Investigation and Genome-Wide Association Analysis of Fusarium Seedling Blight Resistance in Chinese Elite Wheat Lines.
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ABSTRACT:
SUBMITTER: Liu Y
PROVIDER: S-EPMC8635748 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Fusarium head blight (FHB) is a devastating wheat disease worldwide. To decipher the genetic architecture of FHB resistance in Chinese germplasm, a Wheat Association Panel for Scab Research (WAPS) consisting of 240 leading Chinese wheat cultivars and elite lines was genotyped using the 90K single nucleotide polymorphism (SNP) arrays. The FHB response was evaluated in the field nurseries in Wuhan in Hubei Province over four consecutive years from 2014 to 2017. Five quantitative trait loci (QTL) were consistently identified on chromosome arms 1AS, 2DL, 5AS, 5AL, and 7DS using a mixed linear model (MLM), explaining 5.6, 10.3, 5.7, 5.4, and 5.6% of phenotypic variation, respectively. The QTL on 5AS, 5AL, and 7DS QTL are probably novel. The allelic frequency analysis indicated that cultivars from the Middle and Lower Yangtze River Valleys harbored more favorable alleles and were therefore more resistant than those from other regions. To facilitate in-house germplasm screening and marker-assisted selection (MAS), SNP-derived PCR markers were developed for the QTL regions on 1AS, 5AS, and 5AL QTL. In addition to the above five QTL, the WAPS population had a very low frequency of Fhb1, confirming that the gene is not widely used in Chinese wheat breeding programs. The resistant lines and molecular markers developed in this study are resources and information for enhancing FHB resistance in breeding populations by marker-assisted recurrent selection and gene stacking.
| S-EPMC7056811 | biostudies-literature
Project description:Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20-30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26-30% of the total variation (depending on traits: percent severity, coefficient of infection or response type). Similarly, the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24-34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.
| S-EPMC4744023 | biostudies-literature
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
Project description:BackgroundFusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance.ResultsTo characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation.ConclusionInduced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization.
| S-EPMC8228913 | biostudies-literature
Project description:Fusarium head blight (FHB) is a destructive disease of wheat (Triticum aestivum L.), which not only significantly reduces grain yield, but also affects end-use quality. Breeding wheat cultivars with high FHB resistance is the most effective way to control the disease. The Chinese wheat cultivar Jingzhou 66 (JZ66) shows moderately high FHB resistance; however, the genetic basis of its resistance is unknown. A doubled haploid (DH) population consisting 209 lines was developed from a cross of JZ66 and Aikang 58 (AK58), a FHB susceptible wheat cultivar, to identify quantitative trait loci (QTL) that contribute to the FHB resistance. Five field experiments were established across two consecutive crop seasons (2018 and 2019) to evaluate the DH lines and parents for FHB response. The parents and DH population were genotyped with the wheat 55K single-nucleotide polymorphism (SNP) assay. Six QTLs associated with FHB resistance in JZ66 were mapped on chromosome 2DS, 3AS, 3AL, 3DL, 4DS, and 5DL, respectively. Four of the QTL (QFhb.hbaas-2DS, QFhb.hbaas-3AL, QFhb.hbaas-4DS, and QFhb.hbaas-5DL) were detected in at least two environments, and the QTL on 3AL and 5DL might be new. The QTL with major effects, QFhb.hbaas-2DS and QFhb.hbaas-4DS, explained up to 36.2% and 17.6% of the phenotypic variance, and were co-localized with the plant semi-dwarfing loci Rht8 and Rht-D1. The dwarfing Rht8 allele significantly increased spike compactness (SC) and FHB susceptibility causing a larger effect on FHB response than Rht-D1 observed in this study. PCR-based SNP markers for QFhb.hbaas-2DS, QFhb.hbaas-3AL, QFhb.hbaas-4DS, and QFhb.hbaas-5DL, were developed to facilitate their use in breeding for FHB resistance by marker-assisted selection.
