Quantitative trait Loci mapping for adult-plant resistance to powdery mildew in bread wheat

Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133

A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.

Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat

Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020-2021, 2021-2022, and 2022-2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker-trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020-2021 and 2021-2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host-pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars.

Fine mapping of two recessive powdery mildew resistance genes from Aegilops tauschii accession CIae8

KEY MESSAGE

Two recessive powdery mildew resistance loci pmAeCIae8_2DS and pmAeCIae8_7DS from Aegilops tauschii were mapped and two synthesized hexaploid wheat lines were developed by distant hybridization. Wheat powdery mildew (Pm), one of the worldwide destructive fungal diseases, causes significant yield loss up to 30%. The identification of new Pm resistance genes will enrich the genetic diversity of wheat breeding for Pm resistance. Aegilops tauschii is the ancestor donor of sub-genome D of hexaploid wheat. It provides beneficial genes that can be easily transferred into wheat by producing synthetic hexaploid wheat followed by genetic recombination. We assessed the Pm resistance level of 35 Ae. tauschii accessions from different origins. Accession CIae8 exhibited high Pm resistance. Inheritance analysis and gene mapping were performed using F2 and F2:3 populations derived from the cross between CIae8 and a Pm susceptible accession PI574467. The Pm resistance of CIae8 was controlled by two independent recessive genes. Bulked segregate analysis using a 55 K SNP array revealed the SNPs were mainly enriched into genome regions, i.e. 2DS (13.5-20 Mb) and 7DS (4.0-15.5 Mb). The Pm resistance loci were named as pmAeCIae8_2DS and pmAeCIae8_7DS, respectively. By recombinant screening, we narrowed the pmAeCIae8_2DS into a 370-kb interval flanked by markers CINAU-AE7800 (14.89 Mb) and CINAU-AE20 (15.26 Mb), and narrowed the pmAeCIae8_7DS into a 260-kb interval flanked by markers CINAU-AE58 (4.72 Mb) and CINAU-AE25 (4.98 Mb). The molecular markers closely linked with the resistance loci were developed, and two synthesized hexaploid wheat (SHW) lines were produced. These laid the foundation for cloning of the two resistance loci and for transferring the resistance into common wheat.

Resistance to Powdery Mildew Is Conferred by Different Genetic Loci at the Adult-Plant and Seedling Stages in Winter Wheat Line Tianmin 668

Winter wheat line Tianmin 668 was crossed with susceptible cultivar Jingshuang 16 to develop 216 recombinant inbred lines (RILs) for dissecting its adult-plant resistance (APR) and all-stage resistance (ASR) against powdery mildew. The RIL population was genotyped on a 16K genotyping by target sequencing single-nucleotide polymorphism array and phenotyped in six field trials and in the greenhouse. Three loci-QPmtj.caas-2BL, QPmtj.caas-2AS, and QPmtj.caas-5AL-conferring APR to powdery mildew were detected on chromosomes 2BL, 2AS, and 5AL, respectively, of Tianmin 668. The effect of resistance to powdery mildew for QPmtj.caas-2BL was greater than that of the other two loci. A Kompetitive allele-specific PCR marker specific for QPmtj.caas-2BL was developed and verified on 402 wheat cultivars or breeding lines. Results of virulence and avirulence patterns to 17 Blumeria graminis f. sp. tritici isolates, bulked segregant analysis-RNA-sequencing, and a genetic linkage mapping identified a resistance allele at locus Pm4 in Tianmin 668 based on the seedling phenotypes of the RIL population. The PCR-based DNA sequence alignment and cosegregation of the functional marker with the phenotypes of the RIL population demonstrated that Pm4d was responsible for the ASR to isolate Bgt1 in Tianmin 668. The dissection of genetic loci for APR and ASR may facilitate the application of Tianmin 668 in developing powdery mildew-resistant wheat cultivars.

Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta-QTL analysis

Leaf rust, caused by the fungus Puccinia triticina Erikss (Pt), is a destructive disease affecting wheat (Triticum aestivum L.) and a threat to food security. Developing resistant cultivars represents a useful method of disease control, and thus, understanding the genetic basis for leaf rust resistance is required. To this end, a comprehensive bibliographic search for leaf rust resistance quantitative trait loci (QTL) was performed, and 393 QTL were collected from 50 QTL mapping studies. Afterward, a consensus map with a total length of 4,567 cM consisting of different types of markers (simple sequence repeat [SSR], diversity arrays technology [DArT], chip-based single-nucleotide polymorphism [SNP] markers, and SNP markers from genotyping-by-sequencing) was used for QTL projection, and meta-QTL (MQTL) analysis was performed on 320 QTL. A total of 75 MQTL were discovered and refined to 15 high-confidence MQTL (hcmQTL). The candidate genes discovered within the hcmQTL interval were then checked for differential expression using data from three transcriptome studies, resulting in 92 differentially expressed genes (DEGs). The expression of these genes in various leaf tissues during wheat development was explored. This study provides insight into leaf rust resistance in wheat and thereby provides an avenue for developing resistant cultivars by incorporating the most important hcmQTL.

Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53–0.75 and 0.36–0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.

Mapping Powdery Mildew (Blumeria graminis f. sp. tritici) Resistance in Wild and Cultivated Tetraploid Wheats

Wheat is the most widely grown crop and represents the staple food for one third of the world’s population. Wheat is attacked by a large variety of pathogens and the use of resistant cultivars is an effective and environmentally safe strategy for controlling diseases and eliminating the use of fungicides. In this study, a collection of wild and cultivated tetraploid wheats (Triticum turgidum) were evaluated for seedling resistance (SR) and adult plant resistance (APR) to powdery mildew (Blumeria graminis) and genotyped with a 90K single nucleotide polymorphism (SNP) array to identify new sources of resistance genes. The genome-wide association mapping detected 18 quantitative trait loci (QTL) for APR and 8 QTL for SR, four of which were identical or at least closely linked to four QTL for APR. Thirteen candidate genes, containing nucleotide binding sites and leucine-rich repeats, were localized in the confidence intervals of the QTL-tagging SNPs. The marker IWB6155, associated to QPm.mgb-1AS, was located within the gene TRITD1Av1G004560 coding for a disease resistance protein. While most of the identified QTL were described previously, five QTL for APR (QPm.mgb-1AS, QPm.mgb-2BS, QPm.mgb-3BL.1, QPm.mgb-4BL, QPm.mgb-7BS.1) and three QTL for SR (QPm.mgb-3BL.3, QPm.mgb-5AL.2, QPm.mgb-7BS.2) were mapped on chromosome regions where no resistance gene was reported before. The novel QTL/genes can contribute to enriching the resistance sources available to breeders.

Genome-wide association mapping for adult resistance to powdery mildew in common wheat

Blumeria graminis f. sp. tritici, the causal agent of wheat powdery mildew disease, can occur at all stages of the crop and constantly threatens wheat production. To identify candidate resistance genes for powdery mildew, we performed GWAS (genome-wide association studies) on a total set of 329 wheat varieties obtained from different origins. These wheat materials were genotyped using wheat 90K SNP array and evaluated for their resistance in either field or glasshouse condition from 2016 to 2018. Using a mixed linear model, 33 SNP markers of which 14 QTL (quantitative trait loci) were later defined were observed to associate with powdery mildew resistance. Among these, QTL on chromosome 3A, 3B, 6D and 7D were concluded as potentially new QTL. Exploration of candidate genes for new QTL suggested roles of these genes involved in encoding disease resistance and defence-related proteins, and regulating early immune response to the pathogen. Overall, the results reveal that GWAS can be an effective means of identifying marker-trait associations, though further functional validation and fine-mapping of gene candidates are required before creating opportunities for developing new resistant genotypes.

