Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL

Transfer of the high-temperature adult-plant stripe rust resistance gene Yr62 in four Chinese wheat cultivars

Wheat stripe rust is one of the diseases that seriously affect wheat production worldwide. Breeding resistant cultivars is an effective way to control this disease. The wheat stripe rust resistance gene Yr62 has high-temperature adult-plant resistance (HTAP). In this study, PI 660,060, a single Yr62 gene line, was crossed with four Chinese wheat cultivars, LunXuan987 (LX987), Bainongaikang58 (AK58), ZhengMai9023 (ZM9023), and HanMai6172 (H6172). F1 seeds of four cross combinations were planted and self-crossed to develop the advance generations in the field. The seeds of each cross were mixed harvested and about 2400 to 3000 seeds were sown in each generation for F1 to F4 to maintain the maximum possible genotypes. Forty-five lines were selected and evaluated for resistance to stripe rust and agronomic traits, including plant height, number of grains per spike, and tiller number, in F5 and F6. Then, 33 lines with good agronomic traits and high disease resistance were developed to F9 generation. SSR markers Xgwm251 and Xgwm192 flank linked with the Yr62 were used to detect the presence of Yr62 in these 33 F9 lines. Of these, 22 lines were confirmed with the resistance gene Yr62. Finally, nine lines with good agronomic traits and disease resistance were successfully selected. The selected wheat lines in this study provide material support for the future breeding of wheat for stripe rust resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01393-1.

Orthologous receptor kinases quantitatively affect the host status of barley to leaf rust fungi

Global food security depends on cereal crops with durable disease resistance. Most cereals are colonized by rust fungi, which are pathogens of major significance for global agriculture¹. Cereal rusts display a high degree of host specificity and one rust species or forma specialis generally colonizes only one cereal host². Exploiting the non-host status and transferring non-host resistance genes between cereal crop species has been proposed as a strategy for durable rust resistance breeding. The molecular determinants that define the host status to rusts, however, are largely unknown. Here, we show that orthologous genes at the Rphq2 locus for quantitative leaf rust resistance from cultivated barley³ and Rph22 from wild bulbous barley⁴ affect the host status to leaf rusts. Both genes encode lectin receptor-like kinases. We transformed Rphq2 and Rph22 into an experimental barley line that has been bred for susceptibility to non-adapted leaf rusts, which allowed us to quantify resistance responses against various leaf rust species. Rphq2 conferred a much stronger resistance to the leaf rust of wild bulbous barley than to the leaf rust adapted to cultivated barley, while for Rph22 the reverse was observed. We hypothesize that adapted leaf rust species mitigate perception by cognate host receptors by lowering ligand recognition. Our results provide an example of orthologous genes that connect the quantitative host with non-host resistance to cereal rusts. Such genes provide a basis to exploit non-host resistance in molecular breeding.

Identifying a novel powdery mildew resistance gene in a barley landrace from Morocco

Powdery mildew is a barley foliar disease that causes great loss in yield. Because of the limited number of effective resistance genes, efforts to identify new sources of resistance are frequently focused on genetically diversified landraces. The goal of this study was to characterise the powdery mildew resistance gene in barley line 2553-3 selected from the Moroccan landrace. Phytopathological testing against a set of differential pathogen isolates revealed different pattern responses of this gene from those of other known resistance genes. F₂ and F_2:3 (2553-3 × Manchuria) mapping populations were employed to investigate resistance inheritance. Two approaches were applied for the linkage analysis: in the first approach, 22 resistant and 21 susceptible homozygous F₂ plants genotyped by the DArTseq platform (Diversity Arrays Technology, Pty. Ltd.) were used; in the second, 94 F₂ plants were genotyped by converted DArTseq markers and SSRs. Both analyses delineated a new resistance gene on the short arm of chromosome 2H. The authors propose MlMor as a gene symbol for newly characterized powdery mildew resistance genes in barley line 255-3-3. The results presented herein provide a good foundation for the development of closer linkage markers and MAS breeding.

