Aug 2026· Theoretical and Applied Genetics· Vol 139· 0 citations· 73 references
Medicine
TL;DR
The identified SNPs, alleles, haplotypes, and CGs may be used in marker-assisted selection and breeding programs to develop wheat varieties with enhanced resistance to SB.
Abstract
GWAS of 1,273 wheat lines identified a stable MTA 3B_6127880 on 3BS chromosome arm for spot blotch resistance, and the associated candidate genes were differentially expressed in resistant vs. susceptible genotypes. Spot blotch (SB), caused by Bipolaris sorokiniana, poses a threat to global wheat production. We evaluated 1,500 elite wheat lines for SB across two environments to identify genomic regions and candidate genes (CGs) conferring resistance. Disease severity, measured as area under the disease progress curve (AUDPC), was negatively correlated with days to heading (DH) and stay-green traits (SGTs). Genome-wide association studies (GWAS) using three different models (MLM, FarmCPU, BLINK) identified seven and eleven stable MTAs for AUDPC and SGTs, respectively, with three (3B_6127880, 5B_546704556, 5B_546132836) common to both traits. To reduce the confounding effects of DH, a separate GWAS was conducted on a subset of genotypes with similar heading dates, confirming 3B_6127880 as a consistent locus for AUDPC, located near to previously known SB QTLs on 3BS chromosome arm. Several other putative MTAs and haplotypes associated with AUDPC and SGTs were identified. A time-course analysis of CGs associated with the important MTAs revealed differential expression in the resistant (Chirya 3) and susceptible (Sonalika) genotypes under SB infection. The identified SNPs, alleles, haplotypes, and CGs may be used in marker-assisted selection and breeding programs to develop wheat varieties with enhanced resistance to SB.
A new approach to identify environment-specific quantitative trait loci (QTL) using GWAS and the validated resistance gene Yr27 was identified as sole candidate gene for one QTL region of particular relevance for Central European wheat.
Jiao-Jiao Wang, Renate H. Schmidt, Guoliang Li et al.· Theoretical and Applied Gene...· 1 citation
The epidemic expansion of maize white leaf spot (WLS) is a substantial threat to the secure and sustained production of maize. Given its diversity and strong environmental adaptability, WLS has the potential to emerge as a globally prevalent disease affecting maize crops. A detailed exploration of genetic segments and genes that are significantly associated with resistance to WLS in maize, an analysis of the genetic mechanisms underlying maize’s response to this disease, as well as the identification and development of resistant germplasm resources and their promotion and application, are of great practical significance for ensuring the safe production of maize. In this study, a genome-wide association study (GWAS) of 11 related traits in 141 maize accessions was conducted, and a total of 1174 significant single-nucleotide polymorphism (SNP) sites were identified. BSA-Seq (Bulked Segregant Analysis Sequencing) identified 6319 sites and 79 candidate genes. Through comprehensive analysis of GWAS and RNA-Seq data, a total of 13 candidate genes associated with maize white spot resistance, including Zm00001eb093900 and Zm00001eb078490, were identified. This study systematically explored genetic regions and genes significantly linked to white spot resistance in maize, thereby providing novel genetic resources for future molecular design-based breeding and improvement of resistance traits. Furthermore, by correlating field disease incidence with the expression of immune response-related gene products, we developed a rapid evaluation system for maize WLS resistance, in which soil plant analysis development (SPAD) value, Fm, SSC, and POD served as key indicators. Using this system, 5 immune germplasm resources such as QB2229 and NP5366 and 89 highly resistant materials such as QB1923 and Chang7-2 were identified. The accurate evaluation of maize WLS resistance will provide essential resistance sources for subsequent breeding programs. RNA-Seq analysis revealed that systemic acquired resistance to maize WLS involves key pathways, including phenylpropanoid metabolism, as well as the synthesis of secondary metabolites such as flavonoids and glutathione. Further analysis of race-specific resistance indicated that the response of highly resistant maize varieties to WLS is primarily characterized by the accumulation of defense-related substances and enhanced activity across multiple energy metabolism pathways. In contrast, highly susceptible maize lines exhibited more pronounced enrichment in hormone signaling, the mitogen-activated protein kinase (MAPK) signaling pathway, and the metabolism of various amino acids.
Net form net blotch (NFNB), caused by
Pyrenophora teres
f.
teres
(
Ptt
), is a major constraint to barley production. However, the genetic basis of adult plant resistance (APR) and seedling resistance remains incompletely understood. This study aimed to dissect the genetic architecture of NFNB resistance in a diverse panel of 273 spring barley accessions.
APR was evaluated in two contrasting field environments in Kazakhstan, whereas seedling resistance was assessed under greenhouse conditions using two
Ptt
races. Genotyping with the 50K SNP array yielded 31,834 high-quality SNPs. Genome-wide association analyses were performed using four models – MLM, MLMM, FarmCPU, and BLINK – that accounted for population structure and kinship. Candidate genes within QTL intervals were prioritized using transcriptomic data from 16 barley tissues and co-expression network analysis.
Substantial phenotypic variation was observed, with moderate heritability for APR (
h
2
= 50.6%) and seedling resistance (
h
2
= 41.3%), together with strong genotype × environment and genotype × race interactions. In total, 275 marker–trait associations were detected for APR and 48 for seedling resistance. These associations were consolidated into 57 genome-wide significant (P < 1.57E–6) or multi-model-supported QTLs across all seven barley chromosomes, including 39 APR and 18 seedling-resistance QTLs. Forty QTLs co-localized with known resistance genes (
Rpt1
,
Rpt2
,
Rpt3
,
Rpt4
,
Rpt6
,
Rpt8
,
Rpt9
, and
SPN1
) or previously reported net blotch QTLs, whereas 17 were potentially novel. Transcriptomic integration identified 87 highly expressed genes within APR QTL regions and 42 within seedling-resistance QTLs. The potentially novel QTLs
Q_NB_1H.6
,
Q_NB_2H.3
, and
Q_NB_3H.1
harbored genes encoding proteins previously associated with pathogen resistance and stress responses. Co-expression analysis revealed stage-specific transcriptional patterns, with APR-associated genes enriched in regulatory functions and seedling-resistance genes enriched in metabolic and structural functions.