| S-EPMC7465298 | biostudies-literature
Project description:Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, is a devastating disease in wheat (Triticum aestivum L.). Use of host resistance is one of the most effective strategies to minimize the disease damage. Haiyanzhong (HYZ) is a Chinese wheat landrace that shows a high level of resistance to FHB spread within a spike (type II resistance). To map the quantitative trait loci (QTLs) in HYZ and identify markers tightly linked to the QTLs for FHB resistance, a population of 172 recombinant inbred lines (RILs) from a cross between HYZ and Wheaton (FHB susceptible) was genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) derived from genotyping-by-sequencing (GBS), and evaluated for percentage of symptomatic spikelets (PSSs) per spike in three greenhouse experiments. Six QTLs for type II resistance were identified in HYZ, indicating that multiple minor QTLs together can provide a high level of FHB resistance in wheat. The QTL with the largest effect on FHB resistance was mapped on the chromosome arm 5AS, and the other five from HYZ were mapped on the chromosomes 6B, 7D, 3B, 4B and 4D. In addition, two QTLs from Wheaton were mapped on 2B. Critical SNPs linked to the QTLs on chromosomes 5A, 6B, and 2B were converted into KBioscience competitive allele-specific PCR (KASP) assays, which can be used for marker-assisted selection (MAS) to pyramid these QTLs in wheat.
| S-EPMC5038969 | biostudies-literature
Project description:BackgroundFusarium head blight (FHB) is a disease affecting wheat spikes caused by some Fusarium species and leads to cases of severe yield reduction and seed contamination. Identifying resistance genes/QTLs from wheat germplasm may help to improve FHB resistance in wheat production.MethodsOur study evaluated 205 elite winter wheat cultivars for FHB resistance. A high-density 90K SNP array was used for genotyping the panel. A genome-wide association study (GWAS) from cultivars from three different environments was performed using a mixed linear model (MLM).ResultsSixty-six significant marker-trait associations (MTAs) were identified (P < 0.001) on fifteen chromosomes that explained the phenotypic variation ranging from 5.4 to 11.2%. Some important new MTAs in genomic regions involving FHB resistance were found on chromosomes 2A, 3B, 5B, 6A, and 7B. Six MTAs at 92 cM on chromosome 7B were found in cultivars from two different environments. Moreover, there were 11 MTAs consistently associated with diseased spikelet rate and diseased rachis rate as pleiotropic effect loci and D_contig74317_533 on chromosome 5D was novel for FHB resistance. Eight new candidate genes of FHB resistance were predicated in wheat in this study. Three candidate genes, TraesCS5D02G006700, TraesCS6A02G013600, and TraesCS7B02G370700 on chromosome 5DS, 6AS, and 7BL, respectively, were perhaps important in defending against FHB by regulating intramolecular transferase activity, GTP binding, or chitinase activity in wheat, but further validation in needed. In addition, a total of five favorable alleles associated with wheat FHB resistance were discovered. These results provide important genes/loci for enhancing FHB resistance in wheat breeding by marker-assisted selection.
