistance genes into cultivars represents the preferred strategy to combat these diseases. Moreover, achieving collaborative improvement between diseases resistance, abiotic stress, quality, and agronomic and yield traits is difficult in genetic breeding. In this study, the wheat cultivar, Guinong 29 (GN29), showed high resistance to powdery mildew and stripe rust at both seedling and adult plant stages, and was susceptible to leaf rust at the seedling stage but slow resistance at the adult-plant stage. Meanwhile, it has elite agronomic and yield traits, indicating promising coordination ability among multiple diseases resistance and other key breeding traits. To determine the genetic basis of these elite traits, GN29 was tested with 113 molecular markers for 98 genes associated with diseases resistance, stress tolerance, quality, and adaptability. The results indicated that two powdery mildew resistance (Pm) genes, Pm2 and Pm21, confirmed the outstanding resistance to powdery mildew through genetic analysis, marker detection, genomic in situ hybridization (GISH), non-denaturing fluorescence in situ hybridization (ND-FISH), and homology-based cloning; the stripe rust resistance (Yr) gene Yr26 and leaf rust resistance (Lr) genes Lr1 and Lr46 conferred the stripe rust and slow leaf rust resistance in GN29, respectively. Meanwhile, GN29 carries dwarfing genes Rht-B1b and Rht-D1a, vernalization genes vrn-A1, vrn-B1, vrn-D1, and vrn-B3, which were consistent with the phenotypic traits in dwarf characteristic and semi-winter property; carries genes Dreb1 and Ta-CRT for stress tolerance to drought, salinity, low temperature, and abscisic acid (ABA), suggesting that GN29 may also have elite stress-tolerance ability; and carries two low-molecular-weight glutenin subunit genes Glu-B3b and Glu-B3bef which contributed to high baking quality. This study not only elucidated the genetic basis of the elite traits in GN29 but also verified the capability for harmonious improvement in both multiple diseases resistance and other comprehensive traits, offering valuable information for breeding breakthrough-resistant cultivars.

Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene

Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.

Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.)

BACKGROUND

Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR).

RESULTS

Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype.

CONCLUSION

The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.

The Autophagy-Related Musa acuminata Protein MaATG8F Interacts with MaATG4B, Regulating Banana Disease Resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4

Banana is one of the most important fruits in the world due to its status as a major food source for more than 400 million people. Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes substantial losses of banana crops every year, and molecular host resistance mechanisms are currently unknown. We here performed a genomewide analysis of the autophagy-related protein 8 (ATG8) family in a wild banana species. The banana genome was found to contain 10 MaATG8 genes. Four MaATG8s formed a gene cluster in the distal part of chromosome 4. Phylogenetic analysis of ATG8 families in banana, Arabidopsis thaliana, citrus, rice, and ginger revealed five major phylogenetic clades shared by all of these plant species, demonstrating evolutionary conservation of the MaATG8 families. The transcriptomic analysis of plants infected with Foc TR4 showed that nine of the MaATG8 genes were more highly induced in resistant cultivars than in susceptible cultivars. Finally, MaATG8F was found to interact with MaATG4B in vitro (with yeast two-hybrid assays), and MaATG8F and MaATG4B all positively regulated banana resistance to Foc TR4. Our study provides novel insights into the structure, distribution, evolution, and expression of the MaATG8 family in bananas. Furthermore, the discovery of interactions between MaATG8F and MaATG4B could facilitate future research of disease resistance genes for the genetic improvement of bananas.

Genetic architecture of adult-plant resistance to stripe rust in bread wheat (Triticum aestivum L.) association panel

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Phenotyping and Identification of Molecular Markers Associated with Leaf Rust Resistance in the Wheat Germplasm from Kazakhstan, CIMMYT and ICARDA

