Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function

Leaf rust resistance gene Lr34 is likely the most important leaf rust gene characterized to date. It has been characterized as an adult plant resistance gene and is known to enhance the resistance of other leaf rust resistance genes and to condition resistance to a number of other diseases. Located on chromosome 7D, this gene was identified to be one of six co-located genes of which, an ABC transporter was shown to be the only valid candidate. Ten new molecular markers were developed spanning the Lr34 locus, including six novel microsatellite markers (cam), one insertion site-based polymorphism marker (caISBP), two single nucleotide polymorphisms (caSNP), and one gene-specific marker (caIND). Using these new markers and others that were previously published, a comparative fine map of the locus was constructed from five segregating populations representing 1,742 lines. Identification of a susceptible line with a recombination in the 4.9 kb interval between caSNP4 located in the ABC transporter gene and cam8 located just upstream of this gene provided further evidence to support the identity of the ABC transporter as Lr34 by ruling out four of the adjacent genes. Originally, three mutations forming two haplotypes had been described for the ABC transporter gene. A third combination of the three mutations and an additional rare mutation in exon 22 were subsequently described. We identified an additional novel mutation in exon 10 that would cause a frameshift and is likely non-functional. This mutation was only found in Lr34? lines and constituted a novel molecular haplotype. Characterization of two germplasm collections of 700 Triticum aestivum lines permitted us to gain an understanding of the frequency of the ABC haplotypes characterized to date and their distribution in germplasm from and around the world. In addition to the four haplotypes previously described, a fifth haplotype was found in two of the 700 lines from the germplasm collections. These lines displayed the deletion in indel 11 characteristic of Lr34+ lines, but are likely susceptible to leaf rust. Mapping and haplotyping data suggest that of all the markers described herein, marker caIND11 is the best diagnostic marker for marker-assisted selection of Lr34 because it is co-dominant, robust and with the exception of 2/700 lines, it is highly diagnostic. Other markers are also described to provide alternatives for laboratories with different technologies.     

Molecular and phenotypic characterization of seedling and adult plant leaf rust resistance in a world wheat collection

Genetic resistance is the most effective approach to managing wheat leaf rust. The aim of this study was to characterize seedling and adult plant leaf rust resistance of a world wheat collection. Using controlled inoculation with ten races of Puccinia triticina, 14 seedling resistance genes were determined or postulated to be present in the collection. Lr1, Lr3, Lr10 and Lr20 were the most prevalent genes around the world while Lr9, Lr14b, Lr3ka and/or Lr30 and Lr26 were rare. To confirm some gene postulations, the collection was screened with gene-specific molecular markers for Lr1, Lr10, Lr21 and Lr34. Although possessing the Lr1 and/or Lr10 gene-specific marker, 51 accessions showed unexpected high infection types to P. triticina race BBBD. The collection was tested in the field, where rust resistance ranged from nearly immune or highly resistant with severity of 1 % and resistant host response to highly susceptible with severity of 84 % and susceptible host response. The majority of the accessions possessing the adult plant resistance (APR) gene Lr34 had a maximum rust severity of 0–35 %, similar to or better than accession RL6058, a Thatcher-Lr34 near-isogenic line. Many accessions displayed an immune response or a high level of resistance under field conditions, likely as a result of synergy between APR genes or between APR and seedling resistance genes. However, accessions with three or more seedling resistance genes had an overall lower field severity than those with two or fewer. Immune or highly resistant accessions are potential sources for improvement of leaf rust resistance. In addition, some lines were postulated to have known but unidentified genes/alleles or novel genes, also constituting potentially important sources of novel resistance.     

Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens

The locus Lr34/Yr18/Pm38 confers partial and durable resistance against the devastating fungal pathogens leaf rust, stripe rust, and powdery mildew. In previous studies, this broad-spectrum resistance was shown to be controlled by a single gene which encodes a putative ATP-binding cassette transporter. Alleles of resistant and susceptible cultivars differed by only three sequence polymorphisms and the same resistance haplotype was found in the three independent breeding lineages of Lr34/Yr18/Pm38. Hence, we used these conserved sequence polymorphisms as templates to develop diagnostic molecular markers that will assist selection for durable multi-pathogen resistance in breeding programs. Five allele-specific markers (cssfr1–cssfr5) were developed based on a 3 bp deletion in exon 11 of the Lr34-gene, and one marker (cssfr6) was derived from a single nucleotide polymorphism in exon 12. Validation of reference genotypes, well characterized for the presence or absence of the Lr34/Yr18/Pm38 resistance locus, demonstrated perfect diagnostic values for the newly developed markers. By testing the new markers on a larger set of wheat cultivars, a third Lr34 haplotype, not described so far, was discovered in some European winter wheat and spelt material. Some cultivars with uncertain Lr34 status were re-assessed using the newly derived markers. Unambiguous identification of the Lr34 gene aided by the new markers has revealed that some wheat cultivars incorrectly postulated as having Lr34 may possess as yet uncharacterised loci for adult plant leaf and stripe rust resistance. E. S. Lagudah and S. G. Krattinger contributed equally to the work.     

Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses

Fusarium head blight (FHB) is a threat to barley (Hordeum vulgare L.) production in many parts of the world. A number of barley accessions with partial resistance have been reported and used in mapping experiments to identify quantitative trait loci (QTL) associated with FHB resistance. Here, we present a set of barley germplasm that exhibits FHB resistance identified through screening a global collection of 23,255 wild (Hordeum vulgare ssp. spontaneum) and cultivated (Hordeum vulgare ssp. vulgare) accessions. Seventy-eight accessions were classified as resistant or moderately resistant. The collection of FHB resistant accessions consists of 5, 27, 46 of winter, wild and spring barley, respectively. The population structure and genetic relationships of the germplasm were investigated with 1,727 Diversity Array Technology (DArT) markers. Multiple clustering analyses suggest the presence of four subpopulations. Within cultivated barley, substructure is largely centered on spike morphology and growth habit. Analysis of molecular variance indicated highly significant genetic variance among clusters and within clusters, suggesting that the FHB resistant sources have broad genetic diversity. The haplotype diversity was characterized with DArT markers associated with the four FHB QTLs on chromosome 2H bin8, 10 and 13 and 6H bin7. In general, the wild barley accessions had distinct haplotypes from those of cultivated barley. The haplotype of the resistant source Chevron was the most prevalent in all four QTL regions, followed by those of the resistant sources Fredrickson and CIho4196. These resistant QTL haplotypes were rare in the susceptible cultivars and accessions grown in the upper Midwest USA. Some two- and six-rowed accessions were identified with high FHB resistance, but contained distinct haplotypes at FHB QTLs from known resistance sources. These germplasm warrant further genetic studies and possible incorporation into barley breeding programs.     

A single-nucleotide polymorphism that accounts for allelic variation in the Lr34 gene and leaf rust reaction in hard winter wheat

Leaf rust, caused by Puccinia triticina Eriks, is one of the most common and persistent wheat diseases in the US Great Plains. We report that the Lr34 gene was mapped in the center of a QTL for leaf rust reaction and explained 18–35% of the total phenotypic variation in disease severity of adult plants in a Jagger × 2174 population of recombinant inbred lines (RILs) field-tested for 3 years. The sequence of the complete Lr34 gene was determined for the susceptible Jagger allele and for the resistant 2174 allele. The two alleles had exactly the same sequence as the resistant allele reported previously in Chinese Spring at three polymorphic sites in intron 4, exon 11, and exon 12. A G/T polymorphism was found in exon 22, where a premature stop codon was found in the susceptible Jagger allele (Lr34E22s), confirming a previous report, due to a point mutation compared with the resistant 2174 allele (Lr34E22r). We have experimentally demonstrated a tight association between the point mutation at exon 22 of Lr34 and leaf rust susceptibility in a segregating biparental population. A PCR marker was developed to distinguish between the Lr34E22r and Lr34E22s alleles. A survey of 33 local hard winter wheat cultivars indicated that 7 cultivars carry the Lr34E22s allele and 26 cultivars carry the Lr34E22r allele. This study significantly improves our genetic understanding of allelic variation in the Lr34 gene and provides a functional molecular tool to improve leaf rust resistance in a major US wheat gene pool.     

Mapping and characterization of the new adult plant leaf rust resistance gene <Emphasis Type="Italic">Lr77</Emphasis> derived from Santa Fe winter wheat

Key message

A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as Lr77.

Abstract

‘Santa Fe’ is a hard red winter cultivar that has had long-lasting resistance to the leaf rust fungus, Puccinia triticina. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of ‘Thatcher’ (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F₆ recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker IWB10344 had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as Lr77. Kompetitive allele-specific polymerase chain reaction assay markers linked to Lr77 on 3BL should be useful for selection of wheat germplasm with this gene.