| S-EPMC10518165 | biostudies-literature
Project description:Beneficial microorganisms, including members of the Trichoderma genus, are known for their ability to promote plant growth and disease resistance, as well as being alternatives to synthetic inputs in agriculture. In this study, 111 Trichoderma strains were isolated from the rhizospheric soil of Florence Aurore, an ancient wheat variety that was cultivated in an organic farming system in Tunisia. A preliminary ITS analysis allowed us to cluster these 111 isolates into three main groups, T. harzianum (74 isolates), T. lixii (16 isolates) and T. sp. (21 isolates), represented by six different species. Their multi-locus analysis (tef1, translation elongation factor 1; rpb2, RNA polymerase B) identified three T. afroharzianum, one T. lixii, one T. atrobrunneum and one T. lentinulae species. These six new strains were selected to determine their suitability as plant growth promoters (PGP) and biocontrol agents (BCA) against Fusarium seedling blight disease (FSB) in wheat caused by Fusarium culmorum. All of the strains exhibited PGP abilities correlated to ammonia and indole-like compound production. In terms of biocontrol activity, all of the strains inhibited the development of F. culmorum in vitro, which is linked to the production of lytic enzymes, as well as diffusible and volatile organic compounds. An in planta assay was carried out on the seeds of a Tunisian modern wheat variety (Khiar) by coating them with Trichoderma. A significant increase in biomass was observed, which is associated with increased chlorophyll and nitrogen. An FSB bioprotective effect was confirmed for all strains (with Th01 being the most effective) by suppressing morbid symptoms in germinated seeds and seedlings, as well as by limiting F. culmorum aggressiveness on overall plant growth. Plant transcriptome analysis revealed that the isolates triggered several SA- and JA-dependent defense-encoding genes involved in F. culmorum resistance in the roots and leaves of three-week-old seedlings. This finding makes these strains very promising in promoting growth and controlling FSB disease in modern wheat varieties.
| S-EPMC10303082 | biostudies-literature
Project description:Fusarium head blight (FHB) of wheat caused by Fusarium species is a destructive disease, causing grain yield and quality losses. Developing FHB-resistant cultivars is crucial to minimize the extent of the disease. The first objective of this study was incorporation of Fhb1 from a resistant donor into five Polish wheat breeding lines with good agronomical traits and different origins. We also performed a haplotype-based GWAS to identify chromosome regions in derived wheat families associated with Fusarium head blight resistance. As a result of marker-assisted backcrossing (MABC), five wheat combinations were obtained. Fungal inoculation and disease assessment were conducted for two years, 2019 and 2020. In 2019 the average phenotypic response of type II resistance was 2.2, whereas in 2020 it was 2.1. A haploblock-based GWAS performed on 10 phenotypic traits (related to type of resistance, year of experiment and FHB index) revealed nine marker-trait associations (MTA), among which six belong to chromosome 2D, two to 3B and one to 7D. Phenotypic variation (R2) explained by the identified haplotypes in haploblocks ranged from 6% to 49%. Additionally, an association weight matrix (AWM) was created, giving the partial correlation-information theory (PCIT) pipeline of 171 edges and 19 nodes. The resultant data and high level of explained phenotypic variance of MTA create the opportunity for data utilization in MAS.
| S-EPMC9695032 | biostudies-literature
Project description:Fusarium head blight (FHB), caused by Fusarium graminearum, is a very important disease of wheat globally. Damage caused by F. graminearum includes reduced grain yield, reduced grain functional quality, and results in the presence of the trichothecene mycotoxin deoxynivalenol in Fusarium-damaged kernels. The development of FHB resistant wheat cultivars is an important component of integrated management. The objective of this study was to identify QTL for FHB resistance in a recombinant inbred line (RIL) population of the spring wheat cross Kenyon/86ISMN 2137. Kenyon is a Canadian spring wheat, while 86ISMN 2137 is an unrelated spring wheat. The RIL population was evaluated for FHB resistance in six FHB nurseries. Nine additive effect QTL for FHB resistance were identified, six from Kenyon and three from 86ISMN 2137. Rht8 and Ppd-D1a co-located with two FHB resistance QTL on chromosome arm 2DS. A major QTL for FHB resistance from Kenyon (QFhb.crc-7D) was identified on chromosome 7D. The QTL QFhb.crc-2D.4 from Kenyon mapped to the same region as a FHB resistance QTL from Wuhan-1 on chromosome arm 2DL. This result was unexpected since Kenyon does not share common ancestry with Wuhan-1. Other FHB resistance QTL on chromosomes 4A, 4D, and 5B also mapped to known locations of FHB resistance. Four digenic epistatic interactions were detected for FHB resistance, which involved eight QTL. None of these QTL were significant based upon additive effect QTL analysis. This study provides insight into the genetic basis of native FHB resistance in Canadian spring wheat.
| S-EPMC5061752 | biostudies-other