Screening global wheat germplasm with a diverse collection of pathogen races expands the catalog of novel Yr loci and identifies new sources of broad-spectrum resistance against evolving Pst populations. Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against a panel of diverse 20 Pst isolates at the seedling stage and for adult-plant-stage resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 34 overlapped with the previously mapped 1150 Yr loci, confirming the robustness of our GWAS results, while 43 were likely novel. Comparison of the nine adult-plant-stage Yr loci mapped in our study with known APR genes identified only one overlap, with Yr29. Except for Yr29, APR genes Yr18 and Yr36 were detected at low frequencies, indicating that resistance in our panel may arise from less characterized or novel sources. Two wheat lines, lacking widely effective Yr5 and Yr15 alleles, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum ASR alleles. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a threefold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with diverse pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.
Integrating high-throughput phenotyping with multiple complementary GWAS models reduces method-dependent bias and enables reliable identification of novel loci and elite germplasm for durable yellow and leaf rust resistance in wheat. The causal agents of yellow and leaf rust in wheat, Puccinia striiformis f. sp. tritici and Puccinia triticina, pose a serious threat to grain yield and quality worldwide. Growing durable resistant wheat cultivars is an effective protection measure contributing to sustainable agriculture. Many of the known resistance genes, however, have been overcome due to the high genetic diversity and adaptability of pathogen populations. Therefore, the present study aimed to identify novel loci associated with yellow rust and leaf rust in a genome-wide association study using 1984 spring wheat accessions from the German Federal ex situ Genebank. Phenotypic data obtained from a detached-leaf assay were combined with 90,283 genotyping-by-sequencing genome-wide markers. Six significant peak marker-trait associations were identified for yellow rust and leaf rust, respectively. These are located on chromosomes 1D, 2B, 3B, 4A, 4B, 4D, 5A, 6B, and 7D. Six candidate genes were identified close to the identified loci. These findings may be valuable for identifying and deploying genetic resources to broaden the genetic basis of resistance and safeguard durability of resistance against yellow and leaf rust.
Tomato fruit weight is primarily controlled by stable genetic effects and domestication-/improvement-associated loci, including prominent chromosome 5 signals, and integrating SNP, INDEL, and SV diversity improves candidate-locus discovery, biological interpretation, and genomic prediction across environments. Tomato fruit weight (fw) is a major breeding target shaped by domestication, crop improvement, and environmental variation. We investigated the genetic architecture and genomic predictability of fw in the Varitome population representing the tomato domestication continuum, including Solanum pimpinellifolium (SP), S. lycopersicum var. cerasiforme (SLC), and cultivated S. lycopersicum (SLL). Genome-wide SNPs, insertions and deletions (INDELs), and structural variants (SVs) were analyzed individually and in combination to assess their contributions to association mapping, candidate locus discovery, and genomic prediction. Population structure based on all three variant classes clearly separated the domestication groups. Genome-wide association analyses identified 15 SNP, 10 INDEL, and 10 SV loci significantly associated with fw across environments. Several associations co-localized with known fw genes, including fw2.2/CNR, fw3.2/KLUH, fw11.3/CSR, lc/WUSCHEL, and fas/CLAVA3 supporting the biological relevance of the detected signals. Chromosome (Chr) 5 was particularly notable, with a 390-bp deletion at chr5_45,551,023 detected across all four environments and an INDEL at chr5_55,361,233 detected across three environments, suggesting stable improvement-associated candidate loci for fw variation validation. Multiple loci exhibited clear allele-frequency shifts from SP through SLC to SLL, consistent with selection during domestication and improvement, whereas others were detected almost exclusively in cultivated germplasm, suggesting more recent breeding-associated origins. Fw displayed strong genetic control, with genotype explaining more than 92
We mapped key regions of the maize genome that influence the formation of aboveground (aerial) roots, which in some varieties have been associated with symbiosis with nitrogen-fixing bacteria. Modern agriculture relies heavily on chemically synthesized nitrogen fertilizers, which ensure high yields but also carry high economic and environmental costs. Biological nitrogen fixation (BNF) supplies high amounts of nitrogen to legumes, and several avenues of research are underway to extend it to cereal crops. In maize, aerial roots formed in Sierra Mixe landraces have been associated with BNF. However, much of the genetics underlying aerial root morphology remains unknown. Here, we evaluate aerial root morphology traits associated with BNF in three segregating populations derived from crosses between two Midwest-adapted inbred lines and three landraces. Inclusive composite interval mapping (iCIM) with flowering time as a covariate identified 37 quantitative trait loci (QTL) for three aerial root traits (nodes with roots, root size, and roots per node) which exhibit moderately high heritability (H2 = 0.65 to 0.83). The combined proportion of phenotypic variance explained by the detected QTL ranged from 23 to 51