     

The successful application of a marker-assisted wheat breeding strategy

A number of useful marker-trait associations have been reported for wheat. However the number of publications detailing the integrated and pragmatic use of molecular markers in wheat breeding is limited. A previous report by some of these authors showed how marker-assisted selection could increase the genetic gain and economic efficiency of a specific breeding strategy. Here, we present a practical validation of that study. The target of this breeding strategy was to produce wheat lines derived from an elite Australian cultivar ‘Stylet’, with superior dough properties and durable rust resistance donated from ‘Annuello’. Molecular markers were used to screen a BC₁F₁ population produced from a cross between the recurrent parent ‘Stylet’ and the donor parent ‘Annuello’ for the presence of rust resistance genes Lr34/Yr18 and Lr46/Yr29. Following this, marker-assisted selection was applied to haploid plants, prior to chromosome doubling with cochicine, for the rust resistance genes Lr24/Sr24, Lr34/Yr18, height reducing genes, and for the grain protein genes Glu-D1 and Glu-A3. In general, results from this study agreed with those of the simulation study. Genetic improvement for rust resistance was greatest when marker selection was applied on BC₁F₁ individuals. Introgression of both the Lr34/Yr18 and Lr46/Yr29 loci into the susceptible recurrent parent background resulted in substantial improvement in leaf rust and stripe rust resistance levels. Selection for favourable glutenin alleles significantly improved dough resistance and dough extensibility. Marker-assisted selection for improved grain yield, through the selection of recurrent parent genome using anonymous markers, only marginally improved grain yield at one of the five sites used for grain yield assessment. In summary, the integration of marker-assisted selection for specific target genes, particularly at the early stages of a breeding programme, is likely to substantially increase genetic improvement in wheat.     

Molecular markers for wheat leaf rust resistance gene Lr41

Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene Lr41 from T. tauschii has been introgressed into chromosome 2D of several wheat cultivars that are currently under commercial production. To discover molecular markers closely linked to Lr41, a set of near-isogenic lines (NILs) of the hard winter wheat cultivar Century were developed through backcrossing. A population of 95 BC₃F_2:6 NILs were evaluated for leaf rust resistance at both seedling and adult plant stages and analyzed with simple sequence repeat (SSR) markers using bulked segregant analysis. Four markers closely linked to Lr41 were identified on chromosome 2DS; the closest marker, Xbarc124, was about 1 cM from Lr41. Physical mapping using Chinese Spring nullitetrasomic and ditelosomic genetic stocks confirmed that markers linked to Lr41 were on chromosome arm 2DS. Marker analysis in a diverse set of wheat germplasm indicated that primers BARC124, GWM210, and GDM35 amplified polymorphic bands between most resistant and susceptible accessions and can be used for marker-assisted selection in breeding programs.     

Identification of the allelic state of the <Emphasis Type="Italic">Lr34</Emphasis> leaf rust resistance gene in soft winter wheat cultivars developed in Ukraine

The distribution of alleles at the Lr34 locus associated with leaf rust resistance has been studied in soft winter wheat (Triticum aestivum L.) cultivars developed in Ukraine. To determine the allelic state of the Lr34 locus, codominant molecular marker cssfr5 has been used. Cultivars with the revealed Lr34(+) and Lr34(−) alleles have been identified as potentially resistant or susceptible, respectively. A collection of 81 cultivars from the main breeding centers of Ukraine has been examined; the Lr34(+) allele has been revealed in 44% of the tested cultivars. The obtained results have been compared with general data on the leaf rust resistance of wheat cultivars from different countries.     

Phytopathological and molecular genetic identification of leaf rust resistance genes in common wheat accessions with alien genetic material

Leaf rust resistance genes were sought in 23 resistant common wheat accessions with alien genetic material of Aegilops speltoides, Ae. triuncialis, and Triticum kiharae from the Arsenal collection. The genes were identified by common phytopathological tests and PCR analysis with STS markers linked with the known Lr genes. None of the methods identified the resistance genes in two accessions. In the other accessions, the combination of the two methods broadened the spectrum of detectable genes and, in some cases, allowed double verification of the presence of a resistance gene. Most accessions proved to contain several leaf rust resistance genes, combining juvenile and adult plant ones. The accessions were found to contain gene combinations that ensured field resistance (Lr13 + Lr10 and Lr12 + Lr34) and immunity under the conditions of the Non-Chernozem region. Accessions with alien genetic material contained a unique combination of five or six resistance genes. Since the accessions were rich in leaf rust resistance genes, including effective ones, and carried rare combinations of these genes, they were proposed as donors to be universally employed in breeding for immunity in all regions of Russia.     