The results demonstrate that NFNB resistance is polygenic and developmentally stage-dependent, with partly distinct mechanisms underlying adult plant and seedling resistance. The identified QTLs and prioritized candidate genes provide targets for independent validation, functional characterization, and the development of molecular markers to support breeding for durable NFNB resistance in barley.
Y. Genievskaya, A. Maulenbay, A. Zatybekov et al.· Frontiers in Agronomy· 0 citations
Rice (
Oryza sativa
L.) is one of the most important staple crops worldwide, and improving grain yield remains a major objective of rice breeding programs. Yield is a complex quantitative trait influenced by multiple agronomic characteristics, including grain yield per plant (GY), seed setting rate (SSR), plant height (PH), and thousand grain weight (TGW). In this study, a natural population comprising 265 rice accessions was evaluated during two consecutive growing seasons (2022-2023) at one field location, and genome-wide association studies (GWAS) conducted using 4454137 high-quality single nucleotide polymorphisms (SNPs). Best linear unbiased prediction (BLUP) values estimated across the two year-environments were used for association analysis using a mixed linear model (MLM). A total of 102 significant SNPs were identified and consolidated into 20 quantitative trait loci (QTLs), including five associated with GY, four with SSR, ten with PH, and one with TGW. Among them, several loci were co-localized with previously reported genes associated with yield related traits, thereby supporting the reliability of the GWAS results. Candidate gene identification and haplotype analysis further revealed four prioritized genes:
LOC_Os09g28230 (GID1L2)
for GY,
LOC_Os05g09500
for SSR,
LOC_Os03g06930
for PH, and
LOC_Os02g09170
for TGW. Significant phenotypic differences among haplotypes supported the potential involvement of these genes in regulating the natural trait variation. These findings provide insights into the genetic basis of rice yield related traits and offer genetic resources for future validation and breeding. However, because the present study included only two year-environments at one field location, additional multi-environment validation is required before the broader environmental reproducibility or breeding adaptation.
Nan-Sheng Wang, M. Hassan, Kang Li et al.· Frontiers in Plant Science· 0 citations
Sudden death syndrome (SDS), caused by Fusarium virguliforme, is one of the most economically important diseases limiting soybean production worldwide. Although numerous quantitative trait loci (QTL) associated with SDS resistance have been reported, inconsistencies among mapping populations, marker systems, and experimental conditions have hindered the identification of robust resistance loci for soybean improvement. In this study, a comprehensive meta-analysis was conducted to integrate published QTL and identify stable consensus genomic regions associated with SDS resistance. After a systematic literature survey and data curation, 153 QTL derived from 14 linkage-mapping studies were analyzed using a custom R-based workflow, resulting in the identification of 23 consensus meta-QTL (MQTL) distributed across 17 chromosomes. Several MQTL, particularly those located on chromosomes 6, 8, 18, and 20, were supported by multiple independent studies and represented major genomic hotspots for SDS resistance. Physical localization and functional annotation of these MQTL identified 217 candidate genes, including genes predicted to be involved in plant defense, signal transduction, transcriptional regulation, and secondary metabolism. Gene Ontology enrichment analysis identified response to salicylic acid as the only biological process that remained significant after FDR correction, whereas Kyoto Encyclopedia of Genes and Genomes pathway analysis did not identify significantly enriched pathways. Independent support using five published genome-wide association studies further supported several MQTL, especially those on chromosomes 6, 18, and 20, thereby increasing confidence in these genomic regions. The identified MQTL and prioritized candidate genes provide potential genomic resources for future marker development, improvement applications, and functional validation aimed at improving soybean resistance to SDS.
Two novel WSS resistance loci were identified on chromosomes 2B and 5A. Characterization of WSS resistance loci will improve breeders’ ability to select to reduce yield loss due to WSS. Wheat stem sawfly (WSS) is a native grass feeding pest of winter wheat (Triticum aestivum L) which is difficult to control since most of its life cycle occurs within the stem of wheat plants. The only well-characterized genetic resistance to WSS is the solid stem locus (Sst1) on chromosome 3B, which exhibits environmental variability. It is critical to identify novel forms of genetic resistance outside of Sst1 to improve the overall resistance of wheat to WSS. In this study, genome-wide association studies (GWAS) were performed on lines in the Colorado State University wheat breeding program grown between 2014 and 2025 field seasons for three traits of interest: heading date (HD), WSS damage in the form of stem cutting (CUT), and stem solidity (SOLID). Significant marker trait associations (MTA) were identified on chromosomes 2B, 2D, 3A, 3B, 5A, and 5D for CUT and 2A, 3B, 4B, and 6A for SOLID. Significant MTA from these GWAS were used to identify beneficial allelic combinations (AC) for WSS resistance. The stem cutting ACs which had the lowest damage estimates were those in which lines possessed the resistant haplotype at every locus assessed (CUT = 2.35, error = 0.21, N = 56). Lines that had all resistant alleles in the stem solidity ACs showed the same superior estimate (SOLID = 14.7, error = 0.78, N = 22). The positive effects of the identified small-effect MTA on CUT and SOLID indicated the importance of including these loci when breeding for WSS resistance.
Mikayla Hammers, Z. Winn, Brian R. Rice et al.· Theoretical and Applied Gene...· 0 citations
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