Cold tolerance in sorghum is largely stage- and environment-specific yet partially shared genetic control allows improvement across developmental stages with mostly modest, trait-specific trade-offs. Cold tolerance is a major constraint to sorghum production in temperate environments, and its improvement is therefore a key breeding objective. However, cold tolerance varies across developmental stages and environments, and selection based on stage-specific phenotypes may overlook shared genetic components. We analysed a diversity panel of 394 sorghum genotypes evaluated across 10 environments representing three developmental stages using multi-environment mixed models, genome-wide haplotype block analysis, and in silico haplotype stacking. Substantial genotype-by-environment interaction was detected, with the strength of GEI varying markedly across traits. Genetic correlations were high within developmental stages but lower and more variable across stages, indicating that the genetic architecture of cold tolerance-relevant traits is largely stage-dependent. Haplotype block analyses identified both stage- and environment-specific regions, as well as regions shared across stages and environments. In silico stacking of favourable haplotypes for early-stage cold tolerance resulted in nonlinear predicted gains, with strong initial responses at low stacking levels followed by diminishing returns. Correlated responses in yield-related traits were generally positive, whereas flowering time was consistently delayed, indicating a potential trait-specific trade-off in cold tolerance improvement. Sorghum cold tolerance can therefore not be treated as a single uniform trait but rather as a combination of stage-specific and shared genetic components, with implications for multi-stage breeding strategies.
This eight-founder MAGIC population represents a powerful resource for dissecting complex traits in maize, assessing the utility of drought proxy traits, and optimizing low-coverage whole-genome sequencing approaches. Securing sustainable crop production requires the genetic improvement of abiotic stress tolerance. Due to the broad range of environmental factors causing abiotic stress and complex genotype-by-environment interactions, it is crucial to understand the genetic basis of crop yield under suboptimal conditions. Here, we developed a dent maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population comprising 388 doubled-haploid (DH) lines. The population was derived from eight founders with varying stress tolerance, selected from a dent diversity panel evaluated for yield performance across a wide range of European environments. The MAGIC DH lines were genotyped via whole-genome sequencing ( 5× coverage) and evaluated in seven testcross and 14 line per se trials, for grain yield, leaf senescence, leaf rolling, anthesis-silking interval, and six additional agronomic traits. Genetic dissection identified 22 grain yield QTL, explaining 45
Multi-environment QTL analysis uncovered reproducible and novel loci underlying grain color and milling-related recovery traits in foxtail millet, and Seita.5G392600 was prioritized as a putative candidate gene for kernel yellowness and a potential breeding target. Grain appearance and processing quality are major determinants of the market value and end-use performance of foxtail millet, yet the genetic basis of these traits remains incompletely understood, particularly for kernel color and milling-related recovery traits. Here, we used 256 recombinant inbred lines derived from Jingu 21 × Chuang 29 and an ultra-high-density bin map generated by whole-genome resequencing to dissect the genetic architecture of grain color and milling-related recovery traits across eight environments. Three hull color traits (L, a, b), three kernel color traits (L, a, b), and two milling-related recovery traits, percentage of grain weight per panicle (PGWP) and percentage of kernel weight (PKW), were evaluated. In total, 74 QTL occurrences were identified and integrated into 45 distinct QTLs, including 11 reproducible loci detected in at least two environments and 34 environment-specific loci. Based on physical overlap with previously reported regions, 39 QTLs were considered putatively novel, whereas six co-localized with previously reported loci. We also identified seven multi-trait QTL clusters on chromosomes 1, 2, 3, 5, and 9. Candidate gene prioritization identified 11 genes within major QTL intervals. Among them, Seita.5G392600, encoding a putative glycosyltransferase, was prioritized as a putative candidate gene for kernel yellowness based on QTL co-localization, haplotype association, and detectable expression during grain development. The rare haplotype of Seita.5G392600 associated with higher kernel yellowness may provide useful variation for kernel color improvement, although further validation is required. These findings advance our understanding of the genetic architecture of grain appearance and milling-related recovery traits in foxtail millet and provide targets for fine mapping, functional validation, and marker-assisted improvement.