Identification of leaf rust resistance genes in wheat (Triticum aestivum L.) cultivars using molecular markers

A collection of 68 cultivars of common wheat has been screened for leaf rust resistance genes with the use of molecular markers. Markers of genes Lr1, Lr9, Lr10, Lr19, Lr20, Lr21, Lr24, and Lr26 have been used. It has been suggested that allele Xgwm295 be used as a marker for identifying the Lr34 gene. The genes originating from Triticum aestivum L., as well as the Lr26 gene contained in rye translocation 1RS, are the most frequent. Genes originating from wild wheats were rarer in the cultivars studied.     

Fine scale genetic and physical mapping using interstitial deletion mutants of <Emphasis Type="Italic">Lr34</Emphasis><Emphasis Type="Italic">/Yr18</Emphasis>: a disease resistance locus effective against multiple pathogens in wheat

The Lr34/Yr18 locus has contributed to durable, non-race specific resistance against leaf rust (Puccinia triticina) and stripe rust (P. striiformis f. sp. tritici) in wheat (Triticum aestivum). Lr34/Yr18 also cosegregates with resistance to powdery mildew (Pm38) and a leaf tip necrosis phenotype (Ltn1). Using a high resolution mapping family from a cross between near-isogenic lines in the “Thatcher” background we demonstrated that Lr34/Yr18 also cosegregated with stem rust resistance in the field. Lr34/Yr18 probably interacts with unlinked genes to provide enhanced stem rust resistance in “Thatcher”. In view of the relatively low levels of DNA polymorphism reported in the Lr34/Yr18 region, gamma irradiation of the single chromosome substitution line, Lalbahadur(Parula7D) that carries Lr34/Yr18 was used to generate several mutant lines. Characterisation of the mutants revealed a range of highly informative genotypes, which included variable size deletions and an overlapping set of interstitial deletions. The mutants enabled a large number of wheat EST derived markers to be mapped and define a relatively small physical region on chromosome 7DS that carried Lr34/Yr18. Fine scale genetic mapping confirmed the physical mapping and identified a genetic interval of less than 0.5 cM, which contained Lr34/Yr18. Both rice and Brachypodium genome sequences provided useful information for fine mapping of ESTs in wheat. Gene order was more conserved between wheat and Brachypodium than with rice but these smaller grass genomes did not reveal sequence information that could be used to identify a candidate gene for rust resistance in wheat. We predict that Lr34/Yr18 is located within a large insertion in wheat not found at syntenic positions in Brachypodium and rice. W. Spielmeyer and R. P. Singh contributed equally to the study through the “Thatcher” and “Lalbahadur” genetic stocks, respectively.     

Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21

Development and utilization of genetic markers play a pivotal role in marker-assisted breeding of wheat cultivars with pyramids of disease resistance genes. The objective of this study was to develop a closed-tube, gel-free assay for high-throughput genotyping of leaf rust resistance locus Lr21. Polymorphism identified from re-sequencing of a 2.4-kb fragment covering the functional region of the Lr21 gene from the second to the fourth indels was targeted for assay development. The generated sequence data revealed the 88- or 105-bp indel in the first intron of the Lr21 gene in the selected resistant cultivars compared to susceptible US spring and winter wheat cultivars. Allele-specific primers for a KASPar assay were designed around the junction of the indel at position 1,346 bp. The marker was tested on a panel of 384 US wheat lines and found to be effective in differentiating resistant and susceptible genotypes.     

The durable wheat disease resistance gene Lr34 confers common rust and northern corn leaf blight resistance in maize

Maize (corn) is one of the most widely grown cereal crops globally. Fungal diseases of maize cause significant economic damage by reducing maize yields and by increasing input costs for disease management. The most sustainable control of maize diseases is through the release and planting of maize cultivars with durable disease resistance. The wheat gene Lr34 provides durable and partial field resistance against multiple fungal diseases of wheat, including three wheat rust pathogens and wheat powdery mildew. Because of its unique qualities, Lr34 became a cornerstone in many wheat disease resistance programmes. The Lr34 resistance is encoded by a rare variant of an ATP‐binding cassette (ABC) transporter that evolved after wheat domestication. An Lr34‐like disease resistance phenotype has not been reported in other cereal species, including maize. Here, we transformed the Lr34 resistance gene into the maize hybrid Hi‐II. Lr34‐expressing maize plants showed increased resistance against the biotrophic fungal disease common rust and the hemi‐biotrophic disease northern corn leaf blight. Furthermore, the Lr34‐expressing maize plants developed a late leaf tip necrosis phenotype, without negative impact on plant growth. With this and previous reports, it could be shown that Lr34 is effective against various biotrophic and hemi‐biotrophic diseases that collectively parasitize all major cereal crop species.     

