Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

Ye, Xueling; Li, Jian; Cheng, Yukun; Yao, Fangjie; Li, Long; Yu, Changyong; Wang, Yuqi; Wu, Yu; Li, Jing; Wang, Jirui; Jiang, Qiantao; Li, Wei; Ma, Jian; Wei, Yuming; Zheng, Youliang; Chen, Guoyue

doi:10.1186/s12870-019-1764-4

Cited by 39 publications

(48 citation statements)

References 73 publications

(71 reference statements)

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“…Based on the genotyping data generated using the 55K SNP array (Affymetrix Axiom Wheat55K), a total of 44,059 high-quality SNP markers were selected for genetic variation (Additional file 3) [27].…”

Section: Genome-wide Association Analysesmentioning

confidence: 99%

“…3, Additional file 4). The LD half decay distance was 2.12 Mb based on the r 2 values between significant pairs of intra-chromosomal SNP markers with physical distances [27]. 2017.…”

Section: Genome-wide Association Analysesmentioning

confidence: 99%

“…We will further study these candidate genes by genetic mapping or reverse genetics in the future. for stripe rust was the same as Ye et al [27]. In order to reduce the environmental impacts on yieldrelated traits, the best linear unbiased prediction (BLUP) values were calculated based on linear model using the lme4 package in the R program [103].…”

Section: Landraces As Elite Germplasm For Breedingmentioning

confidence: 99%

“…Combined with 44059 effective markers, we identified three potential novel loci and 16 favourable alleles through GWAS analysis, providing reliable markers and elite genetic stocks for molecular marker-assisted breeding.Materials And MethodsPlant materialsA total of 244 wheat accessions (Additional file 2) were used in this study, including 79 landraces and 165 cultivars which have been used or developed by different breeding programs in Sichuan Province since 1997.Evaluation of yield-related traits and stripe rust infection typeThe 244 wheat accessions were evaluated in two locations in Sichuan with different years but all under stripe rust stress: Chongzhou (30°33'37.3" N, 103°38'45.4" E, elevation 513 m) in 2017 (CZ17) and 2018 (CZ18); Mianyang (31°23'N, 104°49'E, elevation 440 m) in 2017 (MY17). All experimental fields were inoculated with mixed urediniospores of the local Pst races, including CYR32, CYR33, CYR34, G22-14, Su11-4, Su11-5, Su11-7[27]. The 244 wheat accessions were also planted in different fields in Chongzhou (30°33'46.3"N, 103°38'38.5"E, elevation 514 m) without inoculation in 2017 (CZ17ck) and 2018 (CZ18ck).…”

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confidence: 99%

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Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

Cheng

et al. 2019

Preprint

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Background As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44059 polymorphic markers from the 55K single nucleotide polymorphism (SNP) chip. Results A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, twenty-one candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. Conclusions QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.

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Section: Genome-wide Association Analysesmentioning

confidence: 99%

“…3, Additional file 4). The LD half decay distance was 2.12 Mb based on the r 2 values between significant pairs of intra-chromosomal SNP markers with physical distances [27]. 2017.…”

Section: Genome-wide Association Analysesmentioning

confidence: 99%

Section: Landraces As Elite Germplasm For Breedingmentioning

confidence: 99%

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confidence: 99%

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Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

Cheng

et al. 2019

Preprint

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“…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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Genomic signatures of selection for resistance to stripe rust in Austrian winter wheat

Morales

Michel

Ametz³

et al. 2021

Theor Appl Genet

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Key message We combined quantitative and population genetic methods to identify loci under selection for adult plant resistance to stripe rust in an Austrian winter wheat breeding population from 2008 to 2018. Abstract Resistance to stripe rust, a foliar disease caused by the fungus P. striiformis f. sp. tritici, in wheat (Triticum aestivum L.) is both qualitatively and quantitatively controlled. Resistance genes confer complete, race-specific resistance but are easily overcome by evolving pathogen populations, while quantitative resistance is controlled by many small- to medium-effect loci that provide incomplete yet more durable protection. Data on resistance loci can be applied in marker-assisted selection and genomic prediction frameworks. We employed genome-wide association to detect loci associated with stripe rust and selection testing to identify regions of the genome that underwent selection for stripe rust resistance in an Austrian winter wheat breeding program from 2008 to 2018. Genome-wide association mapping identified 150 resistance loci, 62 of which showed significant evidence of selection over time. The breeding population also demonstrated selection for resistance at the genome-wide level.

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Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

Cited by 39 publications

References 73 publications

Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

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

Genomic signatures of selection for resistance to stripe rust in Austrian winter wheat

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