Search Results (1,046)

Background: Maize shoot height is an important component of early vigor and plant architecture; however, its genetic basis during seedling development and its relationship with modern breeding remain insufficiently understood. This study aimed to investigate the genetic architecture of maize seedling shoot height across different breeding eras. Methods: Shoot height at 21 days after sowing was evaluated in 363 maize inbred lines representing three breeding eras in China. Genome-wide association analysis was performed to identify loci and candidate genes associated with shoot height variation, and selective sweep analysis was used to detect breeding-era differentiated genomic regions. Results: Modern breeding lines from the 2000–2010s exhibited significantly greater shoot height than lines from earlier breeding periods. Pearson’s correlation analysis revealed that 3-week shoot height showed highly significant positive correlations with plant height and ear height. Selective sweep analysis identified multiple differentiated genomic regions harboring previously reported height- and architecture-related genes, including ZmBR2, ZmLIL1, ZmNA1, ZmTE1, ZmSPL12, ZmBV1, ZmDIL1, ZmKN1 and ZmACS7. The GWAS identified 43 SNPs exceeding the GEC-derived suggestive threshold for shoot height, with the strongest and most continuous association signal located on chromosome 8. GWAS, together with LD analysis, haplotype analysis, and expression profiling, prioritized ZmGDCL (Zm00001d009163) as a promising candidate gene because of its strong association signal, local linkage disequilibrium support, broad expression profile, and significant haplotype effect on shoot height. Conclusions: Our results indicate that maize breeding has reshaped the genetic architecture of seedling shoot growth. ZmGDCL represents a promising candidate gene for future functional studies, while breeding-era differentiated regions provide useful genomic context for understanding maize architecture improvement. Full article

Objectives: To facilitate the innovation and efficient utilization of specialty maize germplasm, this study aimed to systematically evaluate a panel of 222 inbred lines. The objective was to comprehensively characterize phenotypic variation, genetic diversity, and genotype–phenotype associations to screen for representative germplasm resources. Methods: We integrated Best Linear Unbiased Prediction (BLUP) values derived from multi-environment field trials with high-density whole-genome single-nucleotide polymorphism (SNP) data. Population structure and genetic diversity were analyzed, Mantel tests were conducted to assess genotype–phenotype correspondence, and a genome-wide association study (GWAS) was performed to identify significant loci. Results: The population exhibited substantial phenotypic variation, particularly in plant height and tassel traits, with distinct morphological differentiations among specialty types. Genetic diversity analyses revealed varying diversity levels among subpopulations. While Mantel tests indicated a weak overall genotype–phenotype correspondence, specific traits showed significant associations with genetic distance. GWAS successfully identified significant loci associated with plant height and tassel traits. Furthermore, population structure analysis revealed distinct genetic stratification corresponding to specialty types, albeit with a certain degree of admixture. Conclusions: By integrating multi-dimensional phenotypic and genomic profiles, a panel of highly diverse and representative candidate germplasm was identified. These findings provide a crucial theoretical basis for specialty maize breeding and the optimized utilization of germplasm resources. Full article

Background: Internode length (IL), a key component of plant height (PH), plays an important role in achieving the optimal architecture in wheat. However, the genetic mechanisms underlying internode elongation are not well understood. Methods: In this study, a recombinant inbred line (RIL) population derived from a cross between Bainong 4199 (BN4199) and Zhengyinmai 2 (ZYM2) was evaluated for PH and five ILs across two field locations over two years and genotyped using a 120 K liquid-phase chip. Results: A total of 141 quantitative trait loci (QTL) associated with PH and the five ILs were mapped onto 20 chromosomes, except for chromosome 5D. Among these, 37 stable QTL were identified on chromosomes 1B, 2B, 2D, 4B, 5A, 7A, 7B and 7D, accounting for 3.86–25.97% of the phenotypic variation. Meanwhile, 23 co-localized QTL associated with at least two traits were detected, with QTL cluster regions on chromosomes 2D, 4B, 5A, 7A, and 7B. Moreover, the total additive effects of the QTL combinations increased with the number of QTL, which indicates the effectiveness of pyramid breeding. Additionally, based on gene function annotation, the cloning and characterization of rice orthologs, and analysis via the QTG miner module of the wheat integrative gene regulatory network (wGRN) platform, 63 candidate genes (e.g., Rht1, Rht8, TB1 and ZnF-B) were prioritized within the stable QTL intervals, and their tissue expression patterns were analyzed. Conclusions: Collectively, these findings not only deepen our understanding of the genetic basis of PH and ILs in wheat but also lay a foundation for the further validation and functional characterization of candidate genes, enabling the optimization of plant architecture through marker-assisted selection (MAS) to ultimately improve agronomic performance and yield potential. Full article