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.
SlASIL2 can regulate tomato heat tolerance by suppressing the expression of SlHSP20/SlHSP90 and forming protein complexes with SlDREBA4. Tomato (Solanum lycopersicum) is an important vegetable crop with substantial economic value. High-temperature stress severely impacts tomato yield and quality, making it a major constraint on the development of the tomato industry. The DREBA4 transcription factor is thought to play a key role in the high-temperature stress response pathway; however, its regulatory mechanism remains to be fully elucidated. In this study, a combination of genetic and biochemical approaches was used to elucidate the roles of SlDREBA4 and SlASIL2 in regulating the transcription of SlHSP20 and SlHSP90. Further analysis were performed to investigate the function of the SlASIL2 gene using overexpression and silencing systems. Additionally, SlASIL2 was found to suppress the reactive oxygen species (ROS) scavenging system, thereby negatively regulating tomato heat tolerance. Moreover, SlASIL2 directly binds to the promoters of SlHSP20 and SlHSP90, repressing their expression and thereby reducing tomato heat tolerance. Importantly, the interaction between SlDREBA4 and SlASIL2 mitigated the inhibitory effect of SlASIL2 on SlHSP20 and SlHSP90, contributing to the establishment of a stable physiological state in tomatoes under high-temperature conditions. These results indicate that the transcriptional regulation of SlHSP20 and SlHSP90 by SlDREBA4 and SlASIL2, together with the modulation of the ROS scavenging system, collectively fine-tune the tomato response to short-term heat stress. Our findings further expand the understanding of the molecular regulatory network involved in plant heat stress responses.
Vertcillium wilt (VW), a soil-borne disease causing cotton yield loss and fiber quality reduction, is a major stumbling block in cotton production. It is a challenging job to detect key genes associated with major quantitative trait loci (QTL) that can be used to develop VW-resistant varieties. In this study, several genome regions associated with major QTL controlling VW resistance were fine mapped by constructing the high-density genetic map of major QTL regions using Kompetitive Allele-Specific PCR (KASP) markers. Candidate genes were subsequently identified by combining gene annotation, genome resequencing, transcriptome sequencing and qRT-PCR, and functions of several genes associated with major QTL were demonstrated based on gene VIGS silencing and overexpressing. The results showed that six QTL were identified, among which five were regarded as major QTL detected in at least two environments, and four QTL, qVW-D05-1, qVW-D05-2, qVW-D05-3 and qVW-A01-1, were fine mapped to 15.2–241.3 kb physical regions located on chromosome D05 and A01, respectively. Polymerizing of major QTL on different chromosomes showed that the more the resistant QTL were polymerized in a line, the stronger the VW resistance of the line became, and those lines polymerizing 4 resistant QTL showed much higher and more stable VW resistance in each environments, implying the potential of multi-locus QTL polymerization in improving VW resistance. Fifteen candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines were identified to be associated with VW resistance in cotton. Four candidate genes associated with qVW-D05-1 were cloned and conducted function analysis, it was showed that the sequence variation of functional genes, especially the variation resulting in amino acid differences of the domains, might be the molecular mechanisms of VW resistance in cotton.
We evaluated four existing Monte Carlo-based methods for approximating prediction error variances and reliabilities in a multiple-trait genomic prediction model. All four methods yielded consistent approximations of the exact values. Genomic prediction models, such as genomic best linear unbiased prediction (GBLUP), use genomic data to improve the accuracy of estimated genetic values. As the number of genotypes and traits increases, the exact calculation of prediction error variances (PEVs) and reliabilities becomes computationally infeasible due to the need to invert the coefficient matrix of the mixed model equations, whose dimension increases directly with the number of individuals and traits. The objective of this study was to evaluate the applicability of the Monte Carlo (MC) sampling method to approximate PEVs and reliabilities in a multiple-trait GBLUP framework relevant to hybrid breeding. The MC method avoids direct matrix inversion by repeatedly sampling genetic values from their assumed distributions to approximate PEVs. We applied the MC method using four previously published formulas to approximate PEVs and reliabilities. All formulas produced consistent estimates of PEVs and reliabilities, with convergence rates depending on the formula, the level of reliability, and the MC sample size.