Leaf rust (LR) is the most widespread disease of common wheat worldwide. In order to evaluate leaf rust resistance, 70 uncharacterized wheat cultivars and promising lines with unknown leaf rust resistance genes (Lr genes) were exposed to Kazakhstani Puccinia triticina (Pt) races at the seedling stage. Field tests were performed to characterize leaf rust responses at the adult plant growth stage in the 2020-2021 and 2021-2022 cropping seasons. The wheat collection showed phenotypic diversity when tested with two virulent races of Pt. Thirteen wheat genotypes (18.6%) showed high resistance at both seedling and adult plant stages. In most cases, breeding material originating from international nurseries showed higher resistance to LR. Nine Lr genes, viz. Lr9, Lr10, Lr19, Lr26, Lr28, Lr34, Lr37, Lr46, and Lr68, either singly or in combination, were identified in 47 genotypes. Known Lr genes were not detected in the remaining 23 genotypes. The most commonly identified resistance genes were Lr37 (17 cultivars), Lr34 (16 cultivars), and Lr46 (10 cultivars), while Lr19, Lr68, Lr26, and Lr28 were the least frequent. Four Lr genes were identified in Keremet and Hisorok, followed by three Lr genes in Aliya, Rasad, Reke, Mataj, Egana and Almaly/Obri. The molecular screening revealed twenty-nine carriers of a single Lr gene, ten carriers of two genes, six carriers of three genes, and two carriers of four genes. Most of these accessions showed a high and moderate level of APR (Adult plant resistance) and may be utilized for the incorporation of Lr genes in well-adapted wheat cultivars. The most effective combination was Lr37, Lr34, and Lr68, the carriers of which were characterized by a low disease susceptibility index. The obtained results will facilitate breeding programs for wheat resistance in Kazakhstan.

Mapping of quantitative trait loci for leaf rust resistance in the wheat population 'Xinmai 26/Zhoumai 22'

Leaf rust, caused by the fungal pathogen Puccinia triticina (Pt), is one of the major and dangerous diseases of wheat, and has caused serious yield loss of wheat worldwide. Here, we investigated adult-plant resistance (APR) to leaf rust in a recombinant inbred line (RIL) population derived from 'Xinmai 26' and 'Zhoumai 22' over 3 years. Linkage mapping for APR to leaf rust revealed four quantitative trait loci (QTL) in this RIL population. Two QTL, QLr.hnau-2BS and QLr.hnau-3BS were contributed by 'Zhoumai22', whereas QLr.hnau-2DS and QLr.hnau-5AL were contributed by 'Xinmai 26'. The QLr.hnau-2BS covering a race-specific resistance gene Lr13 showed the most stable APR to leaf rust. Overexpression of Lr13 significantly increased APR to leaf rust. Interestingly, we found that a CNL(coiled coil-nucleotide-binding site-leucine-rich repeat)-like gene, TaCN, in QLr.hnau-2BS completely co-segregated with leaf rust resistance. The resistant haplotype TaCN-R possessed half the sequence of the coiled-coil domain of TaCN protein. Lr13 strongly interacted with TaCN-R, but did not interact with the full-length TaCN (TaCN-S). In addition, TaCN-R was significantly induced after Pt inoculation and changed the sub-cellular localization of Lr13 after interaction. Therefore, we hypothesized that TaCN-R mediated leaf rust resistance possibly by interacting with Lr13. This study provides important QTL for APR to leaf rust, and new insights into understanding how a CNL gene modulates disease resistance in common wheat.

Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat

Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.

Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis

BACKGROUND

Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces.

RESULTS

Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions.

CONCLUSIONS

Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.

Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis

Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

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

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

Genetic Basis of Resistance to Warrior (-) Yellow Rust Race at the Seedling Stage in Current Central and Northern European Winter Wheat Germplasm

To evaluate genetic variability and seedling plant response to a dominating Warrior (-) race of yellow rust in Northern and Central European germplasm, we used a population of 229 winter wheat cultivars and breeding lines for a genome-wide association study (GWAS). A wide variation in yellow rust disease severity (based on infection types 1-9) was observed in this panel. Four breeding lines, TS049 (from Austria), TS111, TS185, and TS229 (from Germany), and one cultivar, TS158 (KWS Talent), from Germany were found to be resistant to Warrior (-) FS 53/20 and Warrior (-) G 23/19. The GWAS identified five significant SNPs associated with yellow rust on chromosomes 1B, 2A, 5B, and 7A for Warrior (-) FS 53/20, while one SNP on chromosome 5B was associated with disease for Warrior (-) G 23/19. For Warrior (-) FS 53/20, we discovered a new QTL for yellow rust resistance associated with the marker Kukri_c5357_323 on chromosome 1B. The resistant alleles G and T at the marker loci Kukri_c5357_323 on chromosome 1B and Excalibur_c17489_804 on chromosome 5B showed the largest effects (1.21 and 0.81, respectively) on the severity of Warrior (-) FS 53/20 and Warrior (-) G 23/19. Our results provide the basis for knowledge-based resistance breeding in the face of the enormous impact of the Warrior (-) race on wheat production in Europe.

Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat

Fifteen and eleven loci, with most loci being novel, were identified to associate with seedling and adult resistances, respectively, to the durum-specific races of leaf rust pathogen in cultivated emmer. Leaf rust, caused by Puccinia triticina (Pt), constantly threatens durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum) production worldwide. A Pt race BBBQD detected in California in 2009 poses a potential threat to durum production in North America because resistance source to this race is rare in durum germplasm. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to BBBQD and for adult resistance to a mixture of durum-specific races BBBQJ, CCMSS, and MCDSS in the field, and genotyped the panel using genotype-by-sequencing (GBS) and the 9 K SNP (Single Nucleotide Polymorphism) Infinium array. The results showed 24 and nine accessions consistently exhibited seedling and adult resistance, respectively, with two accessions providing resistance at both stages. We performed genome-wide association studies using 46,383 GBS and 4,331 9 K SNP markers and identified 15 quantitative trait loci (QTL) for seedling resistance located mostly on chromosomes 2B and 6B, and 11 QTL for adult resistance on 2B, 3B and 6A. Of these QTL, one might be associated with leaf rust resistance (Lr) gene Lr53, and two with the QTL previously reported in durum or hexaploid wheat. The remaining QTL are potentially associated with new Lr genes. Further linkage analysis and gene cloning are necessary to identify the causal genes underlying these QTL. The emmer accessions with high levels of resistance will be useful for developing mapping populations and adapted durum germplasm and varieties with resistance to the durum-specific races.

Mapping and characterization of a novel adult-plant leaf rust resistance gene LrYang16G216 via bulked segregant analysis and conventional linkage method

A novel adult-plant leaf rust resistance gene LrYang16G216 on wheat chromosome 6BL was identified and mapped to a 0.59 cM genetic interval by BSA and conventional linkage method. Leaf rust (Puccinia triticina) is one of the most devastating fungal diseases of wheat (Triticum aestivum L.). Discovery and identification of new resistance genes is essential to develop disease-resistant cultivars. An advanced breeding line Yang16G216 was previously identified to confer adult-plant resistance (APR) to leaf rust. In this research, a recombinant inbred line (RIL) population was constructed from the cross between Yang16G216 and a highly susceptible line Yang16M6393, and genotyped with exome capture sequencing and 55 K SNP array. Through bulked segregant analysis (BSA) and genetic linkage mapping, a stable APR gene, designated as LrYang16G216, was detected and mapped to the distal region of chromosome arm 6BL with a genetic interval of 2.8 cM. For further verification, another RIL population derived from the cross between Yang16G216 and a susceptible wheat variety Yangmai 29 was analyzed using the enriched markers in the target interval, and LrYang16G216 was further narrowed to a 0.59 cM genetic interval flanked by the KASP markers Ax109403980 and Ax95083494, corresponding to the physical position 712.34-713.94 Mb in the Chinese Spring reference genome, in which twenty-six disease resistance-related genes were annotated. Based on leaf rust resistance spectrum, mapping data and physical location, LrYang16G216 was identified to be a novel and effective APR gene. The LrYang16G216 with linked markers will be useful for marker-assisted selection in wheat resistance breeding.

Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers

BACKGROUND

During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype.

RESULTS

A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker.

CONCLUSIONS

The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.

A Novel Wheat-Rye 2R (2D) Disomic Substitution Line Pyramids Two Types of Resistance to Powdery Mildew

