Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Source Identification and Genome-Wide Association Analysis of Crown Rot Resistance in Wheat.

ABSTRACT: Crown rot (CR) is a soil-borne disease of wheat in arid and semiarid areas of the world. The incidence rate and severity of CR are increasing with each passing year, which seriously threatens the safety of world wheat production. Here, 522 wheat varieties/lines representing genetic diversity were used to identify and evaluate the resistance source to CR disease. Six varieties, including Zimai 12, Xinong 509, Mazhamai, Sifangmai, and Dawson, were classified as resistant ® to CR. Seventy-nine varieties were classified as moderately resistant (MR) to CR, accounting for 15.13% of the tested varieties. The wheat 660 K SNP array was used to identify resistance loci by genome-wide association analysis (GWAS). A total of 33 SNPs, located on chromosomes 1A, 1B, 1D, 4A, and 4D, were significantly correlated with seedling resistance to CR in two years. Among them, one SNP on chromosome 1A and nine SNPs on chromosome 1B showed most significant resistance to disease, phenotypic variance explained (PVE) by these SNPs were more than 8.45%. Except that significant locus AX-110436287 and AX109621209 on chromosome 1B and AX-94692276 on 1D are close to the already reported QTL, other SNPs are newly discovered resistance loci. These results could lay a strong theoretical foundation for the genetic improvement and breeding for CR resistance in wheat.

SUBMITTER: Pu L

PROVIDER: S-EPMC9329777 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat.

Project description:BackgroundFusarium crown rot (FCR) is a severe and chronic disease in common wheat and is able to cause serious yield loss and health problems to human and livestock.ResultsHere, 234 Chinese wheat cultivars were evaluated in four greenhouse experiments for FCR resistance and genome-wide association studies (GWAS) were performed using the wheat 660 K genotyping assay. The results indicated that most cultivars evaluated showed FCR disease index (DI) of 40-60, while some cultivars showed stably good FCR resistance (DI < 30). GWAS identified 286 SNPs to be significantly associated with FCR resistance, of which 266, 6 and 8 were distributed on chromosomes 6A, 6B and 6D, respectively. The significant SNPs on 6A were located in a 7.0-Mb region containing 51 annotated genes. On the other hand, QTL mapping using a bi-parental population derived from UC1110 and PI610750 detected three QTLs on chromosomes 6A (explaining 7.77-10.17% of phenotypic variation), 2D (7.15-9.29%) and 2A (5.24-6.92%). The 6A QTL in the UC1110/PI610750 population falls into the same chromosomal region as those detected from GWAS, demonstrating its importance in Chinese materials for FCR resistance.ConclusionThis study could provide useful information for utilization of FCR-resistant wheat germplasm and further understanding of molecular and genetics basis of FCR resistance in common wheat.

| S-EPMC6480828 | biostudies-literature

Genome-wide association mapping of Fusarium crown rot resistance in Aegilops tauschii.

Project description:Fusarium crown rot (FCR), caused by various Fusarium species, is a primary fungal disease in most wheat-growing regions worldwide. A. tauschii, the diploid wild progenitor of the D-genome of common wheat, is a reservoir of genetic diversity for improving bread wheat biotic and abiotic resistance/tolerance. A worldwide collection of 286 A. tauschii accessions was used to evaluate FCR resistance. Population structure analysis revealed that 115 belonged to the A. tauschii ssp. strangulata subspecies, and 171 belonged to the A. tauschii ssp. tauschii subspecies. Five accessions with disease index values lower than 20 showed moderate resistance to FCR. These five originated from Afghanistan, China, Iran, Uzbekistan, and Turkey, all belonging to the tauschii subspecies. Genome-wide association mapping using 6,739 single nucleotide polymorphisms (SNPs) revealed that two SNPs on chromosome 2D and four SNPs on chromosome 7D were significantly associated with FCR resistance. Almost all FCR resistance alleles were presented in accessions from the tauschii subspecies, and only 4, 11, and 19 resistance alleles were presented in accessions from the strangulata subspecies. Combining phenotypic correlation analysis and genome-wide association mapping confirmed that FCR resistance loci were independent of flowering time, heading date, and plant height in this association panel. Six genes encoding disease resistance-related proteins were selected as candidates for further validation. The identified resistant A. tauschii accessions will provide robust resistance gene sources for breeding FCR-resistant cultivars. The associated loci/genes will accelerate and improve FCR in breeding programs by deploying marker-assisted selection.

| S-EPMC9562832 | biostudies-literature

Identification of Novel Quantitative Trait Loci Linked to Crown Rot Resistance in Spring Wheat.

Project description:Crown rot (CR), caused by various Fusarium species, is a major disease in many cereal-growing regions worldwide. Fusarium culmorum is one of the most important species, which can cause significant yield losses in wheat. A set of 126 advanced International Maize and Wheat Improvement Center (CIMMYT) spring bread wheat lines were phenotyped against CR for field crown, greenhouse crown and stem, and growth room crown resistance scores. Of these, 107 lines were genotyped using Diversity Array Technology (DArT) markers to identify quantitative trait loci linked to CR resistance by genome-wide association study. Results of the population structure analysis grouped the accessions into three sub-groups. Genome wide linkage disequilibrium was large and declined on average within 20 cM (centi-Morgan) in the panel. General linear model (GLM), mixed linear model (MLM), and naïve models were tested for each CR score and the best model was selected based on quarantine-quarantine plots. Three marker-trait associations (MTAs) were identified linked to CR resistance; two of these on chromosome 3B were associated with field crown scores, each explaining 11.4% of the phenotypic variation and the third MTA on chromosome 2D was associated with greenhouse stem score and explained 11.6% of the phenotypic variation. Together, these newly identified loci provide opportunity for wheat breeders to exploit in enhancing CR resistance via marker-assisted selection or deployment in genomic selection in wheat breeding programs.

| S-EPMC6165080 | biostudies-other

Genome-Wide Association Studies on Chinese Wheat Cultivars Reveal a Novel Fusarium Crown Rot Resistance Quantitative Trait Locus on Chromosome 3BL.

