Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield-related traits in wheat.

Increasing crop yield depends on selecting and utilizing pleiotropic genes/alleles to improve multiple yield-related traits (YRTs) during crop breeding. However, synergistic improvement of YRTs is challenging due to the trade-offs between YRTs in breeding practices. Here, the favourable haplotypes of the TaCYP78A family are identified by analysing allelic variations in 1571 wheat accessions worldwide, demonstrating the selection and utilization of pleiotropic genes to improve yield and related traits during wheat breeding. The TaCYP78A family members, including TaCYP78A3, TaCYP78A5, TaCYP78A16, and TaCYP78A17, are organ size regulators expressed in multiple organs, and their allelic variations associated with various YRTs. However, due to the trade-offs between YRTs, knockdown or overexpression of TaCYP78A family members does not directly increase yield. Favourable haplotypes of the TaCYP78A family, namely A3/5/16/17Ap-Hap II, optimize the expression levels of TaCYP78A3/5/16/17-A across different wheat organs to overcome trade-offs and improve multiple YRTs. Different favourable haplotypes have both complementary and specific functions in improving YRTs, and their aggregation in cultivars under strong artificial selection greatly increase yield, even under various planting environments and densities. These findings provide new support and valuable genetic resources for molecular breeding of wheat and other crops in the era of Breeding 4.0.

Wheat TaSnRK2.10 phosphorylates TaERD15 and TaENO1 and confers drought tolerance when overexpressed in rice.

Wheat (Triticum aestivum) is particularly susceptible to water deficit at the jointing stage of its development. Sucrose non-fermenting 1-related protein kinase 2 (SnRK2) acts as a signaling hub in the response to drought stress, but whether SnRK2 helps plants cope with water deficit via other mechanisms is largely unknown. Here, we cloned and characterized TaSnRK2.10, which was induced by multiple abiotic stresses and phytohormones. Ectopic expression of TaSnRK2.10 in rice (Oryza sativa) conferred drought tolerance, manifested by multiple improved physiological indices, including increased water content, cell membrane stability, and survival rates, as well as decreased water loss and accumulation of H2O2 and malonaldehyde. TaSnRK2.10 interacted with and phosphorylated early responsive to dehydration 15 (TaERD15) and enolase 1 (TaENO1) in vivo and in vitro. TaERD15 phosphorylated by TaSnRK2.10 was prone to degradation by the 26S proteasome, thereby mitigating its negative effects on drought tolerance. Phosphorylation of TaENO1 by TaSnRK2.10 may account for the substantially increased levels of phosphoenolpyruvate (PEP), a key metabolite of primary and secondary metabolism, in TaSnRK2.10-overexpressing rice, thereby enhancing its viability under drought stress. Our results demonstrate that TaSnRK2.10 not only regulated stomatal aperture and the expression of drought-responsive genes, but also enhanced PEP supply and promoted the degradation of TaERD15, all of which enhanced drought tolerance.

An SNP based genotyping assay for genes associated with drought tolerance in bread wheat.

BACKGROUND: SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs. METHODS: Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9. RESULTS: Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments. CONCLUSION: These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts.

TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat.

Cultivating high-yield wheat under limited water resources is crucial for sustainable agriculture in semiarid regions. Amid water scarcity, plants activate drought response signaling, yet the delicate balance between drought tolerance and development remains unclear. Through genome-wide association studies and transcriptome profiling, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor (TF), TabHLH27-A1, as a promising quantitative trait locus candidate for both relative root dry weight and spikelet number per spike in wheat. TabHLH27-A1/B1/D1 knock-out reduced wheat drought tolerance, yield, and water use efficiency (WUE). TabHLH27-A1 exhibited rapid induction with polyethylene glycol (PEG) treatment, gradually declining over days. It activated stress response genes such as TaCBL8-B1 and TaCPI2-A1 while inhibiting root growth genes like TaSH15-B1 and TaWRKY70-B1 under short-term PEG stimulus. The distinct transcriptional regulation of TabHLH27-A1 involved diverse interacting factors such as TaABI3-D1 and TabZIP62-D1. Natural variations of TabHLH27-A1 influence its transcriptional responses to drought stress, with TabHLH27-A1Hap-II associated with stronger drought tolerance, larger root system, more spikelets, and higher WUE in wheat. Significantly, the excellent TabHLH27-A1Hap-II was selected during the breeding process in China, and introgression of TabHLH27-A1Hap-II allele improved drought tolerance and grain yield, especially under water-limited conditions. Our study highlights TabHLH27-A1's role in balancing root growth and drought tolerance, providing a genetic manipulation locus for enhancing WUE in wheat.

