Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches

Key message

BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases.

Abstract

Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920–1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker–trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.

     

Characterization of <Emphasis Type="Italic">Lr75</Emphasis>: a partial,broad-spectrum leaf rust resistance gene in wheat

Key message

Here, we describe a strategy to improve broad-spectrum leaf rust resistance by marker-assisted combination of two partial resistance genes. One of them represents a novel partial adult plant resistance gene, named Lr75.

Abstract

Leaf rust caused by the fungal pathogen Puccinia triticina is a damaging disease of wheat (Triticum aestivum L.). The combination of several, additively-acting partial disease resistance genes has been proposed as a suitable strategy to breed wheat cultivars with high levels of durable field resistance. The Swiss winter wheat cultivar ‘Forno’ continues to show near-immunity to leaf rust since its release in the 1980s. This resistance is conferred by the presence of at least six quantitative trait loci (QTL), one of which is associated with the morphological trait leaf tip necrosis. Here, we used a marker-informed strategy to introgress two ‘Forno’ QTLs into the leaf rust-susceptible Swiss winter wheat cultivar ‘Arina’. The resulting backcross line ‘ArinaLrFor’ showed markedly increased leaf rust resistance in multiple locations over several years. One of the introgressed QTLs, QLr.sfr-1BS, is located on chromosome 1BS. We developed chromosome 1B-specific microsatellite markers by exploiting the Illumina survey sequences of wheat cv. ‘Chinese Spring’ and mapped QLr.sfr-1BS to a 4.3 cM interval flanked by the SSR markers gwm604 and swm271. QLr.sfr-1BS does not share a genetic location with any of the described leaf rust resistance genes present on chromosome 1B. Therefore, QLr.sfr-1BS is novel and was designated as Lr75. We conclude that marker-assisted combination of partial resistance genes is a feasible strategy to increase broad-spectrum leaf rust resistance. The identification of Lr75 adds a novel and highly useful gene to the small set of known partial, adult plant leaf rust resistance genes.

     

Intracoronary boluses of adenosine and sodium nitroprusside in combination reverses slow/no-reflow during angioplasty: a clinical scenario of ischemic preconditioning

No or slow reflow following percutaneous coronary intervention (PCI), despite the presence of a patent epicardial vessel, is a serious complication resulting in increased morbidity and mortality. In the present study, we have evaluated the combination therapy of adenosine and sodium nitroprusside administered as sequential intracoronary (IC) boluses on no-reflow during PCI. Seventy-five high risk acute coronary syndrome patients who underwent PCI with evidence of initial less than TIMI (thrombolysis in myocardial infarction) III flow or developed deterioration in TIMI flow during the procedure were randomized to prophylactic administration of multiple boluses of IC saline solution, adenosine (12 microg/bolus) or the combination of adenosine (12 microg/bolus) and sodium nitroprusside (50 microg/bolus), sequentially. Assessment of TIMI and the TMP (tissue myocardial perfusion) grade was done and major adverse cardiac events (MACE) were assessed at the end of 6 months. Slow or no-reflow was persistent in 70% patients receiving saline solution, 31% patients receiving adenosine, and 4% patient receiving the combination. IC injection with saline solution did not produce improvement in TIMI flow or TMP grade. IC injection with combination resulted in greater improvement of TIMI flow and TMP grade. The crossover of patients with no-reflow in saline solution group or adenosine with combination treatment was associated with reestablishment of TIMI II in 4 and TIMI III in 20 patients. Our data suggest that combination therapy of adenosine and nitroprusside is safe and provides better improvement in coronary flow and MACE as compared with IC adenosine alone in cases of impaired flow during coronary interventions.     

A new leaf rust resistance gene <Emphasis Type="Italic">Lr79</Emphasis> mapped in chromosome 3BL from the durum wheat landrace Aus26582

Key message

A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection.

Abstract

Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3. LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2. LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708 and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3, only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3-linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79. Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels.