Project description:Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum, has emerged as a new threat to wheat production and quality in North China. Genetic enhancement of wheat resistance to FCR remains the most effective approach for disease control. In this study, we phenotyped 435 Chinese wheat cultivars through FCR inoculation at the seedling stage in a greenhouse. Our findings revealed that only approximately 10.8% of the wheat germplasms displayed moderate or high resistance to FCR. A genome-wide association study (GWAS) using high-density 660K SNP led to the discovery of a novel quantitative trait locus on the long arm of chromosome 3B, designated as Qfcr.hebau-3BL. A total of 12 significantly associated SNPs were closely clustered within a 1.05 Mb physical interval. SNP-based molecular markers were developed to facilitate the practical application of Qfcr.hebau-3BL. Among the five candidate FCR resistance genes within the Qfcr.hebau-3BL, we focused on TraesCS3B02G307700, which encodes a protein kinase, due to its expression pattern. Functional validation revealed two transcripts, TaSTK1.1 and TaSTK1.2, with opposing roles in plant resistance to fungal disease. These findings provide insights into the genetic basis of FCR resistance in wheat and offer valuable resources for breeding resistant varieties.

| S-EPMC10974656 | biostudies-literature

Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat.

Project description:Fusarium crown rot (FCR) is one of the most important diseases of wheat (Triticum aestivum L.). FCR is mainly caused by the fungal pathogens Fusarium culmorum and F. pseudograminearum. In order to identify new sources of resistance to FCR and to dissect the complexity of FCR resistance, a panel of 161 wheat accessions was phenotyped under growth room (GR) and greenhouse conditions (GH). Analysis of variance showed significant differences in crown rot development among wheat accessions and high heritability of genotype-environment interactions for GR (0.96) and GH (0.91). Mixed linear model analysis revealed seven novel quantitative trait loci (QTLs) linked to F. culmorum on chromosomes 2AL, 3AS, 4BS, 5BS, 5DS, 5DL and 6DS for GR and eight QTLs on chromosomes on 3AS, 3BS, 3DL, 4BS (2), 5BS, 6BS and 6BL for GH. Total phenotypic variances (R²) explained by the QTLs linked to GR and GH were 48% and 59%, respectively. In addition, five favorable epistasis interactions among the QTLs were detected for both GR and GH with and without main effects. Epistatic interaction contributed additional variation up to 21% under GR and 7% under GH indicating strong effects of environment on the expression of QTLs. Our results revealed FCR resistance responses in wheat to be complex and controlled by multiple QTLs.

| S-EPMC7035263 | biostudies-literature

Genome-wide Association Analysis of Powdery Mildew Resistance in U.S. Winter Wheat.

Project description:Wheat powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is a major fungal disease of wheat worldwide. It can cause considerable yield losses when epidemics occur. Use of genetic resistance is the most effective approach to control the disease. To determine the genomic regions responsible for PM resistance in a set of U.S. winter wheat and identify DNA markers in these regions, we conducted a genome-wide association study on a set of 185 U.S. winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90?K wheat SNP arrays. We identified significant SNP markers linked to nine quantitative trait loci (QTLs) and simple sequence repeats (SSR) markers linked to three QTLs for PM resistance. Most of the QTLs in the US winter wheat population have been reported previously, but some such as these on chromosomes 1A, 6A and 1B have not been reported previously, and are likely new QTLs for PM resistance in U.S. winter wheat. The germplasm with immunity to PM are good sources of resistance for PM resistance breeding and the markers closely linked to the QTLs can be used in marker-assisted selection to improve wheat PM resistance after further validation.

| S-EPMC5603590 | biostudies-literature

Genome-wide association analysis of stripe rust resistance in modern Chinese wheat.

Project description:BackgroundStripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.ResultsStripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation.ConclusionThe resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

| S-EPMC7590722 | biostudies-literature

QTL conferring fusarium crown rot resistance in the elite bread wheat variety EGA Wylie.

Project description:Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. The genetics of FCR resistance in the bread wheat (Triticum eastivum L.) variety EGA Wylie, the most resistant commercial variety available, was studied by QTL mapping. Three populations of recombinant inbred lines were developed with this elite variety as the resistant parent. Four QTL conferring FCR resistance were detected and resistance alleles of all of them were derived from the resistant parent EGA Wylie. One of these loci was located on the short arm of chromosome 5D (designated as Qcrs.cpi-5D). This QTL explains up to 31.1% of the phenotypic variance with an LOD value of 9.6. The second locus was located on the long arm of chromosome 2D (designated as Qcrs.cpi-2D) and explained up to 20.2% of the phenotypic variance with an LOD value of 4.5. Significant effects of both Qcrs.cpi-5D and Qcrs.cpi-2D were detected in each of the three populations assessed. Another two QTL (designated as Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2, respectively) were located on the short arm of chromosome 4B. These two QTL explained up to 16.9% and 18.8% of phenotypic variance, respectively. However, significant effects of Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2 were not detected when the effects of plant height was accounted for by covariance analysis. The elite characteristics of this commercial variety should facilitate the incorporation of the resistance loci it contains into breeding programs.

| S-EPMC4002477 | biostudies-literature

Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis.

Project description:Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

| S-EPMC9929074 | biostudies-literature

Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat.

Project description:Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.

| S-EPMC8260946 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data