RING finger E3 ubiquitin ligase gene TaAIRP2-1B controls spike length in wheat.

E3 ubiquitin ligase genes play important roles in the regulation of plant development. They have been well studied in plants, but have not been sufficiently investigated in wheat. Here, we identified a highly expressed RING finger E3 ubiquitin ligase gene TaAIRP2-1B (ABA-insensitive RING protein 2) in wheat spike. Sequence polymorphism and association analysis showed that TaAIRP2-1B is significantly associated with spike length under various conditions. The genotype with haplotype Hap-1B-1 of TaAIRP2-1B has a longer spike than that of Hap-1B-2, and was positively selected in the process of wheat breeding in China. Moreover, the TaAIRP2-1B-overexpressing rice lines have longer panicles compared with wild-type plants. The expression levels of TaAIRP2-1B in Hap-1B-1 accessions were higher than in Hap-1B-2 accessions. Further study revealed that the expression of TaAIRP2-1B was negatively regulated by TaERF3 (ethylene-responsive factor 3) via binding to the Hap-1B-2 promoter, but not via binding of Hap-1B-1. Additionally, several candidate genes interacting with TaAIRP2-1B were obtained by screening the cDNA library of wheat in yeast cells. It was found that TaAIRP2-1B interacted with TaHIPP3 (heavy metal-associated isoprenylated protein 3) and promoted TaHIPP3 degradation. Our study demonstrates that TaAIRP2-1B controls spike length, and the haplotype Hap-1B-1 of TaAIRP2-1B is a favorable natural variation for spike length enhancement in wheat. This work also provides genetic resources and functional markers for wheat molecular breeding.

The wheat basic helix-loop-helix gene TabHLH123 positively modulates the formation of crown roots and is associated with plant height and 1000-grain weight under various conditions.

Crown roots are the main components of the fibrous root system in cereal crops and play critical roles in plant adaptation; however, the molecular mechanisms underlying their formation in wheat (Triticum aestivum) have not been fully elucidated. In this study, we identified a wheat basic helix-loop-helix (bHLH) protein, TabHLH123, that interacts with the essential regulator of crown root initiation, MORE ROOT in wheat (TaMOR). TabHLH123 is expressed highly in shoot bases and roots. Ectopic expression of TabHLH123 in rice resulted in more roots compared with the wild type. TabHLH123 regulates the expression of genes controlling crown-root development and auxin metabolism, responses, and transport. In addition, we analysed the nucleotide sequence polymorphisms of TabHLH123s in the wheat genome and identified a superior haplotype, TabHLH123-6B, that is associated with high root dry weight and 1000-grain weight, and short plant height. Our study reveals the role of TabHLH123 in controlling the formation of crown roots and provides beneficial insights for molecular marker-assisted breeding in wheat.

Combined linkage analysis and association mapping identifies genomic regions associated with yield-related and drought-tolerance traits in wheat (Triticum aestivum L.).

KEY MESSAGE: Combined linkage analysis and association mapping identified genomic regions associated with yield and drought tolerance, providing information to assist breeding for high yield and drought tolerance in wheat. Wheat (Triticum aestivum L.) is one of the most widely grown food crops and provides adequate amounts of protein to support human health. Drought stress is the most important abiotic stress constraining yield during the flowering and grain development periods. Precise targeting of genomic regions underlying yield- and drought tolerance-responsive traits would assist in breeding programs. In this study, two water treatments (well-watered, WW, and rain-fed water stress, WS) were applied, and five yield-related agronomic traits (plant height, PH; spike length, SL; spikelet number per spike, SNPS; kernel number per spike, KNPS; thousand kernel weight, TKW) and drought response values (DRVs) were used to characterize the drought sensitivity of each accession. Association mapping was performed on an association panel of 304 accessions, and linkage analysis was applied to a doubled haploid (DH) population of 152 lines. Eleven co-localized genomic regions associated with yield traits and DRV were identified in both populations. Many previously cloned key genes were located in these regions. In particular, a TKW-associated region on chromosome 2D was identified using both association mapping and linkage analysis and a key candidate gene, TraesCS2D02G142500, was detected based on gene annotation and differences in expression levels. Exonic SNPs were analyzed by sequencing the full length of TraesCS2D02G142500 in the association panel, and a rare haplotype, Hap-2, which reduced TKW to a lesser extent than Hap-1 under drought stress, and the Hap-2 varieties presented drought-insensitive. Altogether, this study provides fundamental insights into molecular targets for high yield and drought tolerance in wheat.

