Identification and validation of quantitative trait loci for chlorophyll content of flag leaf in wheat under different phosphorus treatments

Identification of a novel dwarfing gene, Rht_m097, on chromosome 4BS in common wheat

Plant height is a crucial agronomic trait in wheat, regulated by multiple genes, and significantly influences plant architecture and wheat yield. In this study, a novel dwarf mutant, designated as m097, was developed and characterized through the treatment of seeds from the common wheat cultivar Jinmai47 with ethyl methanesulfonate (EMS). Microscopic analysis revealed that the dwarf phenotype was attributed to a reduction in the longitudinal cell size of the stem. Similar to the wild type, m097 exhibited sensitivity to exogenous gibberellic acid (GA). Genetic analysis indicated that the reduced plant height in m097 was regulated by a semi-dominant dwarfing gene, Rht_m097. Through bulk segregant analysis (BSA) utilizing the wheat 660K SNP array, Rht_m097 was mapped and confined to a region of approximately 2.58 Mb on chromosome arm 4BS, encompassing 16 high-confidence annotated genes. In addition, transcriptome sequencing (RNA-seq) was conducted on the first internode below the panicle of JM47 and m097 at the jointing stage, leading to the identification of two potential candidate genes exhibiting differential expression. Furthermore, the analysis of gene ontology and metabolic pathways from RNA-seq data indicated that the down-regulated differentially expressed genes (DEGs) in m097 were biologically classified as regulating actin cortical patch organization and assembly. Concurrently, it was observed that the up-regulated DEGs were significantly enriched in various phytohormone metabolic pathways, including those involved in indole-3-acetic acid (IAA) biosynthesis, jasmonic acid biosynthesis, and gibberellin signaling. Overall, this study provides a novel genetic resource for the breeding of dwarf wheat and establishes a foundation for subsequent gene cloning.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01558-0.

Genetic dissection for seedling root-related traits using multiple-methods in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Several quantitative trait loci (QTL) and structural chromosome variations (SCVs) related to seedling root traits were identified using multiple methods, which provided valuable insights to assist breeding efforts in wheat. The root system of wheat affects water and fertilizer use efficiency, stress tolerance, and agronomic traits. Using association analysis and linkage mapping, QTL associated with 11 seedling-stage root traits were identified with single nucleotide polymorphisms (SNPs) and SCVs under both hydroponic nutrient solution culture experiment (NCE) and vermiculite culture experiment (VCE). Except for maximum root length (MRL), the root traits of seedlings under NCE and VCE differed significantly. Root fresh weight (RFW) and root dry weight (RDW) were significantly correlated with most agronomic traits and grain yield. Identification of RFW and RDW by NCE might provide a reference basis for VCE. Co-localization analysis revealed that NCE and VCE simultaneously detected SNP-loci viz. QRdw.sxau-6A, QRd.sxau-1B.2, and QDw.sxau-6A (5.56-8.76% of R2). The SCV-loci Mr1B-3, Mr3A-3 and Mr3A-4 were detected in both NCE and VCE (4.74-9.07% of R2). Furthermore, QRdw.sxau-6A, QSfw.sxau-6A and QRd.sxau-4A were detected using the mixed linear model (MLM), 3 Variance-component multi-locus random-SNP-effect Mixed Linear Mode (3VmrMLM) and rrBLUP. In the association panel, SNPs and SCVs co-localized to 14 MTAs, of which Mr5A-6 and QRd.sxau-5A were significantly associated with root diameter (RD). The association panel and doubled haploid (DH) population co-located 10 QTL, of which QDw.sxau-1D was stably detected. Finally, QDw.sxau-6A and Mg6A-9 overlapped in same genomic location containing candidate genes TraesCS6A02G372300, TraesCS6A02G382900 and TraesCS6A02G365100. The present study contributes novel insights into the genetics of root architecture in wheat.

Mapping of a Quantitative Trait Locus for Stay-Green Trait in Common Wheat

The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross between CH7034 and non-SG SY95-71 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2159 SNP markers was constructed. Then, the chlorophyll content of flag leaf from each RIL was estimated for mapping, and one QTL for SG on chromosome 7D was identified, temporarily named QSg.sxau-7D, with the maximum phenotypic variance explained of 8.81~11.46%. A PCR-based diagnostic marker 7D-16 for QSg.sxau-7D was developed, and the CH7034 allele of 7D-16 corresponded to the higher flag leaf chlorophyll content, while the 7D-16 SY95-71 allele corresponded to the lower value, which confirmed the genetic effect on SG of QSg.sxau-7D. QSg.sxau-7D located in the 526.4~556.2 Mbp interval is different from all the known SG loci on chromosome 7D, and 69 high-confidence annotated genes within the interval expressed throughout the entire period of flag leaf senescence. Moreover, results of an association analysis based on the diagnostic marker showed that there is a positive correlation between QSg.sxau-7D and thousand-grain weight. Our results revealed a novel QTL QSg.sxau-7D whose CH7034 allele had a strong effect on SG, which can be applied in further wheat molecular breeding.