Dynamic QTL for adult plant resistance to powdery mildew in common wheat (Triticum aestivum L.)

Agriculture will benefit from a rigorous characterization of genes for adult plant resistance (APR) since this gene class was recognized to provide more durable protection from plant diseases. The present study reports the identification of APR loci to powdery mildew in German winter wheat cultivars Cortez and Atlantis. Cortez was previously shown to carry all-stage resistance gene Pm3e. To avoid interference of Pm3e in APR studies, line 6037 that lacked Pm3e but showed field resistance from doubled-haploid (DH) population Atlantis/Cortez was used in two backcrosses to Atlantis for the establishment of DH population 6037/Atlantis//Atlantis. APR was assessed in the greenhouse 10, 15, and 20 days after inoculation (dai) from the 4-leaf stage onwards and combined with single-nucleotide polymorphism data in a genome-wide association study (GWAS) and a linkage map-based quantitative trait loci (QTL) analysis. In GWAS, two QTL were detected: one on chromosome 1BL 10 dai, the other on chromosome 2BL 20 dai. In conventional QTL analysis, both QTL were detected with all three disease ratings: the QTL on chromosome 1BL explained a maximum of 35.2% of the phenotypic variation 10 dai, whereas the QTL on chromosome 2BL explained a maximum of 43.5% of the phenotypic variation 20 dai. Compared with GWAS, linkage map-based QTL analysis allowed following the dynamics of QTL action. The two large-effect QTL for APR to powdery mildew with dynamic gene action can be useful for the enhancement of wheat germplasm.

Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B

Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations

CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014-2015 and 2015-2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers. Two common significant quantitative trait loci (QTL) on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3-28.7% and 9.6-15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8-11.5% and 10.8-18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1-8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.

Identification and genetic mapping of PmAF7DS a powdery mildew resistance gene in bread wheat (Triticum aestivum L.)

Gene PmAF7DS confers resistance to wheat powdery mildew (isolate Bgt#211 ); it was mapped to a 14.6-cM interval ( Xgwm350 a- Xbarc184 ) on chromosome 7DS. The flanking markers could be applied in MAS breeding. Wheat powdery mildew (Pm) is caused by the biotrophic pathogen Blumeria graminis tritici (DC.) (Bgt). An ongoing threat of breakdown of race-specific resistance to Pm requires a continuous effort to discover new alleles in the wheat gene pool. Developing new cultivars with improved disease resistance is an economically and environmentally safe approach to reduce yield losses. To identify and characterize genes for resistance against Pm in bread wheat we used the (Arina × Forno) RILs population. Initially, the two parental lines were screened with a collection of 61 isolates of Bgt from Israel. Three Pm isolates Bgt#210 , Bgt#211 and Bgt#213 showed differential reactions in the parents: Arina was resistant (IT = 0), whereas Forno was moderately susceptible (IT = -3). Isolate Bgt#211 was then used to inoculate the RIL population. The segregation pattern of plant reactions among the RILs indicates that a single dominant gene controls the conferred resistance. A genetic map of the region containing this gene was assembled with DNA markers and assigned to the 7D physical bin map. The gene, temporarily designated PmAF7DS, was located in the distal region of chromosome arm 7DS. The RILs were also inoculated with Bgt#210 and Bgt#213. The plant reactions to these isolates showed high identity with the reaction to Bgt#211, indicating the involvement of the same gene or closely linked, but distinct single genes. The genomic location of PmAF7DS, in light of other Pm genes on 7DS is discussed.

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.)

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants. Thus, in addition to PM resistance, these progeny might also carry resistance to stem rust race Ug99.