High Resolution Genetic and Physical Mapping of a Major Powdery Mildew Resistance Locus in Barley

Powdery mildew caused by Blumeria graminis f. sp. hordei is a foliar disease with highly negative impact on yield and grain quality in barley. Thus, breeding for powdery mildew resistance is an important goal and requires constantly the discovery of new sources of natural resistance. Here, we report the high resolution genetic and physical mapping of a dominant race-specific powdery mildew resistance locus, originating from an Ethiopian spring barley accession 'HOR2573,' conferring resistance to several modern mildew isolates. High-resolution genetic mapping narrowed down the interval containing the resistance locus to a physical span of 850 kb. Four candidate genes with homology to known disease resistance gene families were identified. The mapped resistance locus coincides with a previously reported resistance locus from Hordeum laevigatum, suggesting allelism at the same locus in two different barley lines. Therefore, we named the newly mapped resistance locus from HOR2573 as MlLa-H. The reported co-segregating and flanking markers may provide new tools for marker-assisted selection of this resistance locus in barley breeding.

Mapping resistance to powdery mildew in barley reveals a large-effect nonhost resistance QTL

Resistance factors against non-adapted powdery mildews were mapped in barley. Some QTLs seem effective only to non-adapted mildews, while others also play a role in defense against the adapted form. The durability and effectiveness of nonhost resistance suggests promising practical applications for crop breeding, relying upon elucidation of key aspects of this type of resistance. We investigated which genetic factors determine the nonhost status of barley (Hordeum vulgare L.) to powdery mildews (Blumeria graminis). We set out to verify whether genes involved in nonhost resistance have a wide effectiveness spectrum, and whether nonhost resistance genes confer resistance to the barley adapted powdery mildew. Two barley lines, SusBgt_SC and SusBgt_DC, with some susceptibility to the wheat powdery mildew B. graminis f.sp. tritici (Bgt) were crossed with cv Vada to generate two mapping populations. Each population was assessed for level of infection against four B. graminis ff.spp, and QTL mapping analyses were performed. Our results demonstrate polygenic inheritance for nonhost resistance, with some QTLs effective only to non-adapted mildews, while others play a role against adapted and non-adapted forms. Histology analyses of nonhost interaction show that most penetration attempts are stopped in association with papillae, and also suggest independent layers of defence at haustorium establishment and conidiophore formation. Nonhost resistance of barley to powdery mildew relies mostly on non-hypersensitive mechanisms. A large-effect nonhost resistance QTL mapped to a 1.4 cM interval is suitable for map-based cloning.

High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust

Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.

Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei

KEY MESSAGE

Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars.

ABSTRACT

Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43%, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.

A near-isogenic line (NIL) collection in diploid strawberry and its use in the genetic analysis of morphologic, phenotypic and nutritional characters

First near-isogenic line collection in diploid strawberry, a tool for morphologic, phenotypic and nutritional QTL analysis. Diploid strawberry (Fragaria vesca), with a small genome, has a high degree of synteny with the octoploid cultivated strawberry (F. × ananassa), so can be used as a simplified model for genetic analysis of the octoploid species. Agronomically interesting traits are usually inherited quantitatively and they need to be studied in large segregating progenies well characterized with molecular markers. Near-isogenic lines (NILs) are tools to dissect quantitative characters and identify some of their components as Mendelian traits. NILs are fixed homozygous lines that share the same genetic background from a recurrent parent with a single introgression region from a donor parent. Here, we developed the first NIL collection in Fragaria, with F. vesca cv. Reine des Vallées as the recurrent parent and F. bucharica as the donor parent. A collection of 39 NILs was identified using a set of single sequence repeat markers. The NILs had an average introgression of 32 cM (6 % of genome) and were phenotyped over several years in two locations. This collection segregates for agronomic characters, such as flowering, germination, fruit size and shape, and nutritional content. At least 16 QTLs for morphological and reproductive traits, such as round fruits and vegetative propagation, and seven for nutritional traits such as sugar composition and total polyphenol content, were identified. The NIL collection of F. vesca can significantly facilitate understanding of the genetics of many traits and provide insight into the more complex F. × ananassa genome.

