Maize is a critical crop for food, feed, and bioenergy worldwide. This study characterized the genetic diversity and population structure of 212 important inbred lines collected from the Southeast China breeding program using the Maize6H-60K single nucleotide polymorphism (SNP) array. To investigate the genetic architecture of plant height (PH) and ear height (EH), genome-wide association analysis (GWAS) was performed on this population in 2021 and 2022. Cluster analysis and population genetic structure analysis grouped the 212 maize inbred lines into 10 distinct categories. GWAS identified significant associations for PH, EH, and the EH/PH ratio. A total of 40 significant SNP (p < 8.55359 × 10⁻⁷) were detected, including nine associated with PH, with phenotypic variation explained (PVE) ranging from 3.42% to 25.92%. Additionally, 16 SNP were linked to EH, with PVE ranging from 2.49% to 38.49%, and 15 SNP were associated with the EH/PH ratio, showing PVE between 3.43% and 16.83%. Five stable SNP, identified across two or more environments, were further analyzed. Three of these SNP loci are reported for the first time in this study: two loci associated with the PH, AX-108020973, and AX-108022922, as well as one new locus, AX-108096437, which was significantly associated with the EH/PH ratio. Additionally, two other significant SNP (AX-247241325 and AX-108097244) were located within a 2 Mb range of previously identified QTL and/or related SNP. Within the 200 kb confidence intervals of these five stable SNP loci, 76 functionally annotated genes were identified. Further functional analysis indicated that 14 of these genes may play a role in regulating plant morphology, which is primarily involved in hormone synthesis, microtubule development, root growth, and cell division regulation. For instance, the homologous genes GRMZM2G375249 and GRMZM2G076029 in maize correspond to OsPEX1 in rice, a protein similar to extension proteins that are implicated in lignin biosynthesis, plant growth promotion, and the negative regulation of root growth through gibberellin-mediated pathways. The candidate gene corresponding to AX-108097244 is GRMZM2G464754; previous studies have reported its involvement in regulating EH in maize. These findings enhance the understanding of QTL associated with maize plant-type traits and provide a foundation for cloning PH, EH-related genes. Therefore, the results also support the development of functional markers for target genes and the breeding of improved maize varieties.

Research on the flowering habit of rapeseed is important for the selection of varieties adapted to specific ecological environments. Here, quantitative trait loci (QTL) for the days-to-flowering trait were identified using a doubled haploid population of 178 lines derived from a cross between the winter type SGDH284 and the semi-winter type 158A. A linkage map encompassing 3268.01 cM was constructed using 2777 bin markers obtained from next-generation sequencing. The preliminary mapping results revealed 56 QTLs for the days to flowering in the six replicates in the three environments. Twelve consensus QTLs were identified by a QTL meta-analysis, two of which (cqDTF-C02 and cqDTF-C06) were designated as major QTLs. Based on the micro-collinearity of the target regions between B. napus and Arabidopsis, four genes possibly related to flowering time were identified in the cqDTF-C02 interval, and only one gene possibly related to flowering time was identified in the cqDTF-C06 interval. A tightly linked insertion–deletion marker for the cqFT-C02 locus was developed. These findings will aid the breeding of early maturing B. napus varieties.

Seed reserve mobilization is a crucial physiological process during seed germination. Enhancing the reserve mobilization in sweet corn is vital for seed germination and seedling growth. In this study, a genome-wide association analysis (GWAS) was conducted to predict candidate genes for regulating the weight of mobilized reserved seeds (WMRS) and kernel weight (KW) in sweet corn. GWAS was performed using the BLINK model with the maize 56K SNP chip. The results indicated that there was a positive correlation between the WMRS and KW, with coefficients of variation of 68.18% and 44.63%. Association analysis identified thirteen SNPs associated with two traits, and linkage disequilibrium analysis revealed that eight of these SNPs were in strong linkage. A total of 298 candidate genes were identified within the confidence interval, of which 79 were annotated. About 20 candidate genes were identified through the comparison of homologous genes in Arabidopsis. These genes were enriched in regulating ribosome biogenesis, signal transduction, hormone synthesis, and RNA degradation processes. This study provides important insights into the genetic mechanisms governing germination traits in sweet corn, aiding further research into the localization and cloning of genes involved in the mobilization of reserve materials.

The valine glutamine (VQ) proteins are transcription cofactors involved in various aspects of plant biology, including growth, development, and stress resistance, making them an attractive target for genetic engineering aimed at enhancing plant resilience and productivity. However, comprehensive reports or systematic studies on VQ cofactors in Salix suchowensis remain lacking. In this study, we analyzed SsVQ genes using bioinformatics methods based on the Salix suchowensis genome database. Expression profiles were further investigated through qRT-PCR under six treatments: PEG, NaCl, 40 °C, ABA, SA, and MeJA. A total of 39 SsVQ genes were identified, with phylogenetic analysis classifying them into seven groups. Collinearity analysis suggested that SsVQ gene amplification primarily resulted from whole genome duplication (WGD) or segmental duplication events. Ka/Ks ratios indicated that willow VQ genes have undergone predominantly purifying selection. Gene structure analysis revealed that SsVQ genes are intronless. Multiple sequence alignment showed that SsVQ19 shares similarity with PtVQ27, containing a hydrophilic threonine (T) residue preceding the VQ amino acid residues. Furthermore, genes within each group exhibited conserved structures and VQ motifs. Promoter and expression analyses suggested the potential roles of SsVQ genes in regulating willow responses to environmental stresses and hormonal signals. Most SsVQ genes displayed differential expression at specific time points, with six members (SsVQ2, SsVQ9, SsVQ12, SsVQ23, SsVQ32, and SsVQ34) showing sustained high-amplitude expression profiles across treatments. Notably, SsVQ34 demonstrated pronounced transcriptional induction under PEG stress, with expression levels upregulated by 62.29-fold (1 h), 49.21-fold (6 h), 99.9-fold (12 h), and 201.50-fold (24 h). Certain SsVQ genes showed co-expression under abiotic/hormonal stresses, implying synergistic functions. Paralogous gene pairs exhibited stronger co-expression than non-paralogous pairs. This study provides novel insights into the structural and functional characteristics of the VQ gene family in Salix suchowensis, establishing a foundation for future research on the stress-resistance mechanisms of willow VQ genes.

Salinization stress poses a major environmental factor that adversely affects maize (Zea mays L.) growth and development. Thus, identifying and utilizing alkaline tolerance-related genes in maize is crucial for enhancing resistance to alkaline stress. In this study, a genome-wide association study (GWAS) was conducted to analyze alkali tolerance in seedlings, focusing on biomass-related traits at the seedling stage across a panel of 212 maize inbred lines. The analysis found nine single-nucleotide polymorphism (SNP) loci significantly associated with alkali tolerance during the seedling stage. Within the confidence intervals of these loci, 57 genes with clear functional annotations were identified, among which eight were predicted to be involved in alkali tolerance based on functional annotation and homology analysis. qRT-PCR expression validation of selected candidate genes revealed that the relative expression level of GRMZM2G028089 was similar between in L99 and M-J244-3 lines. In contrast, the expression levels of GRMZM2G071196, GRMZM2G313162 and GRMZM5G883126 were higher in the L99 line compared to M-J244-3, suggesting their potential positive regulatory roles in the response to alkaline stress. These findings provide important theoretical support for the targeted breeding of alkali-resistant maize varieties.