Genetic diversity within maize inbred populations is essential for sustaining genetic gain in breeding programmes. This study evaluated 280 maize inbred lines with two checks using an augmented block design (22 × 14). At harvest, 271 lines and two checks were analysed, with nine entries excluded due to poor survival. Using both descriptive (24) and quantitative (19) traits, significant variations were observed across many traits. Descriptive traits varied among the genotypes, as revealed by graphical analysis and correlation heatmaps. The likelihood ratio test (LRT) for lines showed significant differences for several quantitative traits with moderate–high heritability, while anthesis–silking interval, tassel length, ear position, ear aspect, bad husk cover, number of plants, and number of ears per plant exhibited low heritability. High genetic advance as a percentage of the mean was observed for grain yield, plant height, grain texture, number of plants, number of kernels, and grain weight per plant. Positive associations were observed among genotypic coefficient of variation, genetic advance, and heritability. Grain yield showed significant positive correlations with yield-related traits and morphological traits, but negative correlations with flowering traits. The first 10 principal components explained 86.17% of total variation, with flowering traits contributing most to variability in PC 1. Cluster analysis grouped genotypes into 10 clusters, with substantial genetic divergence within and between cluster groups. In conclusion, the study revealed considerable genetic diversity, supporting the selection of superior parents in breeding programmes and developing improved maize varieties to enhance productivity. Full article

Maize (Zea mays L.), a typical thermophilic crop originating from tropical regions, exhibits an inherent sensitivity to low-temperature stress. Cold stress severely restricts maize seed germination, seedling growth, the physiological metabolism, and the final grain yield, which greatly limits its geographical cultivation range and sustainable industrial development. Elucidating the molecular regulatory mechanisms underlying maize cold tolerance and excavating cold-resistant functional genes are essential for the molecular breeding of cold-tolerant maize varieties and expanding maize planting areas in high-latitude and low-temperature-prone regions. In this study, using the strongly cold-tolerant maize inbred line B144 as the experimental material, we cloned the ZmMAPKKKA gene (NCBI accession: LOC103651289) and systematically screened and verified its cold-stress-specific interacting proteins via multiple molecular biological assays. The full-length coding sequence (CDS) of ZmMAPKKKA is 1134 bp, encoding a 377-amino-acid protein with a predicted molecular weight of 40.37 kDa. The quantitative real-time PCR (qRT-PCR) results demonstrated that the ZmMAPKKKA expression was significantly upregulated by 16.56-fold in maize roots after 12 h of low-temperature treatment, indicating a tissue-specific and robust cold response in root tissues. A total of 25 interacting proteins were identified through yeast two-hybrid screening, among which three stress-responsive proteins, including a protein kinase (LOC100286253), a protein phosphatase 2C (PP2C) (LOC542176), and a NAC transcription factor (LOC118474710), were selected for subsequent verification. The Pull-Down, Co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) assays consistently confirmed that ZmMAPKKKA specifically interacts with these three proteins both in vitro and in vivo under cold stress conditions. This study is the first to construct a ZmMAPKKKA-centered protein interaction module in the maize mitogen-activated protein kinase (MAPK) cascade under cold stress, establishing a novel kinase–phosphatase–transcription factor regulatory cascade that improves the current understanding of cold signal transduction mechanisms in maize. Homologous genes of ZmMAPKKKA in gramineous crops including rice (Oryza sativa) and sorghum (Sorghum bicolor) have been proven to participate in diverse abiotic stress responses, suggesting the conserved functional roles of MAPKKK family genes across gramineous species. Collectively, our findings provide comprehensive insights into the molecular mechanism of the maize MAPK signaling pathway mediating cold stress adaptation and supply valuable functional gene resources for cold-tolerant maize germplasm innovation and molecular breeding. Full article