DIW1 encoding a clade I PP2C phosphatase negatively regulates drought tolerance by de-phosphorylating TaSnRK1.1 in wheat.

Drought seriously impacts wheat production (Triticum aestivum L.), while the exploitation and utilization of genes for drought tolerance are insufficient. Leaf wilting is a direct reflection of drought tolerance in plants. Clade A PP2Cs are abscisic acid (ABA) co-receptors playing vital roles in the ABA signaling pathway, regulating drought response. However, the roles of other clade PP2Cs in drought tolerance, especially in wheat, remain largely unknown. Here, we identified a gain-of-function drought-induced wilting 1 (DIW1) gene from the wheat Aikang 58 mutant library by map-based cloning, which encodes a clade I protein phosphatase 2C (TaPP2C158) with enhanced protein phosphatase activity. Phenotypic analysis of overexpression and CRISPR/Cas9 mutant lines demonstrated that DIW1/TaPP2C158 is a negative regulator responsible for drought resistance. We found that TaPP2C158 directly interacts with TaSnRK1.1 and de-phosphorylates it, thus inactivating the TaSnRK1.1-TaAREB3 pathway. TaPP2C158 protein phosphatase activity is negatively correlated with ABA signaling. Association analysis suggested that C-terminal variation of TaPP2C158 changing protein phosphatase activity is highly correlated with the canopy temperature, and seedling survival rate under drought stress. Our data suggest that the favorable allele with lower phosphatase activity of TaPP2C158 has been positively selected in Chinese breeding history. This work benefits us in understanding the molecular mechanism of wheat drought tolerance, and provides elite genetic resources and molecular markers for improving wheat drought tolerance.

Modified expression of TaCYP78A5 enhances grain weight with yield potential by accumulating auxin in wheat (Triticum aestivum L.).

Increasing grain yield has always been the primary goal of crop breeding. KLUH/CYP78A5 has been shown to affect seed size in several plant species, but the relevant molecular mechanism is still unclear and there are no reports of this gene contributing to yield. Here, we demonstrate that modified expression of TaCYP78A5 can enhance wheat grain weight and grain yield per plant by accumulating auxin. TaCYP78A5 is highly expressed in maternal tissues, including ovary and seed coat during wheat development. The constitutive overexpression of TaCYP78A5 leads to significantly increased seed size and weight but not grain yield per plant due to the strengthening of apical dominance. However, localized overexpression of TaCYP78A5 in maternal integument enhances grain weight and grain yield per plant by 4.3%-18.8% and 9.6%-14.7%, respectively, in field trials. Transcriptome and hormone metabolome analyses reveal that TaCYP78A5 participates in auxin synthesis pathway and promotes auxin accumulation and cell wall remodelling in ovary. Phenotype investigation and cytological observation show that localized overexpression of TaCYP78A5 in ovary results in delayed flowering and prolonged proliferation of maternal integument cells, which promote grain enlargement. Moreover, naturally occurring variations in the promoter of TaCYP78A5-2A contribute to thousand-grain weight (TGW) and grain yield per plant of wheat;TaCYP78A5-2A haplotype Ap-HapII with higher activity is favourable for improving grain weight and grain yield per plant and has been positively selected in wheat breeding. Then, a functional marker of TaCYP78A5 haplotype Ap-HapII is developed for marker-assisted selection in wheat grain and yield improvement.

TaMOR is essential for root initiation and improvement of root system architecture in wheat.

Optimal root system architecture is beneficial for water-fertilizer use efficiency, stress tolerance and yield improvement of crops. However, because of the complexity of root traits and difficulty in phenotyping deep roots, the study on mechanisms of root development is rarely reported in wheat (Triticum aestivum L.). In this study, we identified that the LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene TaMOR (MORE ROOT in wheat) determines wheat crown root initiation. The mor mutants exhibited less or even no crown root, dwarfism, less grain number and lodging caused by few roots. The observation of cross sections showed that crown root initiation is inhibited in the mor mutants. Molecular assays revealed that TaMOR interacts with the auxin response factor ARF5 to directly induce the expression of the auxin transporter gene PIN2 (PIN-FORMED 2) in the root base to regulate crown root initiation. In addition, a 159-bp MITE (miniature inverted-repeat transposable element) insertion causing DNA methylation and lower expression of TaMOR-B was identified in TaMOR-B promoter, which is associated with lower root dry weight and shorter plant height. The results bring new light into regulation mechanisms of crown root initiation and offer a new target for the improvement of root system architecture in wheat.