Soybean is one of the major sources of high-quality protein and oil and plays a crucial role in ensuring nutritional and economic security. The rapidly increasing population, soybean supply–demand imbalance, and yield losses due to soil salinity collectively necessitate the development of salt-tolerant cultivars. Perennial wild Glycine species harbor-rich genetic diversity and constitute a reservoir of stress-tolerant genes. This study systematically characterized the COBL gene family in the salt-resilient Glycine tabacina (Labill.) Benth., a wild soybean that tolerates 500 mM NaCl with 100
A nuclear-localized G2-like transcription factor, TaGLK-A1 (TraesCS7A02G539600), was identified as a strong candidate gene for grain fructan content in wheat using GWAS, linkage mapping and transcriptome analysis. Fructans, a type of natural polysaccharides or oligosaccharides polymerized from fructose molecules, play important physiological roles in crops and confer great health benefits to humans. In this study, we detected 78 stable loci associated with fructan content across all 21 wheat chromosomes across three environments and in the BLUE, explaining 4.4–10.0
The tassel glume closure1 (tgc1) mutant was identified and mapped, and ZmKAO1, which encodes an ent-kaurenoic acid oxidase, is the key candidate gene. Tassel glume timely opening is a key trait that influences cross-pollination and hybrid breeding. However, in maize (Zea mays L.), the related genes regulating this process remain largely unexplored. Here, we identified tassel glume closure1 (tgc1), a recessive mutant that exhibits tassel glume closure, anther non-extrusion, and no pollen shedding at the adult-plant stage. Anatomical and scanning electron microscopy (SEM) observations revealed that the tgc1 mutant phenotype is caused by the hindrance of filament elongation and lodicule swelling. We mapped the tgc1 locus and determined that Zm00001eb379120, which encodes ent-kaurenoic acid oxidase1 (ZmKAO1), is the key candidate gene of tgc1. Transcriptome analysis revealed that gibberellin (GA) biosynthesis was disrupted in tgc1 tassel, and exogenous application of GA3 can fully rescue the tgc1 mutant phenotype. Based on the tgc1 mutant, we propose the novel Pseudo-Genic Male Sterility (GMS) Two-Line (PGTL) system for maize hybrid seed production. These findings enrich our understanding of ZmKAO1 function in tassel glume timely opening and provide a new germplasm resource and a promising technical approach for maize commercial hybrid seed production.
A genotypic pattern for breeding wheat with ideal plant architecture. Breeding wheat with reduced leaf angle represents a promising strategy for developing lines tolerant to high planting density, mitigating the adverse effects of shade avoidance and thus increasing yield potential. However, the molecular mechanisms underlying the reduced leaf angle phenotype remain poorly understood. In this study, a wheat mutant with a reduced leaf angle, designated lad1 and exhibiting impaired sensitivity to brassinosteroids (BRs), was isolated from an EMS-induced mutant library. Phenotypic analysis revealed that the reduced leaf angle in lad1 plants is due to a decrease in the size of lamina joint cells. Genetic mapping and cloning identified Talad1-A1, a single recessive nuclear gene located on chromosome 2A, is responsible for the variation in leaf angle. Furthermore, Rht8 and Rht-D1b have been shown to contribute significantly to leaf angle regulation. These findings deepen our understanding of the genetic and molecular mechanisms controlling leaf angle in wheat and provide a potential molecular selection strategy for the developing elite wheat varieties adapted to high-density planting.
Stem structural investment enhances grain size and yield under drought, challenging the traditional view of vegetative-reproductive trade-offs. Antagonistic pleiotropy at the SSt1 locus reveals a genetic constraint between stem diameter and solidness. Incorporating genotype-by-environment into genomic selection models improves prediction accuracy by 46.5
Plants respond to environmental stress by integrating epigenetic regulation with reactive oxygen species (ROS) signaling. This review examines the bidirectional interactions between epigenetic mechanisms and ROS homeostasis in plant stress adaptation, with a particular emphasis on drought resistance. Four epigenetic mechanisms, including histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, control the expression of ROS-related genes, while in turn, ROS also alter chromatin structure and DNA methylation patterns. We propose that these interactions take the form of dynamic regulatory networks rather than one-way pathways, where changes in DNA methyltransferases and demethylation factors via ROS create reversible epigenetic states. This bilateral regulation can establish self-strengthening circuits that are capable of providing immediate responses to recurring stress. However, there is still a significant lack of knowledge, including the inconsistent reproducibility of stress priming protocols in studies, the incomplete understanding of how global oxidative stress induces epigenetic changes at specific sites, and the limited capacity for transgenerational transmission of stress-induced modifications. We review the evidence for epigenetic memory in plant stress responses, distinguish recurring adaptive plasticity from random variation, and highlight key mechanistic research directions for developing seasonally resilient crops through targeted epigenetic strategies.