QTL mapping of adult-plant resistances to stripe rust and leaf rust in Chinese wheat cultivar Bainong 64

Stripe rust and leaf rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. and P. triticina, respectively, are devastating fungal diseases of common wheat (Triticum aestivum L.). Chinese wheat cultivar Bainong 64 has maintained acceptable adult-plant resistance (APR) to stripe rust, leaf rust and powdery mildew for more than 10 years. The aim of this study was to identify quantitative trait loci/locus (QTL) for resistance to the two rusts in a population of 179 doubled haploid (DH) lines derived from Bainong 64 × Jingshuang 16. The DH lines were planted in randomized complete blocks with three replicates at four locations. Stripe rust tests were conducted using a mixture of currently prevalent P. striiformis races, and leaf rust tests were performed with P. triticina race THTT. Leaf rust severities were scored two or three times, whereas maximum disease severities (MDS) were recorded for stripe rust. Using bulked segregant analysis (BSA) and simple sequence repeat (SSR) markers, five independent loci for APR to two rusts were detected. The QTL on chromosomes 1BL and 6BS contributed by Bainong 64 conferred resistance to both diseases. The loci identified on chromosomes 7AS and 4DL had minor effects on stripe rust response, whereas another locus, close to the centromere on chromosome 6BS, had a significant effect only on leaf rust response. The loci located on chromosomes 1BL and 4DL also had significant effects on powdery mildew response. These were located at the same positions as the Yr29/Lr46 and Yr46/Lr67 genes, respectively. The multiple disease resistance locus for APR on chromosome 6BS appears to be new. All three genes and their closely linked molecular markers could be used in breeding wheat cultivars with durable resistance to multiple diseases.

Partial resistance to powdery mildew in German spring wheat 'Naxos' is based on multiple genes with stable effects in diverse environments

Powdery mildew is one of the most important wheat diseases in temperate regions of the world. Resistance breeding is considered to be an economical and environmentally benign way to control this disease. The German spring wheat cv. 'Naxos' exhibits high levels of partial and race non-specific resistance to powdery mildew in the field and is a valuable source in resistance breeding. The main objective of the present study was to map the genetic factors behind the resistance in Naxos, based on a population of recombinant inbred lines (RIL) from a cross with the susceptible CIMMYT breeding line SHA3/CBRD. Powdery mildew severity was evaluated in six field trials in Norway and four field trials in China. The major quantitative trait locus (QTL) with resistance from Naxos was detected close to the Pm3 locus on 1AS in all environments, and explained up to 35% of the phenotypic variation. Naxos was shown to carry another major QTL on 2DL and minor ones on 2BL and 7DS. QTL with resistance from SHA3/CBRD were detected on 1RS, 2DLc, 6BL and 7AL. The QTL on the 1B/1R translocation showed highly variable effects across environments corresponding to known virulence differences against Pm8. SHA3/CBRD was shown to possess the Pm3 haplotype on 1AS, but none of the known Pm3a-g alleles. The RIL population did not provide any evidence to suggest that the Pm3 allele of SHA3/CBRD acted as a suppressor of Pm8.

Collinearity-based marker mining for the fine mapping of Pm6, a powdery mildew resistance gene in wheat

The genome sequences of rice (Oryza sativa L.) and Brachypodium distachyon and the comprehensive Triticeae EST (Expressed Sequence Tag) resources provide invaluable information for comparative genomics analysis. The powdery mildew resistance gene, Pm6, which was introgressed into common wheat from Triticum timopheevii, was previously mapped to the wheat chromosome bin of 2BL [fraction length (FL) 0.50-1.00] with limited DNA markers. In this study, we saturated the Pm6 locus in wheat using the collinearity-based markers by extensively exploiting these genomic resources. All wheat ESTs located in the bin 2BL FL 0.50-1.00 and their corresponding orthologous genes on rice chromosome 4 were firstly used to develop STS (Sequence Tagged Site) markers. Those identified markers that flanked the Pm6 locus were then used to identify the collinear regions in the genomes of rice and Brachypodium. Triticeae ESTs with orthologous genes in these collinear regions were further used to develop new conserved markers for the fine mapping of Pm6. Using two F(2) populations derived from crosses of IGVI-465 × Prins and IGVI-466 × Prins, we mapped a total of 29 markers to the Pm6 locus. Among them, 14 markers were co-segregated with Pm6 in the IGVI-466/Prins population. Comparative genome analysis showed that the collinear region of the 29 linked markers covers a ~5.6-Mb region in chromosome 5L of Brachypodium and a ~6.0-Mb region in chromosome 4L of rice. The marker order is conserved between rice and Brachypodium, but re-arrangements are present in wheat. Comparative mapping in the two populations showed that two conserved markers (CINAU123 and CINAU127) flanked the Pm6 locus, and an LRR-receptor-like protein kinase cluster was identified in the collinear regions of Brachypodium and rice. This putative resistance gene cluster provides a potential target site for further fine mapping and cloning of Pm6. Moreover, the newly developed conserved markers closely linked to Pm6 can be used for the marker-assisted selection (MAS) of Pm6 in wheat breeding programs.