Functional variability of the Lr34 durable resistance gene in transgenic wheat

Breeding for durable disease resistance is challenging, yet essential to improve crops for sustainable agriculture. The wheat Lr34 gene is one of the few cloned, durable resistance genes in plants. It encodes an ATP binding cassette transporter and has been a source of resistance against biotrophic pathogens, such as leaf rust (Puccinina triticina), for over 100 years. As endogenous Lr34 confers quantitative resistance, we wanted to determine the effects of transgenic Lr34 with specific reference to how expression levels affect resistance. Transgenic Lr34 wheat lines were made in two different, susceptible genetic backgrounds. We found that the introduction of the Lr34 resistance allele was sufficient to provide comparable levels of leaf rust resistance as the endogenous Lr34 gene. As with the endogenous gene, we observed resistance in seedlings after cold treatment and in flag leaves of adult plants, as well as Lr34‐associated leaf tip necrosis. The transgene‐based Lr34 resistance did not involve a hypersensitive response, altered callose deposition or up‐regulation of PR genes. Higher expression levels compared to endogenous Lr34 were observed in the transgenic lines both at seedling as well as adult stage and some improvement of resistance was seen in the flag leaf. Interestingly, in one genetic background the transgenic Lr34‐based resistance resulted in improved seedling resistance without cold treatment. These data indicate that functional variability in Lr34‐based resistance can be created using a transgenic approach.     

Two haplotypes of resistance gene analogs have been conserved during evolution at the leaf rust resistance locus Lr10in wild and cultivated wheat

The isolation of genes of agronomic interest such as disease resistance genes is a central issue in wheat research. A good knowledge of the organization and evolution of the genome can greatly help in defining the best strategies for efficient gene isolation. So far, very few wheat disease resistance loci have been studied at the molecular level and little is known about their evolution during polyploidization and domestication. In this study, we have analyzed the haplotype structure at loci orthologous to the leaf rust resistance locus Lr10 in hexaploid wheat which spans 350 kb in diploid wheat. Two haplotypes (H1, H2) were defined by the presence (H1) or the absence (H2) of two different resistance gene analogs (rga1, rga2) at this locus on chromosome 1AS. Both haplotypes were found in a collection of 113 wild and cultivated diploid and polyploid wheat lines and they do not reflect phylogenetic relationships. This indicates an ancient origin for this disease resistance locus and the independent conservation of the two haplotypes throughout the evolution of the wheat genome. Finally, the coding regions of the H1 haplotype RGAs are extremely conserved in all the species. This suggests a selective pressure for maintaining the structural and functional configuration of this haplotype in wheat. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0051-9. Electronic Publication     

15个小麦农家品种抗叶锈基因分析

本研究旨在明确小麦农家品种中可能含有的抗叶锈病基因,为抗源的选择和利用提供理论依据。以15个小麦农家品种、感病对照品种郑州5389和36个含有已知抗叶锈病基因的载体品种为材料,苗期接种19个具有鉴别力的叶锈菌生理小种进行基因推导,同时利用12个与抗叶锈病基因紧密连锁的分子标记进行分析。为明确其成株期抗性,分别于2016-2017年和2017-2018年在河北保定对小麦农家品种、感病对照品种郑州5389与慢锈品种SAAR进行田间接种,调查并记录田间严重度及普遍率。基因推导和分子标记检测结果显示,在15个小麦农家品种中共检测到7个抗叶锈病基因,其中部分品种还有多个抗性基因,如红狗豆含有Lr1和Lr46;黄花麦含有Lr13和Lr34;大白麦含有Lr14b和Lr26;洋麦含有Lr37和Lr46;成都光头含有Lr34和Lr46;墨脱麦和西山扁穗含有Lr26和Lr46。部分品种含有1个成株期慢叶锈病抗性基因,如同家坝小麦、武都白茧儿、边巴春麦-6、白花麦含有Lr34;红抢麦、白扁穗和白火麦含有Lr46。这些携带有效抗叶锈病基因的农家品种,可为小麦抗叶锈病育种提供抗源。     

Association mapping of leaf rust resistance loci in a spring wheat core collection

Key message

We identified 15 potentially novel loci in addition to previously characterized leaf rust resistance genes from 1032 spring wheat accessions. Targeted AM subset panels were instrumental in revealing interesting loci.