Plant height is a key component of sunflower (Helianthus annuus L.) plant architecture. It strongly influences lodging resistance, mechanized harvestability, and yield stability. However, the genetic basis of plant height in sunflowers remains underexplored. This study aimed to develop an F₂ population consisting of 715 individuals from a cross between the dwarf inbred line 150A and the tall inbred line PT326. Bulked segregant analysis coupled with whole-genome resequencing was employed to identify loci associated with plant height. Using three complementary analytical methods, a major quantitative trait locus, qPH15, was identified on chromosome 15. This locus was subsequently fine-mapped, using Kompetitive Allele Specific PCR (KASP) markers and recombinant screening in F₂ and F₃ populations, narrowing it to a 64.66-kb region containing three annotated genes. Among these, HanXRQr2_Chr15g0707451, which encodes an NAC transcription factor designated HaNAC7, was identified as the most promising candidate gene. Haplotype analysis of HaNAC7 across 148 sunflower accessions revealed 4 polymorphic sites defining 6 haplotypes with substantial differences in plant height. The shortest haplotypes, Hap2 and Hap3, were associated with reduced plant height and were predominantly found in Asian germplasm. These findings suggest that HaNAC7 is a strong candidate gene underlying qPH15 and provide useful molecular markers and favorable allelic resources for improving sunflower plant architecture. Full article

Nitrogen use efficiency (NUE) is a major determinant of maize (Zea mays L.) productivity and sustainability, yet the regulatory changes associated with modern breeding remain incompletely understood. Here, we used breeding-era transcriptomic data from 137 elite Chinese maize inbred lines to identify transcriptional regulators associated with maize NUE. Breeding-era expression shifts in NUE effector genes were modest but tissue-specific, pointing to pathway-level transcriptional rewiring during modern breeding. Focusing on the first leaf above the uppermost ear at silking, we identified 69 breeding-era-responsive genes, including 10 transcription factors, and prioritized ZmSPL19 through Pearson correlation analysis with curated NUE-related genes. ZmSPL19 expression declined during modern breeding and showed a nitrate-repressed expression, with lower transcript abundance under nitrogen-sufficient conditions and rapid downregulation upon nitrate resupply. Loss of ZmSPL19 function promoted primary root elongation, biomass accumulation, leaf nitrogen content, soil–plant analysis development (SPAD), photosynthetic rate, kernel number, and grain yield under nitrogen-sufficient conditions. These results identify ZmSPL19 as a breeding-associated negative regulator of growth and yield formation under nitrogen-sufficient conditions and support the value of a breeding-informed strategy for discovering regulators with potential relevance to maize NUE improvement. Full article

Maize is one of the most widely cultivated crops worldwide and is extensively used for animal feed and industrial applications. Plant height (PH) and ear height (EH) are critical determinants of lodging resistance and tolerance to high planting density, and coordinated regulation of these traits is essential for yield improvement. In this study, 479 maize inbred lines from Northeast and North China were genotyped using 7861 single-nucleotide polymorphism (SNP) markers to perform a genome-wide association study (GWAS). After controlling for population structure and relatedness, the mixed linear model (MLM) identified 20 loci significantly associated with PH on chromosomes 2, 4, 5, 6, 7, and 8, and 8 loci associated with EH on chromosomes 2, 3, 4, and 7. A total of 23 candidate genes were identified, including PLATZ8, pectin methylesterase 36, and leucine-rich repeat extensin 14. Gene Ontology (GO) enrichment analysis revealed significant enrichment in biological and molecular functions such as DNA binding, pectinesterase activity, zinc ion binding, ATP binding, and uniporter activity. Bioinformatic characterization of the two most likely candidate genes, Zm00001d002726 and Zm00001d015394, showed that both possess a typical compact four-exon structure. Functional prediction indicated that Zm00001d002726 encodes a pectinesterase/pectinase, potentially regulating cell elongation through pectin degradation and remodeling of the cell wall. Pectinesterase activity may influence PH and EH by mediating pectin demethylation within the cell wall. In contrast, Zm00001d015394 encodes a PLATZ family transcription factor that may regulate downstream gene expression through DNA-binding activity. These findings provide insight into the genetic architecture and potential molecular mechanisms underlying PH and EH in maize and offer a foundation for future breeding efforts. Full article

Soil salinization severely restricts rice growth and global grain production, posing a serious threat to food security. Dongxiang wild rice serves as an important genetic resource for improving salt tolerance in rice. In this study, a backcross inbred line (BIL) population derived from Dongxiang wild rice DY80 and an indica restorer line R974 were used to detect QTLs for salt tolerance at the germination and seedling stages. Four QTLs related to germination-stage salt tolerance and three QTLs for seedling-stage salt tolerance were identified, among which qSTS5 on chromosome 5 showed the largest effect with a LOD score of 8.0 and a phenotypic contribution rate of 14.8%. An F_2:3 population was further constructed to validate qSTS5, which increased its LOD value to 10.4 and phenotypic variation explanation rate to 18.5%, and the locus was finally delimited to a 2.3 Mb interval. Transcriptome analysis identified eight differentially expressed genes (DEGs) within the qSTS5 region under salt stress. Sequence comparison between the parents revealed that three DEGs had no coding-region variations, while the other five showed nucleotide polymorphisms leading to amino acid changes. Among them, Os05g0349800 encodes a LEA protein, a typical stress-responsive gene, and harbors a frameshift mutation in DY80. Combined with its induced expression pattern under salt stress, this gene was considered the most promising candidate for qSTS5. This study not only provides a stable major QTL for rice breeding for salt tolerance but also lays a foundation for dissecting the molecular mechanism of salt tolerance in Dongxiang wild rice. Full article