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

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

Quantitative trait loci mapping for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64

Adult-plant resistance (APR) is an effective means of controlling powdery mildew in wheat. In the present study, 406 simple-sequence repeat markers were used to map quantitative trait loci (QTLs) for APR to powdery mildew in a doubled-haploid (DH) population of 181 lines derived from the cross Bainong 64xJingshuang 16. The DH lines were planted in a randomized complete block design with three replicates in Beijing and Anyang during the 2005-06 and 2007-08 cropping seasons. Artificial inoculations were carried out in Beijing using the highly virulent Blumeria graminis f. sp. tritici isolate E20. Disease severities on penultimate leaves were scored twice in Beijing whereas, at Anyang, maximum disease severities (MDS) were recorded following natural infection. Broad-sense heritabilities of MDS and areas under the disease progress curve were 0.89 and 0.77, respectively, based on the mean values averaged across environments. Composite interval mapping detected four QTLs for APR to powdery mildew on chromosomes 1A, 4DL, 6BS, and 7A; these were designated QPm.caas-1A, QPm.caas-4DL, QPm.caas-6BS, and QPm.caas-7A, respectively, and explained 6.3 to 22.7% of the phenotypic variance. QTLs QPm.caas-4DL and QPm.caas-6BS were stable across environments with high genetic effects on powdery mildew response, accounting for 15.2 to 22.7% and 9.0 to 13.2% of the phenotypic variance, respectively. These results should be useful for the future improvement of powdery mildew resistance in wheat.

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

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

The adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29 are important determinants of partial resistance to powdery mildew in bread wheat line Saar

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.

The adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29 are important determinants of partial resistance to powdery mildew in bread wheat line Saar

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.

Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure

Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype x environment interaction, thereby making possible the identification of markers contributing to both additive and additive x additive interaction effects of traits.

Seedling and Slow Rusting Resistance to Stripe Rust in Chinese Common Wheats

Identification of seedling and slow stripe rust resistance genes is important for gene pyramiding, gene deployment, and developing slow-rusting wheat cultivars to control the disease. A total of 98 Chinese lines were inoculated with 26 pathotypes of Puccinia striiformis f. sp. tritici for postulation of stripe rust resistance genes effective at the seedling stage. A total of 135 wheat lines were planted at two locations to characterize their slow rusting responses to stripe rust in the 2003-2004 and 2004-2005 cropping seasons. Genes Yr2, Yr3a, Yr4a, Yr6, Yr7, Yr9, Yr26, Yr27, and YrSD, either singly or in combinations, were postulated in 72 lines, whereas known resistance genes were not identified in the other 26 accessions. The resistance genes Yr9 and Yr26 were found in 42 and 19 accessions, respectively. Yr3a and Yr4a were detected in two lines, and four lines may contain Yr6. Three lines were postulated to possess YrSD, one carried Yr27, and one may possess Yr7. Thirty-three lines showed slow stripe rusting resistance at two locations in both seasons.