     

Genotyping of Indian <Emphasis Type="Italic">Yersinia pestis</Emphasis> strains by MLVA and repetitive DNA sequence based PCRs

India experienced two plague outbreaks in Gujarat and Maharastra during 1994 and then in the Shimla district of Himachal Pradesh during 2002. Yersinia pestis strains recovered from rodents and pneumonic patients during the 1994 outbreaks, pneumonic patients from the 2002 Shimla outbreak and rodents trapped on the Deccan Plateau during a surveillance activity carried out in 1998 were characterized by MLVA, ERIC-PCR and ERIC-BOX-PCR. MLVA genotyping of Indian Y. pestis strains revealed strains of 2 Orientalis, 1 Mediaevalis and 1 Antiqua genotypes distributed in three distinct branches corresponding to their biovar. The Orientalis genotype strains recovered from the 1994 outbreaks and 1998 surveillance activity clustered in one branch while the Antiqua biovar strains from the Shimla outbreak and the Mediaevalis strain recovered from a rodent trapped on the Deccan Plateau region during surveillance formed the other branches. The Orientalis Y. pestis strains recovered from rodents and patients from the 1994 plague outbreaks exhibited similar MLVA, ERIC-PCR and ERIC-BOX-PCR profiles and these were closely related to the Orientalis strains recovered from the rodents trapped on the Deccan Plateau. These data provide evidence for the possible linkage between the Y. pestis strains resident in the endemic region and those that were associated with the 1994 plague outbreaks. Mediaevalis and Antiqua biovars also were recovered from the environmental reservoir on the Deccan Plateau and from the pneumonic patients of 2002 plague outbreak. Therefore, as in Central Asian and African regions, Antiqua and Mediaevalis biovars seem to be well established in the Indian subcontinent as well. ERIC-PCR DNA fingerprinting delineated genotypes similar to those defined by MLVA. Thus ERIC-PCR appears to have the potential to be used as a molecular marker in the molecular epidemiological investigations of plague.     

Development of wheat–Aegilops speltoides recombinants and simple PCR-based markers for Sr32 and a new stem rust resistance gene on the 2S#1 chromosome

Key message

Wheat– Aegilops speltoides recombinants carrying stem rust resistance genes Sr32 and SrAes1t effective against Ug99 and PCR markers for marker-assisted selection.

Abstract

Wild relatives of wheat are important resources for new rust resistance genes but underutilized because the valuable resistances are often linked to negative traits that prevent deployment of these genes in commercial wheats. Here, we report ph1b-induced recombinants with reduced alien chromatin derived from E.R. Sears’ wheat–Aegilops speltoides 2D-2S#1 translocation line C82.2, which carries the widely effective stem rust resistance gene Sr32. Infection type assessments of the recombinants showed that the original translocation in fact carries two stem rust resistance genes, Sr32 on the short arm and a previously undescribed gene SrAes1t on the long arm of chromosome 2S#1. Recombinants with substantially shortened alien chromatin were produced for both genes, which confer resistance to stem rust races in the TTKSK (Ug99) lineage and representative races of all Australian stem rust lineages. Selected recombinants were back crossed into adapted Australian cultivars and PCR markers were developed to facilitate the incorporation of these genes into future wheat varieties. Our recombinants and those from several other labs now show that Sr32, Sr39, and SrAes7t on the short arm and Sr47 and SrAes1t on the long arm of 2S#1 form two linkage groups and at present no rust races are described that can distinguish these resistance specificities.     

Mapping of durable stripe rust resistance in a durum wheat cultivar Wollaroi

Wollaroi, an Australian durum wheat cultivar, produced a low stripe rust response and the alternative parent Bansi was highly susceptible. The Wollaroi/Bansi recombinant inbred line (RIL) population was phenotyped across three consecutive crop seasons. A genetic map of the Wollaroi/Bansi RIL population comprising 799 markers (diversity arrays technology and simple sequence repeat markers) was used to determine the genomic location of stripe rust resistance genes carried by the cultivar Wollaroi. Composite interval mapping detected three consistent quantitative trait loci (QTL) in chromosomes 2A, 3B and 5B. These QTL were named QYr.sun-2A, QYr.sun-3B and QYr.sun-5B. Another QTL, QYr.sun-1B, was detected only in the 2009 crop season. QTL in chromosomes 1B, 2A, 3B and 5B explained on average 6, 9.3, 26.7 and 8.7 %, respectively, of the variation in stripe rust response. All QTL were contributed by Wollaroi. RILs carrying these QTL singly produced intermediate stripe rust severities ranging from 46.2 to 55.7 %, whereas RILs with all four QTL produced the lowest disease severity (34.3 %). The consistently low stripe rust response of Wollaroi for 20 years demonstrated the durability of the resistance loci involved. The QTL combination detected in this study is being transferred to common wheat.