TaGSNE, a WRKY transcription factor, overcomes the trade-off between grain size and grain number in common wheat and is associated with root development.

Wheat is one of the world's major staple food crops, and breeding for improvement of grain yield is a priority under the scenarios of climate change and population growth. WRKY transcription factors are multifaceted regulators in plant growth, development, and responses to environmental stimuli. In this study, we identify the WRKY gene TaGSNE (Grain Size and Number Enhancer) in common wheat, and find that it has relatively high expression in leaves and roots, and is induced by multiple abiotic stresses. Eleven single-nucleotide polymorphisms were identified in TaGSNE, forming two haplotypes in multiple germplasm collections, named as TaGSNE-Hap-1 and TaGSNE-Hap-2. In a range of different environments, TaGSNE-Hap-2 was significantly associated with increases in thousand-grain weight (TGW; 3.0%) and spikelet number per spike (4.1%), as well as with deeper roots (10.1%) and increased root dry weight (8.3%) at the mid-grain-filling stage, and these were confirmed in backcross introgression populations. Furthermore, transgenic rice lines overexpressing TaGSNE had larger panicles, more grains, increased grain size, and increased grain yield relative to the wild-type control. Analysis of geographic and temporal distributions revealed that TaGSNE-Hap-2 is positively selected in China and Pakistan, and TaGSNE-Hap-1 in Europe. Our findings demonstrate that TaGSNE overcomes the trade-off between TGW/grain size and grain number, leading us to conclude that these elite haplotypes and their functional markers could be utilized in marker-assisted selection for breeding high-yielding varieties.

How Many Faces Does the Plant U-Box E3 Ligase Have?

Ubiquitination is a major type of post-translational modification of proteins in eukaryotes. The plant U-Box (PUB) E3 ligase is the smallest family in the E3 ligase superfamily, but plays a variety of essential roles in plant growth, development and response to diverse environmental stresses. Hence, PUBs are potential gene resources for developing climate-resilient crops. However, there is a lack of review of the latest advances to fully understand the powerful gene family. To bridge the gap and facilitate its use in future crop breeding, we comprehensively summarize the recent progress of the PUB family, including gene evolution, classification, biological functions, and multifarious regulatory mechanisms in plants.

A transposon in the vacuolar sorting receptor gene TaVSR1-B promoter region is associated with wheat root depth at booting stage.

Root depth, as an important component of root architecture, plays a significant role in growth, grain yield determination and abiotic stress tolerance in crop plants, but its genetic basis remains poorly elucidated. In this study, a panel composed of 323 wheat (Triticum aestivum L.) accessions was assessed for variation in root depth and genotyped with the Wheat 660K SNP Array. GWAS (genome-wide association study) detected significant association between a 125 bp miniature inverted-repeat transposable element (MITE) in the promoter of the TaVSR1-B gene with root depth at the booting stage. We showed that the MITE repressed TaVSR1-B expression by DNA methylation and H3K27 tri-methylation. The roles of TaVSR1-B in root growth were verified by altered expression of the gene in transgenic wheat, rice and a tavsr1 TILLING mutant. Increased TaVSR1-B expression made the root elongation zone shorter and the differentiation zone longer, leading to deeper root. This work provides novel insight into the genetic basis of variation in root depth and a promising target for genetic improvement of root architecture in wheat.

Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat.

Kernel number per spike determined by the spike or inflorescence development is one important agricultural trait for wheat yield that is critical for global food security. While a few important genes for wheat spike development were identified, the genetic regulatory mechanism underlying supernumerary spikelets (SSs) is still unclear. Here, we cloned the wheat FRIZZY PANICLE (WFZP) gene from one local wheat cultivar. WFZP is specifically expressed at the sites where the spikelet meristem and floral meristem are initiated, which differs from the expression patterns of its homologs FZP/BD1 in rice and maize, indicative of its functional divergence during species differentiation. Moreover, WFZP directly activates VERNALIZATION1 (VRN1) and wheat HOMEOBOX4 (TaHOX4) to regulate the initiation and development of spikelet. The haplotypes analysis showed that the favourable alleles of WFZP associated with spikelet number per spike (SNS) were preferentially selected during breeding. Our findings provide insights into the molecular and genetic mechanisms underlying wheat spike development and characterize the WFZP as elite resource for wheat molecular breeding with enhanced crop yield.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance.

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Genetic insights into natural variation underlying salt tolerance in wheat.