Marker assisted separation of resistance genes Rph22 and Rym16 (Hb) from an associated yield penalty in a barley: Hordeum bulbosum introgression line

The resistance genes Rph22 and Rym16 (Hb) transferred into barley from Hordeum bulbosum have been separated from a large yield penalty locus that was present in the original introgression line '182Q20'. The Hordeum bulbosum introgression line '182Q20' possesses resistance to barley leaf rust (Rph22) and Barley mild mosaic virus (Rym16 (Hb) ) located on chromosome 2HL. Unfortunately, this line also carries a considerable yield penalty compared with its barley genetic background 'Golden Promise'. Quantitative trait locus (QTL) mapping of the components of yield (total yield, thousand grain weight, hectolitre weight, percentage screenings and screened yield) was performed using 75 recombinant lines derived from the original '182Q20' introgression line. A QTL for the yield penalty was located in the proximal region of the introgressed segment. Marker assisted selection targeting intraspecific recombination events between overlapping H. bulbosum introgression segments was used to develop the lines '372E' and '372H' which feature genetically small introgressions around Rph22. Further yield trials validated the separation of both Rph22 and Rym16 (Hb) from the proximal yield penalty. These results, combined with molecular markers closely linked to Rph22 and Rym16 (Hb) , make these resistance genes more attractive for barley breeding.

Detection of QTLs for salt tolerance in Asian barley (Hordeum vulgare L.) by association analysis with SNP markers

Two hundred ninety-six Asian barley (Hordeum vulgare L.) accessions were assessed to detect QTLs underlying salt tolerance by association analysis using a 384 single nucleotide polymorphism (SNP) marker system. The experiment was laid out at the seedling stage in a hydroponic solution under control and 250 mM NaCl solution with three replications of four plants each. Salt tolerance was assessed by leaf injury score (LIS) and salt tolerance indices (STIs) of the number of leaves (NL), shoot length (SL), root length (RL), shoot dry weight (SDW) and root dry weight (RDW). LIS was scored from 1 to 5 according to the severity of necrosis and chlorosis observed on leaves. There was a wide variation in salt tolerance among Asian barley accessions. LIS and STI (SDW) were the most suitable traits for screening salt tolerance. Association was estimated between markers and traits to detect QTLs for LIS and STI (SDW). Seven significant QTLs were located on chromosomes 1H (2 QTLs), 2H (2 QTLs), 3H (1 QTL), 4H (1 QTL) and 5H (1 QTL). Five QTLs were associated with LIS and 2 QTLs with STI (SDW). Two QTLs associated with LIS were newly identified on chromosomes 3H and 4H.

Effects of stacked quantitative resistances to downy mildew in lettuce do not simply add up

KEY MESSAGE

In a stacking study of eight resistance QTLs in lettuce against downy mildew, only three out of ten double combinations showed an increased resistance effect under field conditions. Complete race nonspecific resistance to lettuce downy mildew, as observed for the nonhost wild lettuce species Lactuca saligna, is desired in lettuce cultivation. Genetic dissection of L. saligna's complete resistance has revealed several quantitative loci (QTL) for resistance with field infection reductions of 30-50 %. To test the effect of stacking these QTL, we analyzed interactions between homozygous L. saligna CGN05271 chromosome segments introgressed into the genetic background of L. sativa cv. Olof. Eight different backcross inbred lines (BILs) with single introgressions of 30-70 cM and selected predominately for quantitative resistance in field situations were intercrossed. Ten developed homozygous lines with stacked introgression segments (double combinations) were evaluated for resistance in the field. Seven double combinations showed a similar infection as the individual most resistant parental BIL, revealing epistatic interactions with 'less-than-additive' effects. Three double combinations showed an increased resistance level compared to their parental BILs and their interactions were additive, 'less-than-additive' epistatic and 'more-than-additive' epistatic, respectively. The additive interaction reduced field infection by 73 %. The double combination with a 'more-than-additive' epistatic effect, derived from a combination between a susceptible and a resistant BIL with 0 and 30 % infection reduction, respectively, showed an average field infection reduction of 52 %. For the latter line, an attempt to genetically dissect its underlying epistatic loci by substitution mapping did not result in smaller mapping intervals as none of the 22 substitution lines reached a similar high resistance level. Implications for breeding and the inheritance of L. saligna's complete resistance are discussed.