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is a devastating disease of wheat that seriously affects yield and quality worldwide. Because of the extensive growth of wheat cultivars with homogeneous genetic background, exploring novel resistant resources from wheat relatives has become important for increasing the genetic diversity of wheat. Rye (Secale cereale) is a wheat relative possessing abundant resistance genes because of its high variation. Wheat line AL69, resistant to powdery mildew, was developed by crossing, backcrossing, and self-pollination for multiple generations between hexaploid triticale Zhongsi 237 and common wheat cultivar Zimai 17. Through genomic in situ hybridization (GISH) and multicolor fluorescence in situ hybridization (FISH), nondenaturing FISH, multicolor GISH, and selection with specific molecular markers, AL69 was determined to be a wheat-rye 2R (2D) disomic substitution line. Testing with different B. graminis f. sp. tritici isolates and genetic analysis showed that the all-stage resistance (also called seedling resistance) of AL69 was conferred by the cataloged powdery mildew resistance gene Pm4b derived from Zimai 17, and its adult-plant resistance was derived from the alien chromosome 2R of Zhongsi 237, which was found to be different from the previously reported rye-derived Pm genes, including Pm7 on 2RL. In addition, AL69 showed improved spike number per plant, spike length, fertile spikelet number per spike, kernel number per spike, and grain yield per plant compared with its wheat parent Zimai 17. An elite line S251 combining powdery mildew resistance with excellent agronomic performance was selected from the progenies of AL69 and wheat cultivar Jimai 22. Therefore, AL69 has two types of resistance genes to powdery mildew and improved agronomic traits through pyramiding and thus can be used as a promising genetic stock for wheat breeding.

Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing

Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to characterize new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single, incompletely dominant gene designated as Yr84. Through bulked segregant analysis sequencing (BSA-Seq) we identified a 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used to design genetic markers for recombinant screening, further refining the interval of Yr84 to a 2.3-3.3 Mb in tetraploid wheat genomes. This interval contains 34 candidate genes encoding for protein domains involved in disease resistance responses. Furthermore, KASP markers closely-linked to Yr84 were developed to facilitate marker-assisted selection for rust resistance breeding.

Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan

Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50−60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars.

Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.)

In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.

Genome-Wide Screening of Broad-Spectrum Resistance to Leaf Rust (Puccinia triticina Eriks) in Spring Wheat (Triticum aestivum L.)

Wheat leaf rust (LR) causes significant yield losses worldwide. In Egypt, resistant cultivars began to lose their efficiency in leaf rust resistance. Therefore, a diverse spring wheat panel was evaluated at the seedling stage to identify new sources of broad-spectrum seedling resistance against the Egyptian Puccinia triticina (Pt) races. In three different experiments, seedling evaluation was done using Pt spores collected from different fields and growing seasons. Highly significant differences were found among experiments confirming the presence of different races population in each experiment. Highly significant differences were found among the tested genotypes confirming the ability to select superior genotypes. Genome-wide association study (GWAS) was conducted for each experiment and a set of 87 markers located within 48 gene models were identified. The identified gene models were associated with disease resistance in wheat. Five gene models were identified to resist all Pt races in at least two experiments and could be identified as stable genes under Egyptian conditions. Ten genotypes from five different countries were stable against all the tested Pt races but showed different degrees of resistance.

Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.)

Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [-log₁₀(P) ≥ 3], which explained 5.91-15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding.

Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.)

A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.

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.

Meta-QTLs and candidate genes for stripe rust resistance in wheat

In bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders' MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning.

Linkage and association mapping and Kompetitive allele-specific PCR marker development for improving grain protein content in wheat

Linkage and association mapping identified nine candidate intervals for wheat GPC, and large-scale association mapping based on 9 corresponding KASP markers and 1163 F₄ breeding lines revealed 3 significant markers. Wheat grain protein content (GPC) is an important quality indicator. The GPC of wheat grown in the middle and lower reaches of the Yangtze River is often low. Marker-assisted selection (MAS) is an effective tool for improving quantitative traits; however, most markers have not been effectively applied in GPC improvement except Gpc-B1, although many loci associated with GPC were identified. In this study, linkage analysis using a recombinant inbred line population from the cross of core parents of Ningmai 9 and Yangmai 158 and association mapping using the local cultivated varieties were performed and nine candidate intervals were identified. The appropriate kompetitive allele-specific PCR (KASP) markers associated with GPC were successfully developed and screened in 1163 F4 breeding lines. Three markers, Kgpc-2B, Kgpc-2D, and Kgpc-4A, were validated to be significantly related to GPC by large-scale association mapping, and they were combined to achieve the highest efficiency to enhance GPC. We applied these markers in 164 F6 breeding lines and obtained 15 lines with high GPC, indicating their high selective efficiency. Further, strategies for gene exploration in the three significant intervals were proposed. These results were expected to provide a novel route for improving GPC in wheat quality breeding.