Background: During maize anthesis, heat stress severely limits productivity—particularly under humid conditions where high humidity suppresses transpirational cooling, forcing tissues to endure direct thermal load. Methods: Using field enclosures to impose enclosure-imposed humid heat shock (EHS), we screened 135 maize inbred lines for flowering-stage yield resilience, using grain weight per ear at maturity under EHS relative to the corresponding control (CK) condition as the primary selection criterion. Based on this screen, we selected two tolerant (R025, R100) and two sensitive (R133, R135) genotypes for data-independent acquisition mass spectrometry (DIA-MS) profiling of the tassel-subtending leaf. Results: At baseline, the selected tolerant lines exhibited a constitutively distinct proteomic state, including lower abundance of light-harvesting complex components and higher abundance or detection frequency of several regulatory proteins, including SRK2E/OST1 and HSF-B2a. Under sustained EHS, the selected sensitive lines showed extensive proteomic disruption, including reduced abundance of photosynthesis-related proteins and oxidative phosphorylation, together with increased abundance of proteins associated with endoplasmic reticulum stress responses and protein turnover. In contrast, the selected tolerant lines displayed a more constrained acclimation response, characterized by relative maintenance of photosynthesis-related proteins together with selective increases in chaperone systems (HSP90/sHSPs) and benzoxazinoid biosynthesis-related proteins. Several proteins showed switch-like detection patterns between the selected tolerant and sensitive lines, including TMEM97-like and a peptidyl-prolyl isomerase, indicating potentially distinct regulatory states. Conclusions: These findings suggest that tolerant performance under enclosure-imposed heat stress is associated with a pre-conditioned proteomic state and enhanced protein homeostasis (proteostasis) buffering capacity that may help preserve photosynthetic function during flowering-stage stress. The identified proteins should be regarded as candidate markers requiring further functional validation before any application in breeding programs aimed at improving adaptation to increasingly frequent heat-stress events. Full article

Plant architecture is a critical agronomic trait in watermelon (Citrullus lanatus), with vine length directly influencing planting density, light interception, and field management efficiency. Short-vine forms have become important agronomic targets in breeding due to their advantages of high-density planting, efficient light utilization, and simplified field management. In this study, a dwarf mutant, designated PKH207, was identified from an ethyl methanesulfonate (EMS)-mutagenized population of the watermelon inbred line G42. The mutant exhibited significantly reduced plant height and shortened internodes due to decreased cell expansion in stem tissues. Genetic analysis indicated that the dwarf phenotype in PKH207 is controlled by a single recessive gene, which was named Cldw2 (Citrullus lanatus dwarf mutant 2). Using a population of 558 F₂ plants, bulked segregant analysis sequencing (BSA-seq) and linkage mapping delimited the causal locus to a 540.6 kb region on chromosome 10. Within this interval, a single-nucleotide polymorphism (SNP) mutation was identified in the gene ClG42_10g0100600, encoding an α-tubulin, and this gene was determined to be the candidate gene for the dwarf phenotype. Transcriptome analysis revealed that this mutation significantly disrupts key biological processes, including cell wall biosynthesis, microtubule cytoskeleton organization, and auxin signaling pathways, contributing to the dwarfism phenotype. This study identifies a novel dwarfing allele in cucurbits and provides a direct molecular target for breeding compact watermelon cultivars suited to high-density production. Full article