Developing salt-tolerant crop varieties is one of the important approaches to cope with increasing soil salinization worldwide. In this study, a diversity panel of 323 wheat accessions and 150 doubled haploid lines were phenotyped for salt-responsive morphological and physiological traits across two growth stages. The comprehensive salt tolerance of each wheat accession was evaluated based on principal component analysis. A total of 269 associated loci for salt-responsive traits and/or salt tolerance indices were identified by genome-wide association studies using 395 675 single nucleotide polymorphisms, among which 22 overlapping loci were simultaneously identified by biparental quantitative trait loci mapping. Two novel candidate genes ROOT NUMBER 1 (TaRN1) and ROOT NUMBER 2 (TaRN2) involved in root responses to salt stress fell within overlapping loci, showing different expression patterns and a frameshift mutation (in TaRN2) in contrasting salt-tolerant wheat genotypes. Moreover, the decline in salt tolerance of Chinese wheat varieties was observed from genetic and phenotypic data. We demonstrate that a haplotype controlling root responses to salt stress has been diminished by strong selection for grain yield, which highlights that linkage drag constrains the salt tolerance of Chinese wheat. This study will facilitate salt-tolerant wheat breeding in terms of elite germplasm, favorable alleles and selection strategies.

The wheat SHORT ROOT LENGTH 1 gene TaSRL1 controls root length in an auxin-dependent pathway.

The root is the main organ for water and nutrient uptake and sensing environmental stimuli in the soil. The optimization of root system architecture contributes to stress tolerance and yield improvement. ERF (ETHYLENE RESPONSIVE FACTOR) is one of the plant-specific transcription factor families associated with various developmental processes and stress tolerance. We cloned a novel ERF transcription factor gene TaSRL1 (SHORT ROOT LENGTH 1) from wheat (Triticum aestivum) which is mainly expressed in root. Ectopic expression of TaSRL1 in rice resulted in short root length and plant height. TaSRL1 regulated expression of genes related to auxin synthesis, transport, and signaling. Further studies revealed that TaSRL1 induced expression of the auxin transport gene TaPIN2 by directly binding to its promoter, while the interaction of TaSRL1 and TaTIFY9 repressed TaPIN2 expression. Sequence polymorphisms and association analysis showed that TaSRL1-4A was associated with root depth and angle, plant height, and 1000-grain weight of wheat. The haplotype Hap-4A-2 with shallow roots, short plant height, and high 1000-grain weight has been positively selected in the Chinese wheat breeding process. We demonstrated that TaSRL1 functions as a direct regulator of TaPIN2 in the auxin-dependent pathway, and integrates auxin and jasmonate signaling by interacting with TaTIFY9 to repress root growth. Furthermore, the molecular marker of TaSRL1-4A is valuable for the improvement of the root system, plant architecture, and yield in the wheat breeding process.

Exploitation of Drought Tolerance-Related Genes for Crop Improvement.

Drought has become a major threat to food security, because it affects crop growth and development. Drought tolerance is an important quantitative trait, which is regulated by hundreds of genes in crop plants. In recent decades, scientists have made considerable progress to uncover the genetic and molecular mechanisms of drought tolerance, especially in model plants. This review summarizes the evaluation criteria for drought tolerance, methods for gene mining, characterization of genes related to drought tolerance, and explores the approaches to enhance crop drought tolerance. Collectively, this review illustrates the application prospect of these genes in improving the drought tolerance breeding of crop plants.

The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli.

Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.

Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population.

BACKGROUND: Human demand for wheat will continue to increase together with the continuous global population growth. Agronomic traits in wheat are susceptible to environmental conditions. Therefore, in breeding practice, priority is given to QTLs of agronomic traits that can be stably detected across multiple environments and over many years. RESULTS: In this study, QTL analysis was conducted for eight agronomic traits using an introgression line population across eight environments (drought stressed and well-watered) for 5 years. In total, 44 additive QTLs for the above agronomic traits were detected on 15 chromosomes. Among these, qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A were detected across seven, six, five, five and four environments, respectively. The means in the phenotypic variation explained by these five QTLs were 12.26, 9.51, 7.77, 7.23, and 8.49%, respectively. CONCLUSIONS: We identified five stable QTLs, which includes qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A. They play a critical role in wheat agronomic traits. One of the dwarf genes Rht14, Rht16, Rht18 and Rht25 on chromosome 6A might be the candidate gene for qPH-6A. The qHD-1A and qHD-2D were novel stable QTLs for heading date and they differed from known vernalization genes, photoperiod genes and earliness per se genes.