Balanced, relationship-based omission, multi-environment predictions, and pedigree-genomic matrices improve genomic predictions, highlighting breeder’s ability to influence performance through strategic training set design and model choice. Genomic prediction is increasingly applied in plant breeding, yet its robustness under sparse testing in hybrid breeding programs of winter oilseed rape (Brassica napus L.) lacks evidence. We evaluated the effects of data omission strategies, prediction schemes and models on genomic prediction accuracy and selection consistency. Seven omission scenarios were assessed for three traits with contrasting genetic architectures, using the correlation between observed and predicted phenotypes and Cohen’s κ as complementary metrics for genomic prediction accuracy and selection consistency. Both declined systematically with increased data omission, although both metrics only correlated moderately. Balanced omission across environments outperformed unbalanced strategies by stabilizing variance estimation and preserving heritability. Our relationship-informed omission strategy further improved prediction performance, yielding higher and more stable prediction accuracies. Models based on combined pedigree–genomic relationship matrices enabled the inclusion of non-genotyped parental lines and further improved prediction performance. Multi-environment predictions using GCA + SCA models were consistently superior to per-environment predictions and GCA-only models; however, responses were trait-specific. Overall, our results demonstrate that informed omission strategies and model choices substantially influence the performance of genomic prediction under data reduction. Relationship-based balanced omission represents a promising selection approach that balances prediction performance with resource efficiency.
Plant height is a key determinant of wheat plant architecture that affect lodging resistance and grain yield. The GA-responsive (GAR) dwarfing gene Rht5 was previously shown to decrease plant height without compromise of wheat seedling vigor and considered as a promising candidate gene for breeding wheat varieties in water-limited conditions. However, the mechanisms underlying Rht5-mediated dwarfism are unclear. In this study, we investigated the genetic effects of Rht5 on wheat growth and development using recombinant inbred lines (RILs) and found that Rht5 reduces plant height through inhibition of cell proliferation while it promotes cell elongation. The dual functions of Rht5 on cell growth during wheat stem elongation were associated with the alteration of the homeostasis of endogenous growth-promoting phytohormones cytokinins and gibberellins. Transcriptome analysis of Rht5 RILs and their parental lines identified TaGAD2 (glutamate decarboxylase), encoding a functional glutamate decarboxylase localized at the plasma membrane that catalyzes γ-aminobutyric acid (GABA) biosynthesis, as a potential downstream regulator of Rht5-mediated dwarfism. Functional assays demonstrated that overexpression of TaGAD2 could reduce plant height while TaGAD2 knockdown increased plant height and improved lodging resistance, indicating a negative role of TaGAD2 in controlling wheat plant height. We also conducted haplotype analysis of TaGAD2 in a natural wheat population and identified TaGAD2H1 as a potential favorable allele for wheat dwarfing breeding without compromising grain number. Our study provides new insights into the molecular mechanism of the Rht5-mediated plant height regulatory pathway and valuable gene resource for the genetic improvement of wheat plant architecture. Rht5 regulates wheat plant height and yield-related traits partly through modulation of a downstream gene TaGAD2, which controls GABA biosynthesis and influences stem elongation, lodging resistance, and photosynthetic performance.
The transition from vegetative to reproductive growth, marked by flowering, is a pivotal developmental switch in plants, whereby the age pathway serves as an important regulatory mechanism governing this process. In this study, we screened a late-flowering mutant from EMS mutagenesis in Chinese cabbage. The late-flowering phenotype was unaffected by photoperiod, vernalization and GA3 treatments, and obvious changes occurred at the transcriptional levels of age flowering pathway-related genes, which indicated that the mutant trait was mediated by the age pathway. Causal gene BrDDB1A, involved in UV-induced DNA damage recognition and repair, was identified via MutMap and KASP techniques, and its function was verified by sequencing analysis of two allelic mutants. BrDDB1A was located in the nucleus. UV-B delayed the flowering time of the WT but not that of the mutant, suggesting BrDDB1A was involved in UV-B-mediated flowering delay of Chinese cabbage.