Pre-harvest sprouting (PHS) in wheat is a significant global challenge influenced by climate. This study aimed to decipher the genetic underpinnings of PHS and identify resistance genes using 309 recombinant inbred lines (RILs) derived from the “Berkut” × “Worrakatta” cross. Methods: Phenotypic assessment of PHS traits was performed using the whole-spike sprouting method across various environments, complemented by quantitative trait loci (QTL) analysis employing a wheat 50 K SNP chip. Results showed high PHS rates in both parental lines across multiple environments. Progeny exhibited substantial variation in PHS rates, with coefficients of variation ranging from 0.16 to 0.19 and phenotypic variation ranging from 23.92% to 100%, suggesting pronounced transgressive segregation. Nine QTLs associated with PHS were identified on chromosomes 1AL, 1DL, 2AL, 2AS, 2BS, 3DS, 4BL, and 7BL. These loci accounted for 2.67% to 6.39% of the phenotypic variation. Notably, the enhancer alleles at four loci—1DL, 2BS, 4BL, and 7BL—originated from “Worrakatta”, and “Berkut” contributed the enhancer alleles at the remaining five loci. Two QTLs, QPHS.xjau-1AL.1 and QPHS.xjau-1AL.2, were stable across multiple environments. Specifically, QPHS.xjau-1AL.1 was present in three environments and explained 3.86% to 6.39% of the phenotypic variation, while QPHS.xjau-1AL.2 appeared in one environment under average conditions, explaining 2.67% to 4.87% of the variation. Our study also identified eight candidate genes associated with wheat PHS, including those encoding Myb transcription factors that influence flavonoid biosynthesis and grain color, as well as genes involved in stress response and gibberellin biosynthesis, which are crucial for plant growth and development. These genes represent vital targets for enhancing wheat PHS resistance. Full article

Drought stress significantly constrains crop productivity and yield stability. Sorghum (Sorghum bicolor L. Moench), a C4 cereal widely cultivated in arid and semi-arid regions, exhibits high water-use efficiency and remarkable drought tolerance. Understanding both the impacts of drought and the plant’s response mechanisms is essential for enhancing drought resilience in this crop. In this study, physiological changes and differential protein accumulation were analyzed in leaves of the sorghum inbred line BT × 623 under 10% PEG-6000-induced drought stress. The physiological adaptation to drought was characterized by improved water retention and mitigation of oxidative damage through the synergistic action of antioxidant enzymes. Using two-dimensional electrophoresis (2-DE) and MALDI-TOF-TOF mass spectrometry, 43 protein spots were successfully identified, corresponding to 38 unique proteins differentially expressed under osmotic stress. These proteins function in diverse biological processes, including protein synthesis, processing, and degradation; photosynthesis; carbohydrate and energy metabolism; transcriptional regulation; stress and defense; lipid and membrane metabolism; and amino acid metabolism. Proteomic profiling revealed that the coordinated modulation of multiple functional groups, such as those involved in photosynthesis, energy metabolism, transcriptional adjustment, ROS scavenging, and protein turnover, underpins sorghum’s osmotic stress adaptation. These findings provide key insights into the drought resistance mechanisms of sorghum at both physiological and proteomic levels. Full article

Maize has a long generation cycle and sensitivity to photoperiod, which limit breeding efficiency. An LED plant factory with suitable light conditions provides a promising approach to overcoming challenges in speed breeding. This study optimized the LED light environment to enhance growth and tassel development in the maize inbred line from the V3 to V9 stages. Six lighting treatments were tested, combining three light intensities (800, 1200, and 1600 μmol m⁻² s⁻¹) and two photoperiods (10 h d⁻¹ and 12 h d⁻¹). Treatment with a light intensity of 1600 μmol m⁻² s⁻¹ and a photoperiod of 10 h d⁻¹ resulted in the highest shoot fresh weight (396.9 g per plant), shoot dry weight (42.4 g per plant), leaf area (51.3 dm² per plant), and stomatal length (34.6 μm), as well as improved photosystem performance. Furthermore, this treatment promoted tassel development, with the tassel length at the V9 stage being 45.8% longer than that under the treatment with a light intensity of 800 μmol m⁻² s⁻¹ and a photoperiod of 10 h d⁻¹. These findings establish an optimized lighting strategy that significantly enhances the growth and tassel development of maize inbred lines from the V3 to V9 stages, providing a suitable light environment for maize speed breeding in plant factory systems. Full article

Objectives: Low-temperature stress has become a key factor severely restricting seedling growth in wheat, highlighting the growing importance of research on low-temperature tolerance in wheat. Most previous studies focused on the aboveground organs, and only a minority specifically targeted the roots. Methods: In this study, a recombinant inbred line population derived from a cross between DH118 and Jinmai 919 was used to dissect the genetic regulatory mechanism underlying root growth and development in wheat seedlings under low-temperature conditions. Results: A total of 9 QTLs associated with low-temperature tolerance coefficient were identified; among them, QCi.saw-2B and QCi.saw-5B were validated to be significantly associated with cold tolerance in a natural population including 289 wheat accessions. Moreover, 13 candidate genes from QTL intervals regulating root growth and development under low-temperature stress were further identified based on RNA sequencing. Conclusions: These results provide a foundation for further exploring the regulatory mechanism of root growth and development in wheat under low-temperature stress. Full article