A first step toward the development of a barley NAM population and its utilization to detect QTLs conferring leaf rust seedling resistance

We suggest multi-parental nested association mapping as a valuable innovation in barley genetics, which increases the power to map quantitative trait loci and assists in extending genetic diversity of the elite barley gene pool. Plant genetic resources are a key asset to further improve crop species. The nested association mapping (NAM) approach was introduced to identify favorable genes in multi-parental populations. Here, we report toward the development of the first explorative barley NAM population and demonstrate its usefulness in a study on mapping quantitative trait loci (QTLs) for leaf rust resistance. The NAM population HEB-5 was developed from crossing and backcrossing five exotic barley donors with the elite barley cultivar 'Barke,' resulting in 295 NAM lines in generation BC1S1. HEB-5 was genetically characterized with 1,536 barley SNPs. Across HEB-5 and within the NAM families, no deviation from the expected genotype and allele frequencies was detected. Genetic similarity between 'Barke' and the NAM families ranged from 78.6 to 83.1 %, confirming the backcrossing step during population development. To explore its usefulness, a screen for leaf rust (Puccinia hordei) seedling resistance was conducted. Resistance QTLs were mapped to six barley chromosomes, applying a mixed model genome-wide association study. In total, four leaf rust QTLs were detected across HEB-5 and four QTLs within family HEB-F23. Favorable exotic QTL alleles reduced leaf rust symptoms on two chromosomes by 33.3 and 36.2 %, respectively. The located QTLs may represent new resistance loci or correspond to new alleles of known resistance genes. We conclude that the exploratory population HEB-5 can be applied to mapping and utilizing exotic QTL alleles of agronomic importance. The NAM concept will foster the evaluation of the genetic diversity, which is present in our primary barley gene pool.

Fine mapping quantitative resistances to downy mildew in lettuce revealed multiple sub-QTLs with plant stage dependent effects reducing or even promoting the infection

KEY MESSAGE

Three regions with quantitative resistance to downy mildew of non-host and wild lettuce species, Lactuca saligna , disintegrate into seventeen sub-QTLs with plant-stage-dependent effects, reducing or even promoting the infection. Previous studies on the genetic dissection of the complete resistance of wild lettuce, Lactuca saligna, to downy mildew revealed 15 introgression regions that conferred plant stage dependent quantitative resistances (QTLs). Three backcross inbred lines (BILs), carrying an individual 30-50 cM long introgression segment from L. saligna in a cultivated lettuce, L. sativa, background, reduced infection by 60-70 % at young plant stage and by 30-50 % at adult plant stage in field situations. We studied these three quantitative resistances in order to narrow down their mapping interval and determine their number of loci, either single or multiple. We performed recombinant screenings and developed near isogenic lines (NILs) with smaller overlapping L. saligna introgressions (substitution mapping). In segregating introgression line populations, recombination was suppressed up to 17-fold compared to the original L. saligna × L. sativa F 2 population. Recombination suppression depended on the chromosome region and was stronger suppressed at the smallest introgression lengths. Disease evaluation of the NILs revealed that the resistance of all three BILs was not explained by a single locus but by multiple sub-QTLs. The 17 L. saligna-derived sub-QTLs had a smaller and plant stage dependent resistance effect, some segments reducing; others even promoting downy mildew infection. Implications for lettuce breeding are outlined.

Rph22: mapping of a novel leaf rust resistance gene introgressed from the non-host Hordeum bulbosum L. into cultivated barley (Hordeum vulgare L.)

A resistance gene (Rph22) to barley leaf rust caused by Puccinia hordei was introgressed from the non-host species Hordeum bulbosum into cultivated barley. The H. bulbosum introgression in line '182Q20' was located to chromosome 2HL using genomic in situ hybridisation (GISH). Using molecular markers it was shown to cover approximately 20 % of the genetic length of the chromosome. The introgression confers a very high level of resistance to P. hordei at the seedling stage that is not based on a hypersensitive reaction. The presence of the resistance gene increased the latency period of the leaf rust fungus and strongly reduced the infection frequency relative to the genetic background cultivar 'Golden Promise'. An F2 population of 550 individuals was developed and used to create a genetic map of the introgressed region and to determine the map position of the underlying resistance gene(s). The resistance locus, designated Rph22, was located to the distal portion of the introgression, co-segregating with markers H35_26334 and H35_45139. Flanking markers will be used to reduce the linkage drag, including gene(s) responsible for a yield penalty, around the resistance locus and to transfer the gene into elite barley germplasm. This genetic location is also known to harbour a QTL (Rphq2) for non-hypersensitive leaf rust resistance in the barley cultivar 'Vada'. Comparison of the 'Vada' and H. bulbosum resistances at this locus may lead to a better understanding of the possible association between host and non-host resistance mechanisms.

