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Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

ABSTRACT: Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New Zealand near Lincoln in 2014. The populations were genotyped with the 90K Infinium iSelect assay and quantitative trait loci (QTL) analysis was performed. A high density consensus map generated based on 14 doubled haploid populations and integrating SNP and SSR markers was used to compare QTL identified in different populations. AC Cadillac contributed QTL on chromosomes 2A, 3B and 7B (2 loci), Carberry on 1A, 2B (2 loci), 2D, 4B (2 loci), 5A, 6A, 7A and 7D, Lillian on 4A and 7D, Stettler on 2D and 6B, Vesper on 1B, 1D, 2A, 6B and 7B (2 loci), and Red Fife on 7A and 7B. Lillian contributed to a novel locus QLr.spa-4A, and similarly Carberry at QLr.spa-5A. The discovery of novel leaf rust resistance QTL QLr.spa-4A and QLr.spa-5A, and several others in contemporary Canada Western Red Spring wheat varieties is a tremendous addition to our present knowledge of resistance gene deployment in breeding. Carberry demonstrated substantial stacking of genes which could be supplemented with the genes identified in other cultivars with the expectation of increasing efficacy of resistance to leaf rust and longevity with little risk of linkage drag.

SUBMITTER: Bokore FE

PROVIDER: S-EPMC7141615 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

Bokore Firdissa E FE Knox Ron E RE Cuthbert Richard D RD Pozniak Curtis J CJ McCallum Brent D BD N'Diaye Amidou A DePauw Ron M RM Campbell Heather L HL Munro Catherine C Singh Arti A Hiebert Colin W CW McCartney Curt A CA Sharpe Andrew G AG Singh Asheesh K AK Spaner Dean D Fowler D B DB Ruan Yuefeng Y Berraies Samia S Meyer Brad B

PloS one 20200408 4

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurse ...[more]

PMID: 32267842

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Project description:BackgroundLeaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers.ResultsThe collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S-90S, however some cultivars showed a high level of leaf rust resistance (SR?<?20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15?K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai?=?2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population.ConclusionsThis study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.

Project description:Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace "KU3067" displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5-17.2 and 12.6-19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9-20.5 and 5.4-12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.

Project description:Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Project description:The Canada Western Red Spring wheat (Triticum aestivum L.) cultivars AAC Concord, AAC Prevail, CDC Hughes, Lillian, Glenlea, and elite line BW961 express a spectrum of resistance to leaf rust caused by Puccinia triticina Eriks. This study aimed to identify and map the leaf rust resistance of the cultivars using three doubled haploid populations, AAC Prevail/BW961 (PB), CDC Hughes/AAC Concord (HC), and Lillian/Glenlea (LG). The populations were evaluated for seedling resistance in the greenhouse and adult plant disease response in the field at Morden, MB for 3 years and genotyped with the 90K wheat Infinium iSelect SNP array. Genetic maps were constructed to perform QTL analysis on the seedling and field leaf rust data. A total of three field leaf rust resistance QTL segregated in the PB population, five in the HC, and six in the LG population. In the PB population, BW961 contributed two QTL on chromosomes 2DS and 7DS, and AAC Prevail contributed a QTL on 4AL consistent across trials. Of the five QTL in HC, AAC Concord contributed two QTL on 4AL and 7AL consistent across trials and a QTL on 3DL.1 that provided seedling resistance only. CDC Hughes contributed two QTL on 1DS and 3DL.2. Lillian contributed four QTL significant in at least two of the three trials on 2BS, 4AL, 5AL, and 7AL, and Glenlea two QTL on 4BL and 7BL. The 1DS QTL from CDC Hughes, the 2DS from BW961, the 4AL from the AAC Prevail, AAC Concord, and Lillian, and the 7AL from AAC Concord and Lillian conferred seedling leaf rust resistance. The QTL on 4AL corresponded with Lr30 and was the same across cultivars AAC Prevail, AAC Concord, and Lillian, whereas the 7AL corresponding with LrCen was coincident between AAC Concord and Lillian. The 7DS and 2DS QTL in BW961 corresponded with Lr34 and Lr2a, respectively, and the 1DS QTL in CDC Hughes with Lr21. The QTL identified on 5AL could represent a novel gene. The results of this study will widen our knowledge of leaf rust resistance genes in Canadian wheat and their utilization in resistance breeding.

Dataset Information

Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

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Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

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