Genome wide association mapping of stripe rust resistance in Afghan wheat landraces

Manickavelu, Alagu; Joukhadar, Reem; Jighly, Abdulqader; Lan, Caixia; Espino, Julio Huerta; Stanikzai, Ahmad Shah; Kilian, Andrzej; Singh, Ravi P.; Ban, Tomohiro

doi:10.1016/j.plantsci.2016.07.018

Cited by 37 publications

(39 citation statements)

References 49 publications

(59 reference statements)

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“…All positions are approximations, and thus should be treated as guidelines for future studies. The detailed information of relationships between the QTL identified in this study and previously mapped Yr genes and QTL are based on this result integrated by the BioMercator V4.2 and described in the unpublished data of our research group (Table 3 and Additional file 6) the extent of genetic diversity and the genetic basis of responses to stripe rust in wheat may improve the effectiveness of exploration of genetic resources and enrich breeding for durable stripe rust resistance in wheat [60]. In the current study, 93 Northern Chinese wheat landraces were surveyed under four environments and challenged with a mixture of Pst isolates.…”

Section: Discussionmentioning

confidence: 93%

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Yao

Xue-mei

et al. 2019

BMC Genet

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Background: Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. Results: Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage. Conclusions: The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.

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Section: Discussionmentioning

confidence: 93%

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Yao

Xue-mei

et al. 2019

BMC Genet

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“…Another simulation was conducted in order to compare the output from PolySim to a real wheat data set, which is a well‐described allohexaploid species (2 n = 6 x = 42), based on LD and He measurements of SNP markers (Manickavelu, Jighly, & Ban, ; Manickavelu et al., ). The simulation was performed for 1,000 individuals, for each of the allohexaploid genomes and its known progenitors.…”

Section: Methodsmentioning

confidence: 99%

“…Selfing rate was set to 90% (outcrossing 10%) as multiple studies reported variable outcrossing rates for wheat up to 10.6% (Hanson, Mallory‐Smith, Shafii, Thill, & Zemetra, ; Lawrie, Matus‐Cádiz, & Hucl, ). We assumed that our wheat population has a high outcrossing rate because of the massive diversity reported in this germplasm (Manickavelu et al., , ). The simulation was run for 30,000 generations, during which the three diploids emerged after 6,000; 6,200 and 10,000 generations; the allotetraploid evolved after 12,000 generations; and the allohexaploid genome appeared at generation 18,000.…”

Section: Methodsmentioning

confidence: 99%

Insights into population genetics and evolution of polyploids and their ancestors

Jighly

Lin

Forster

et al. 2018

Molecular Ecology Resources

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We have developed the first comprehensive simulator for polyploid genomes (PolySim) and demonstrated its value by performing large-scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating single nucleotide polymorphisms, minor allele frequency, heterozygosity, R and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent (MV) pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. MV formation can homogenize allotetraploid subgenomes, but this homogenization requires a higher MV rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations, which, in combination with quantitative genetics tools, can be used to investigate the power of genomewide association, genomic selection or breeding programme designs in these species.

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“…As a result of changes in the predominant races and emergence of new races, many wheat cultivars have become susceptible to stripe rust, thus accelerating the cultivar turnover frequency [7]. Mining of novel genetic resources and the breeding of diseaseresistant cultivars is an effective, economic and environmentally friendly strategy to control stripe rust in wheat [7,12].…”

Section: Introductionmentioning

confidence: 99%

“…They have a greater diversity of genes that respond to abiotic and biotic stresses, such as growth habit; cold; heat or drought tolerance; early growth vigor; competition with weeds and disease tolerance [27]. They could be used as important resources for stripe-rust resistance breeding [12,20,[28][29][30][31]. However, relatively few studies have investigated genetic diversity and stripe rust resistance in wheat landraces from the southern autumnsown spring wheat zone of China.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Mapping Reveals Potential Novel Loci Controlling Stripe-rust Resistance in a Chinese Wheat Landrace Diversity Panel From the Southern Autumn-sown Spring Wheat Zone

Wang

Cheng

et al. 2020

Preprint

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Background:Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe-rust resistance genes and cultivation of resistant varieties are considered to be the most effective approaches to control this disease. In this study, we evaluated the infection type (IT), disease severity (DS) and area under the disease progress curve (AUDPC) of 143 Chinese wheat landrace accessions for stripe-rust resistance. Assessments were undertaken in five environments at the adult-plant stage with Pst mixture races under field conditions, in addition, IT was assessed at the seedling stage with two prevalent Pst races (CYR32 and CYR34) under controlled greenhouse conditions. Results:Seventeen accessions showed stable high-level resistance to stripe rust across all environments under field tests,while four accessions showed resistance to the Pst races CYR32 and CYR34 at the all-stage.Combining phenotypic data from the field and greenhouse trials with 6404 markers covering the whole genome, we detected 17quantitative trait locus(QTLs) on 11 chromosomes for IT associated with seedling resistance and 15 QTLs on seven chromosomes for IT, final disease severityor AUDPC associated with adult-plant resistance. Four stable QTLs detected on four chromosomes, which explained 9.99%–23.30% of the phenotypic variation, were simultaneously associated with seedling and adult-plant resistance. Integrating a linkage map of stripe-rust resistance in wheat, 29 QTLs overlapped with previously reported genes or QTLs, while two and oneQTLs conferring seedling and adult-plant resistancerespectively were mapped distantly from previously reported stripe rust resistance genes or QTLs and may be novel resistantloci. Conclusions:Our results provided an integrated view of stripe rust resistance resources in a Chinese wheat landrace diversity panel from the southern autumn-sown spring wheat zone.The identified resistant accessions and resistance loci will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.

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Genome wide association mapping of stripe rust resistance in Afghan wheat landraces

Cited by 37 publications

References 49 publications

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Insights into population genetics and evolution of polyploids and their ancestors

Genome-wide Association Mapping Reveals Potential Novel Loci Controlling Stripe-rust Resistance in a Chinese Wheat Landrace Diversity Panel From the Southern Autumn-sown Spring Wheat Zone

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