Proteomic characterization of the Rph15 barley resistance gene-mediated defence responses to leaf rust

Background

Leaf rust, caused by the biotrophic fungal pathogen Puccinia hordei, is one of the most important foliar disease of barley (Hordeum vulgare) and represents a serious threat in many production regions of the world. The leaf rust resistance gene Rph15 is of outstanding interest for resistance breeding because it confers resistance to over 350 Puccinia hordei isolates collected from around the world. Molecular and biochemical mechanisms responsible for the Rph15 effectiveness are currently not investigated. The aim of the present work was to study the Rph15-based defence responses using a proteomic approach.

Results

Protein pattern changes in response to the leaf rust pathogen infection were investigated in two barley near isogenic lines (NILs), Bowman (leaf rust susceptible) and Bowman-Rph15 (leaf rust resistant), differing for the introgression of the leaf rust resistance gene Rph15. Two infection time points, 24 hours and four days post inoculation (dpi), were analysed. No statistically significant differences were identified at the early time point, while at 4 dpi eighteen protein spots were significantly up or down regulated with a fold-change equal or higher than two in response to pathogen infection. Almost all the pathogen-responsive proteins were identified in the Bowman-Rph15 resistant NIL. Protein spots were characterized by LC-MS/MS analysis and found to be involved in photosynthesis and energy metabolism, carbohydrate metabolism, protein degradation and defence. Proteomic data were complemented by transcriptional analysis of the respective genes. The identified proteins can be related to modulation of the photosynthetic apparatus components, re-direction of the metabolism to sustain defence responses and deployment of defence proteins.

Conclusions

The identification of leaf rust infection-modulated defence responses restricted to the resistant NIL support the hypothesis that basal defence responses of Bowman, but not the Rph15 resistance gene-based ones, are suppressed or delayed by pathogen effectors to levels below the detection power of the adopted proteomic approach. Additionally, Rph15-mediated resistance processes identified mainly resides on a modulation of primary metabolism, affecting photosyntesis and carbohydrate pool.

Evidence for a minor gene-for-minor gene interaction explaining nonhypersensitive polygenic partial disease resistance

ABSTRACT Partial resistance is a quantitative type of resistance that, by definition of Parlevliet, is not based on hypersensitivity. It is largely pathotype nonspecific, although some minor isolate-specific responses have been reported. In order to elucidate the isolate specificity of individual genes for partial resistance, three barley recombinant inbred line mapping populations were analyzed for resistance to the leaf rust fungus Puccinia hordei. The mapping populations were inoculated with one isolate avirulent and two isolates virulent to resistance gene Rph7g. Six significant quantitative trait loci (QTLs) were detected. Of these, two (Rphq3 and Rphq11) were detected with only the avirulent isolate (1.2.1.) and one (Rphq18) only with both virulent isolates (CO-04 and 28.1). The effectiveness of these QTLs was tested with 14 isolates, using a tester set of genotypes containing alleles for resistance or susceptibility for these QTLs. QTL Rphq18 was effective to only two isolates, CO-04 and 28.1, whereas Rphq3 and Rphq11 were ineffective to CO-04 and 28.1 but effective to all other isolates, except one. This resulted in a significant Person's differential interaction, which is a hallmark of a gene-for-gene interaction. The minor gene-for-minor gene interaction is not based on hypersensitivity and there is no evidence that the resistance is based on genes belonging to the nucleotide-binding leucine-rich repeat class.

High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay

Genetically well-characterized mapping populations are a key tool for rapid and precise localization of quantitative trait loci (QTL) and subsequent identification of the underlying genes. In this study, a set of 73 introgression lines (S42ILs) originating from a cross between the spring barley cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. v. ssp. spontaneum) was subjected to high-resolution genotyping with an Illumina 1536-SNP array. The array enabled a precise localization of the wild barley introgressions in the elite barley background. Based on 636 informative SNPs, the S42IL set represents 87.3% of the wild barley genome, where each line contains on average 3.3% of the donor genome. Furthermore, segregating high-resolution mapping populations (S42IL-HRs) were developed for 70 S42ILs in order to facilitate QTL fine-mapping and cloning. As a case study, we used the developed genetic resources to rapidly identify and fine-map the novel locus thresh-1 on chromosome 1H that controls grain threshability. Here, the recessive wild barley allele confers a difficult to thresh phenotype, suggesting that thresh-1 played an important role during barley domestication. Using a S42IL-HR population, thresh-1 was fine-mapped within a 4.3cM interval that was predicted to contain candidate genes involved in regulation of plant cell wall composition. The set of wild barley introgression lines and derived high-resolution populations are ideal tools to speed up the process of mapping and further dissecting QTL, which ultimately clears the way for isolating the genes behind QTL effects.

Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

BACKGROUND

The barley-Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL) for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs) have been developed that combine two QTL, Rphq2 and Rphq3, the largest effects detected in a recombinant-inbred-line (RIL) population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown.

RESULTS

An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi) with Puccinia hordei. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq2 and Rphq3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (HvERF4) was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that Rphq2 or Rphq3 contains a trans-eQTL that modulates expression of HvERF4. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s) contained within Rphq2 or Rphq3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of Ph-responsive genes and that hormone-related signalling pathways are actively involved in response to Puccinia hordei.

CONCLUSIONS

Differential gene expression between QTL-NILs identifies genes predominantly located within the target region(s) providing both transcriptional and positional candidate genes for the QTL. Genetically mapping the differentially expressed genes relative to the QTL has the potential to discover trans-eQTL mediated regulatory relays initiated from genes within the QTL regions.

The phenotypic expression of QTLs for partial resistance to barley leaf rust during plant development

Partial resistance is generally considered to be a durable form of resistance. In barley, Rphq2, Rphq3 and Rphq4 have been identified as consistent quantitative trait loci (QTLs) for partial resistance to the barley leaf rust pathogen Puccinia hordei. These QTLs have been incorporated separately into the susceptible L94 and the partially resistant Vada barley genetic backgrounds to obtain two sets of near isogenic lines (NILs). Previous studies have shown that these QTLs are not effective at conferring disease resistance in all stages of plant development. In the present study, the two sets of QTL-NILs and the two recurrent parents, L94 and Vada, were evaluated for resistance to P. hordei isolate 1.2.1 simultaneously under greenhouse conditions from the first leaf to the flag leaf stage. Effect of the QTLs on resistance was measured by development rate of the pathogen, expressed as latency period (LP). The data show that Rphq2 prolongs LP at the seedling stage (the first and second leaf stages) but has almost no effect on disease resistance in adult plants. Rphq4 showed no effect on LP until the third leaf stage, whereas Rphq3 is consistently effective at prolonging LP from the first leaf to the flag leaf. The changes in the effectiveness of Rphq2 and Rphq4 happen at the barley tillering stage (the third to fourth leaf stages). These results indicate that multiple disease evaluations of a single plant by repeated inoculations of the fourth leaf to the flag leaf should be conducted to precisely estimate the effect of Rphq4. The present study confirms and describes in detail the plant development-dependent effectiveness of partial resistance genes and, consequently, will enable a more precise evaluation of partial resistance regulation during barley development.

Peroxidase profiling reveals genetic linkage between peroxidase gene clusters and basal host and non-host resistance to rusts and mildew in barley

BACKGROUND

Higher plants possess a large multigene family encoding secreted class III peroxidase (Prx) proteins. Peroxidases appear to be associated with plant disease resistance based on observations of induction during disease challenge and the presence or absence of isozymes in resistant vs susceptible varieties. Despite these associations, there is no evidence that allelic variation of peroxidases directly determines levels of disease resistance.

METHODOLOGY/PRINCIPAL FINDINGS

The current study introduces a new strategy called Prx-Profiling. We showed that with this strategy a large number of peroxidase genes can be mapped on the barley genome. In order to obtain an estimate of the total number of Prx clusters we followed a re-sampling procedure, which indicated that the barley genome contains about 40 peroxidase gene clusters. We examined the association between the Prxs mapped and the QTLs for resistance of barley to homologous and heterologous rusts, and to the barley powdery mildew fungus. We report that 61% of the QTLs for partial resistance to P. hordei, 61% of the QTLs for resistance to B. graminis and 47% of the QTLs for non-host resistance to other Puccinia species co-localize with Prx based markers.