Abstract

Leaf rust is a common disease of wheat, consistently reducing yields in many wheat-growing regions of the world. Although fungicides are commonly applied to wheat in the United States (US), genetic resistance can provide less expensive, yet effective control of the disease. Our objectives were to map leaf rust resistance genes in a large core collection of spring wheat accessions selected from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection (NSGC), determine whether previously characterized race-nonspecific resistance genes could be identified with our panel, and evaluate the use of targeted panels to identify seedling and adult plant resistance (APR) genes. Association mapping (AM) detected five potentially novel leaf rust resistance loci on chromosomes 2BL, 4AS, and 5DL at the seedling stage, and 2DL and 7AS that conditioned both seedling and adult plant resistance. In addition, ten potentially novel race-nonspecific resistance loci conditioned field resistance and lacked seedling resistance. Analyses of targeted subsets of the accessions identified additional loci not associated with resistance in the complete core panel. Using molecular markers, we also confirmed the presence and effectiveness of the race-nonspecific genes Lr34, Lr46, and Lr67 in our panel. Although most of the accessions in this study were susceptible to leaf rust in field and seedling tests, many resistance loci were identified with AM. Through the use of targeted subset panels, more loci were identified than in the larger core panels alone.

     

QTL for spot blotch resistance in bread wheat line Saar co-locate to the biotrophic disease resistance loci Lr34 and Lr46

Spot blotch caused by Bipolaris sorokiniana is a major disease of wheat in warm and humid wheat growing regions of the world including south Asian countries such as India, Nepal and Bangladesh. The CIMMYT bread wheat line Saar which carries the leaf tip necrosis (LTN)-associated rust resistance genes Lr34 and Lr46 has exhibited a low level of spot blotch disease in field trials conducted in Asia and South America. One hundred and fourteen recombinant inbred lines (RILs) of Avocet (Susceptible) × Saar, were evaluated along with parents in two dates of sowing in India for 3 years (2007–2008 to 2009–2010) to identify quantitative trait loci (QTL) associated with spot blotch resistance, and to determine the potential association of Lr34 and Lr46 with resistance to this disease. Lr34 was found to constitute the main locus for spot blotch resistance, and explained as much as 55 % of the phenotypic variation in the mean disease data across the six environments. Based on the large effect, the spot blotch resistance at this locus has been given the gene designation Sb1. Two further, minor QTL were detected in the sub-population of RILs not containing Lr34. The first of these was located about 40 cM distal to Lr34 on 7DS, and the other corresponded to Lr46 on 1BL. A major implication for wheat breeding is that Lr34 and Lr46, which are widely used in wheat breeding to improve resistance to rust diseases and powdery mildew, also have a beneficial effect on spot blotch.     

Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum and Aegilops tauschii

Spontaneous sequence changes and the selection of beneficial mutations are driving forces of gene diversification and key factors of evolution. In highly dynamic co-evolutionary processes such as plant-pathogen interactions, the plant’s ability to rapidly adapt to newly emerging pathogens is paramount. The hexaploid wheat gene Lr34, which encodes an ATP-binding cassette (ABC) transporter, confers durable field resistance against four fungal diseases. Despite its extensive use in breeding and agriculture, no increase in virulence towards Lr34 has been described over the last century. The wheat genepool contains two predominant Lr34 alleles of which only one confers disease resistance. The two alleles, located on chromosome 7DS, differ by only two exon-polymorphisms. Putatively functional homoeologs and orthologs of Lr34 are found on the B-genome of wheat and in rice and sorghum, but not in maize, barley and Brachypodium. In this study we present a detailed haplotype analysis of homoeologous and orthologous Lr34 genes in genetically and geographically diverse selections of wheat, rice and sorghum accessions. We found that the resistant Lr34 haplotype is unique to the wheat D-genome and is not found in the B-genome of wheat or in rice and sorghum. Furthermore, we only found the susceptible Lr34 allele in a set of 252 Ae. tauschii genotypes, the progenitor of the wheat D-genome. These data provide compelling evidence that the Lr34 multi-pathogen resistance is the result of recent gene diversification occurring after the formation of hexaploid wheat about 8,000 years ago.