Genetic Foundation of Leaf Senescence: Insights from Natural and Cultivated Plant Diversity

Leaf senescence, the final stage of leaf development, is crucial for plant fitness as it enhances nutrient reutilization, supporting reproductive success and overall plant adaptation. Understanding its molecular and genetic regulation is essential to improve crop resilience and productivity, particularly in the face of global climate change. This review explores the significant contributions of natural genetic diversity to our understanding of leaf senescence, focusing on insights from model plants and major crops. We discuss the physiological and adaptive significance of senescence in plant development, environmental adaptation, and agricultural productivity. The review emphasizes the importance of natural genetic variation, including studies on natural accessions, landraces, cultivars, and artificial recombinant lines to unravel the genetic basis of senescence. Various approaches, from quantitative trait loci mapping to genome-wide association analysis and in planta functional analysis, have advanced our knowledge of senescence regulation. Current studies focusing on key regulatory genes and pathways underlying natural senescence, identified from natural or recombinant accession and cultivar populations, are highlighted. We also address the adaptive implications of abiotic and biotic stress factors triggering senescence and the genetic mechanisms underlying these responses. Finally, we discuss the challenges in translating these genetic insights into crop improvement. We propose future research directions, such as expanding studies on under-researched crops, investigating multiple stress combinations, and utilizing advanced technologies, including multiomics and gene editing, to harness natural genetic diversity for crop resilience.

Effect of High Nighttime Temperatures on Growth, Yield, and Quality of Two Wheat Cultivars During the Whole Growth Period

It is a consensus that Earth's climate has been warming. The impact of global warming is asymmetric, that is, there is more substantial warming in the daily minimum surface air temperature and lower warming in the maximum surface air temperature. Previous studies have reported diurnal temperature differences greatly affecting winter wheat yield. However, only a few studies have investigated the impact of global warming on the growth and yield of winter wheat, yet the influence of night warming on quality has not been deeply evaluated. In this study, two wheat cultivars were used as materials: Jimai 44 (JM44) with strong gluten and Jimai 22 (JM22) with medium gluten, to explore the effects of high nighttime temperatures (HNTs) on the growth, yield, and quality of wheat. The results show that HNTs significantly shortened seedling emergence and anthesis periods in both cultivars compared with ambient temperatures (ATs). In addition, HNTs increased the respiration rate at anthesis and grain-filling stages, impeding wheat pollination and grain maturity. HNTs also accelerated leaf senescence and increased the number of sterile spikelets and plant height, but decreased the effective tiller number, the number of spikes per unit area, and grains per spike. As a result, the grain yield of JM22 and JM44 was decreased by 24.6% and 21.2%, respectively. Moreover, HNTs negatively influenced the flour quality of the two wheat cultivars. The current findings provide new insights into the effects of HNTs on the growth, development, yield, and quality of different wheat genotypes during the whole growth period.

Chlorophyll Fluorescence in Wheat Breeding for Heat and Drought Tolerance

The constantly growing need to increase the production of agricultural products in changing climatic conditions makes it necessary to accelerate the development of new cultivars that meet the modern demands of agronomists. Currently, the breeding process includes the stages of genotyping and phenotyping to optimize the selection of promising genotypes. One of the most popular phenotypic methods is the pulse-amplitude modulated (PAM) fluorometry, due to its non-invasiveness and high information content. In this review, we focused on the opportunities of using chlorophyll fluorescence (ChlF) parameters recorded using PAM fluorometry to assess the state of plants in drought and heat stress conditions and predict the economically significant traits of wheat, as one of the most important agricultural crops, and also analyzed the relationship between the ChlF parameters and genetic markers.

Quantitative Trait Loci Mapping of Heading Date in Wheat under Phosphorus Stress Conditions

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments.