CONCLUSIONS/SIGNIFICANCE

We conclude that Prx-Profiling was effective in finding the genetic location of Prx genes on the barley genome. The finding that QTLs for basal resistance to rusts and powdery mildew fungi tend to co-locate with Prx clusters provides a base for exploring the functional role of Prx-related genes in determining natural differences in levels of basal resistance.

Pathogen race determines the type of resistance response in the stripe rust-Triticum dicoccoides pathosystem

Wild relatives of crop plants may serve as a promising source for screening for new disease resistance genes that can be utilized in breeding programs. Triticum dicoccoides, the wild progenitor of most cultivated wheats, was shown to harbor many resistance genes against the major diseases attacking cultivated wheat. Stripe rust is a devastating fungal disease that attacks wheat in many regions of the world. New races of Puccinia striiformis Westend. f. sp. tritici, the causative agent of stripe rust, have overcome most of the known Yr resistance genes in wheat. Therefore, there is a need to search for new resistance genes in the T. dicoccoides gene pool. A set of 120 T. dicoccoides accessions, collected from 13 populations representing different habitats in Israel and vicinity, was tested for resistance to three prevalent stripe rust races (38E134, 6E16 and 6E0). Of these 120 accessions, 14, 8 and 12% were resistant to races 38E134, 6E16 and 6E0, respectively, while 57, 2 and 4% were moderately resistant to these races, respectively. A unique resistance was found in the population of Mt Hermon where >80% of the accessions showed resistance to all races. Distribution of infection types (ITs) of race 38E134 showed a normal distribution that can fit a quantitative pattern of response, while the distributions of ITs of races 6E16 and 6E0 had excess of extreme values and therefore showing a qualitative pattern of response. anova testing the main factor effects and interaction showed significant effects of population, race and their interaction on IT. Significant positive correlations were obtained between the resistance to races 6E16 and 6E0 and humidity variables of the collections sites, while resistance to race 38E134 was positively correlated with temperature variables. These results show that the pathogen race can determine the type of resistance response, qualitative or quantitative, in the stripe rust-T. dicoccoides pathosystem. The obtained results also reveal that the distribution of resistance to different pathogen races can be affected by different climatic factors.

Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum

Leaf stripe of barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley districts. Two barley segregating populations represented by 103 recombinant inbred lines (RILs) of the cross L94 (susceptible) x Vada (resistant) and 194 RILs of the cross Arta (susceptible) x Hordeum spontaneum 41-1 (resistant) were analysed with two highly virulent leaf stripe isolates, Dg2 and Dg5, to identify loci for P. graminea resistance. A major gene with its positive allele contributed by Vada and H. spontaneum 41-1 was detected in both populations and for both pathogen isolates on chromosome 2HL explaining 44.1 and 91.8% R (2), respectively for Dg2 and Dg5 in L94 x Vada and 97.8 and 96.1% R (2), respectively for Dg2 and Dg5 in Arta x H. spontaneum 41-1. Common markers in the gene region of the two populations enabled map comparison and highlighted an overlapping for the region of the resistance locus. Since the map position of the resistance locus identified in this report is the same as that for the leaf stripe resistance gene Rdg1a, mapped earlier in Alf and derived from the 'botanical' barley line H. laevigatum, we propose that leaf stripe resistance in Vada and H. spontaneum 41-1 is governed by the same gene, namely by Rdg1a, and that Rdg1a resistance could be traced back to H. spontaneum, the progenitor of cultivated barley. PCR-based molecular markers that can be used for marker-assisted selection (MAS) of Rdg1a were identified. An Rdg1a syntenic interval with the rice chromosome arm 4L was identified on the basis of rice orthologs of EST-based barley markers. Analysis of the rice genes annotated into the syntenic interval did not reveal sequences strictly belonging to the major class (nucleotide-binding site plus leucine-rich repeat) of the resistance genes. Nonetheless, four genes coding for domains that are present in the major disease-resistance genes, namely receptor-like protein kinase and ATP/GTP-binding proteins, were identified together with a homolog of the barley powdery mildew resistance gene mlo. Three (out of five) homologs of these genes were mapped in the Rdg1a region in barley and the mlo homolog map position was tightly associated with the LOD score peak in both populations.

Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana

Retrotransposons (RTEs) are a principal component of most eukaryotic genomes, representing 50%-80% of some grass genomes. RTE sequences have been shown to be preferentially present in disease resistance gene clusters in plants. Arabidopsis thaliana has over 1,600 annotated RTE sequences and 56 of these appear to be expressed because of the exact expressed sequence tag (EST) matches and the presence of intact open reading frames. Of the 22 represented in the Affymetrix ATH1 array, AtCOPIA4 was found to be expressed at a higher level than all other RTEs across different developmental stages. Since AtCOPIA4 is located in the RPP5 gene cluster and is adjacent to RPP4 which confers resistance to the downy mildew oomycete Hyaloperonospora parasitica isolate EMWA1, we evaluated AtCOPIA4 mutants for resistance to this pathogen. T-DNA insertional and antisense knockout of AtCOPIA4 was found to reduce the resistance of wild type plants by 2-4 folds. Our results suggest that retrotransposon can be exapted to participate in plant defense response.

Basal host resistance of barley to powdery mildew: connecting quantitative trait Loci and candidate genes

The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of fungal haustoria. It is not known which of these candidate genes have allelic variation that contributes to the natural variation in powdery mildew resistance, because many of them may be highly conserved within the barley species and may act downstream of the basal resistance reaction. Twenty-two expressed sequence tag or cDNA clone sequences that are likely to play a role in the barley-Blumeria interaction based on transcriptional profiling, gene silencing, or overexpression data, as well as mlo, Ror1, and Ror2, were mapped and considered candidate genes for contribution to basal resistance. We mapped the quantitative trait loci (QTL) for powdery mildew resistance in six mapping populations of barley at seedling and adult plant stages and developed an improved high-density integrated genetic map containing 6,990 markers for comparing QTL and candidate gene positions over mapping populations. We mapped 12 QTL at seedling stage and 13 QTL at adult plant stage, of which four were in common between the two developmental stages. Six of the candidate genes showed coincidence in their map positions with the QTL identified for basal resistance to powdery mildew. This co-localization justifies giving priority to those six candidate genes to validate them as being responsible for the phenotypic effects of the QTL for basal resistance.

Quantitative disease resistance and quantitative resistance Loci in breeding

Quantitative disease resistance (QDR) has been observed within many crop plants but is not as well understood as qualitative (monogenic) disease resistance and has not been used as extensively in breeding. Mapping quantitative trait loci (QTLs) is a powerful tool for genetic dissection of QDR. DNA markers tightly linked to quantitative resistance loci (QRLs) controlling QDR can be used for marker-assisted selection (MAS) to incorporate these valuable traits. QDR confers a reduction, rather than lack, of disease and has diverse biological and molecular bases as revealed by cloning of QRLs and identification of the candidate gene(s) underlying QRLs. Increasing our biological knowledge of QDR and QRLs will enhance understanding of how QDR differs from qualitative resistance and provide the necessary information to better deploy these resources in breeding. Application of MAS for QRLs in breeding for QDR to diverse pathogens is illustrated by examples from wheat, barley, common bean, tomato, and pepper. Strategies for optimum deployment of QRLs require research to understand effects of QDR on pathogen populations over time.

Nonhost and basal resistance: how to explain specificity?

Nonhost resistance to plant pathogens can be constitutive or induced by microbes. Successful pathogens suppress microbe-induced plant defences by delivering appropriate effectors, which are apparently not sufficiently effective on nonhost plant species, as can be concluded from the strong host specificity of many biotroph plant pathogens. Such effectors act on particular plant targets, such as promoters or motifs in expressed sequences. Despite much progress in the elucidation of the molecular aspects of nonhost resistance to plant pathogens, very little is known about the genes that determine whether effectors can or cannot suppress the basal defence. In hosts they can, in nonhosts they cannot. The targets determining the host status of plants can be identified in inheritance studies. Recent reports have indicated that nonhost resistance is inherited polygenically, and exhibits strong similarity and association with the basal resistance of plants to adapted pathogens.

Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust

A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0-85 cM and 4H, 125-170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166-181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.

Structure-function analysis of the barley genome: the gene-rich region of chromosome 2HL

A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies, making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy, frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region. Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion-deletion polymorphism levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome 2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points in the rice genome sequence.