Genome-wide association studies dissect low-phosphorus stress response genes underling field and seedling traits in maize

Phosphorus (P) is an essential element for plant growth, and its deficiency can cause decreased crop yield. This study systematically evaluated the low-phosphate (Pi) response traits in a large population at maturity and seedling stages, and explored candidate genes and their interrelationships with specific traits. The results revealed a greater sensitivity of seedling maize to low-Pi stress compared to that at maturity stage. The phenotypic response patterns to low-Pi stress at different stages were independent. Chlorophyll content was found to be a potential indicator for screening low-Pi-tolerant materials in the field. A total of 2900 and 1446 significantly associated genes at the maturity and seedling stages were identified, respectively. Among these genes, 972 were uniquely associated with maturity traits, while 330 were specifically detected at the seedling stage under low-Pi stress. Moreover, 768 and 733 genes were specifically associated with index values (low-Pi trait/normal-Pi trait) at maturity and seedling stage, respectively. Genetic network diagrams showed that the low-Pi response gene Zm00001d022226 was specifically associated with multiple primary P-related traits under low-Pi conditions. A total of 963 out of 2966 genes specifically associated with traits under low-Pi conditions or index values were found to be induced by low-Pi stress. Notably, ZmSPX4.1 and ZmSPX2 were sharply up-regulated in response to low-Pi stress across different lines or tissues. These findings advance our understanding of maize's response to low-Pi stress at different developmental stages, shedding light on the genes and pathways implicated in this response.

Combining Genetic and Phenotypic Analyses for Detecting Bread Wheat Genotypes of Drought Tolerance through Multivariate Analysis Techniques

Successfully promoting drought tolerance in wheat genotypes will require several procedures, such as field experimentations, measuring relevant traits, using analysis tools of high precision and efficiency, and taking a complementary approach that combines analyses of phenotyping and genotyping at once. The aim of this study is to assess the genetic diversity of 60 genotypes using SSR (simple sequence repeat) markers collected from several regions of the world and select 13 of them as more genetically diverse to be re-evaluated under field conditions to study drought stress by estimating 30 agro-physio-biochemical traits. Genetic parameters and multivariate analysis were used to compare genotype traits and identify which traits are increasingly efficient at detecting wheat genotypes of drought tolerance. Hierarchical cluster (HC) analysis of SSR markers divided the genotypes into five main categories of drought tolerance: four high tolerant (HT), eight tolerant (T), nine moderate tolerant (MT), six sensitive (S), and 33 high sensitive (HS). Six traits exhibit a combination of high heritability (>60%) and genetic gain (>20%). Analyses of principal components and stepwise multiple linear regression together identified nine traits (grain yield, flag leaf area, stomatal conductance, plant height, relative turgidity, glycine betaine, polyphenol oxidase, chlorophyll content, and grain-filling duration) as a screening tool that effectively detects the variation among the 13 genotypes used. HC analysis of the nine traits divided genotypes into three main categories: T, MT, and S, representing three, five, and five genotypes, respectively, and were completely identical in linear discriminant analysis. But in the case of SSR markers, they were classified into three main categories: T, MT, and S, representing five, three, and five genotypes, respectively, which are both significantly correlated as per the Mantel test. The SSR markers were associated with nine traits, which are considered an assistance tool in the selection process for drought tolerance. So, this study is useful and has successfully detected several agro-physio-biochemical traits, associated SSR markers, and some drought-tolerant genotypes, coupled with our knowledge of the phenotypic and genotypic basis of wheat genotypes.

Wheat Grains as a Sustainable Source of Protein for Health

Protein deficiency is recognized among the major global health issues with an underestimation of its importance. Genetic biofortification is a cost-effective and sustainable strategy to overcome global protein malnutrition. This study was designed to focus on protein-dense grains of wheat (Triticum aestivum L.) and identify the genes governing grain protein content (GPC) that improve end-use quality and in turn human health. Genome-wide association was applied using the 90k iSELECT Infinium and 35k Affymetrix arrays with GPC quantified by using a proteomic-based technique in 369 wheat genotypes over three field-year trials. The results showed significant natural variation among bread wheat genotypes that led to detecting 54 significant quantitative trait nucleotides (QTNs) surpassing the false discovery rate (FDR) threshold. These QTNs showed contrasting effects on GPC ranging from -0.50 to +0.54% that can be used for protein content improvement. Further bioinformatics analyses reported that these QTNs are genomically linked with 35 candidate genes showing high expression during grain development. The putative candidate genes have functions in the binding, remobilization, or transport of protein. For instance, the promising QTN AX-94727470 on chromosome 6B increases GPC by +0.47% and is physically located inside the gene TraesCS6B02G384500 annotated as Trehalose 6-phosphate phosphatase (T6P), which can be employed to improve grain protein quality. Our findings are valuable for the enhancement of protein content and end-use quality in one of the major daily food resources that ultimately improve human nutrition.