Search Results (1,263)

Climate change has intensified drought events, compromising popcorn production, particularly in tropical regions. This study aimed to identify popcorn inbred lines with superior water-use efficiency and responsiveness, and to examine the relationships among morpho-agronomic traits associated with expanded popcorn volume per hectare (VP). Fifty inbred lines were evaluated under well-watered (WW) and water-stressed (WS) conditions across two cropping seasons (2020 and 2021). Water deficit was imposed at pre-anthesis, with the permanent wilting point occurring during early reproductive stages in 2020 and during grain filling in 2021. Principal component analysis and efficiency/responsiveness classification were used to characterize line performance. Significant genotype × water condition × season interactions affected all traits. Water stress reduced VP by 75% in 2020 and 46% in 2021, reflecting the differing timing of stress. Line L477 showed high efficiency and responsiveness, while genotypes such as L213, L221, and L222 were inefficient and non-responsive in both years. Under WW, VP was mainly associated with hundred-grain weight, ear length, and grain number per row, whereas under WS, ear diameter and number of rows per ear were the strongest contributors, indicating that the available genetic variability is more effectively exploited through selective morpho-agronomic criteria tailored to each water scenario. Contrasting crosses between efficient and non-responsive lines (L325 and L481) and inefficient but responsive lines (L513, L625, and L689) are recommended to support the development of hybrids that combine high yield under irrigation with resilience under water-stress conditions. Full article

Fusarium wilt (FW), caused by Fusarium oxysporum, poses a significant threat to mungbean (Vigna radiata L.), impacting its yield and quality. In this study, a recombinant inbred line (RIL) population was developed by crossing the highly resistant cultivar Weilv 9002-341 with the highly susceptible line V1128. Assessment of resistance revealed a continuous variation in the average disease index within the resulting population, consistent with the inheritance pattern of quantitative traits. Leveraging an F_2:3 segregating population, we conducted linkage mapping analysis and bulked segregant analysis by sequencing, leading to the construction of a genetic linkage map and the identification of a region correlated with resistance. Within this region, 14 novel simple sequence repeat markers were designed to enable refined mapping. A putative resistance locus, spanning 0.17 Mb and encompassing 19 annotated genes, was precisely located. Ultimately, two genes were identified as high-priority candidates conferring resistance. The results of this study lay the foundation for the functional investigation of genes associated with resistance to Fusarium wilt disease in mungbean. Full article

Seed coat color in peanut (Arachis hypogaea L.) is a critical agronomic trait that affects both nutritional quality and market appeal. In this study, we identified two bHLH transcription factor genes, AhWSC1a and AhWSC1b, homologues of Arabidopsis TRANSPARENT TESTA 8, as indispensable gatekeepers of basal flavonoid pigmentation. QTL-seq analysis of a recombinant inbred line population derived from a black-testa parent (S3) and a white-testa parent (S2) revealed that recessive loss-of-function mutations in both AhWSC1a/1b abolish proanthocyanidin biosynthesis, resulting in a white testa. Integrated metabolomic and transcriptomic profiling confirmed the absence of proanthocyanidins and a strong repression of late anthocyanin-pathway genes (DFR, LDOX) in the mutants. Molecular assays further demonstrated that AhWSC1 physically interacts with the R2R3-MYB regulator AhTc1 to form a functional MBW complex that activates AhDFR and AhLDOX transcription. In this research, we also found that the black testa phenotype may arise from elevated AhTc1 expression associated with a structural variant (SV); however, in the SV background, the introduction of ahwsc1a/1b mutant leads to a significant suppression of AhTc1 expression. Notably, because AhWSC1 is transcriptionally silent in hairy-root systems, overexpression of AhTc1 alone failed to induce these late-stage anthocyanin biosynthesis genes, highlighting AhWSC1 as an indispensable, rate-limiting hub of anthocyanin biosynthesis pathway regulation. Collectively, our findings establish AhWSC1a and AhWSC1b as master regulators of peanut testa pigmentation, elucidate the molecular basis of classical white testa inheritance, and provide genetic targets for precision-breeding of nutritionally enhanced cultivars. Full article

In order to screen high-quality processed tomato germplasm resources, the present research measured the content of quality indicators—lycopene, soluble solids, total acidity, total sugar, and vitamin C—in mature fruits of 113 processed tomato high-generation inbred lines. Comprehensive evaluations of germplasm quality were conducted through genetic diversity analysis, correlation analysis, principal component analysis, and cluster analysis. The results indicated that the variability of the five quality traits in the materials under test was relatively high, with a range of variation from 12.21% to 39.04%. Total sugar exhibited the greatest variation, while soluble solids content showed the least variation. The genetic diversity index ranged from 1.899 to 2.064, with total sugar, vitamin C, and lycopene showing high genetic variation. Soluble solids content was significantly positively correlated with lycopene, total sugar, and total acidity, while lycopene content was significantly positively correlated with total sugar. Vitamin C showed weaker correlations with other traits, but exhibited a significant negative correlation with total sugar. Total acidity had relatively simple correlations with other traits, being significantly correlated only with soluble solids. The three principal components extracted from the principal component analysis all had eigenvalues above 0.8%, contributing to a cumulative contribution rate of 77.435%. Through cluster analysis, the tested materials were divided into six major groups at an Euclidean distance of 15. Group I serves as candidate materials for breeding varieties with good basic quality and high vitamin C content. Group II stood out in terms of high sugar and lycopene content, suitable for developing tomato sauce or juice products with high vibrancy and sweetness. Group III had a high nutritional value and vibrant color, serving as core germplasm resources for breeding high-end processing-specific varieties. Group IV had high soluble solids content, making it a parent source for improving the viscosity and flavor of sauce tomatoes. Group V was suitable for specific formulations requiring high acidity or as breeding materials for high-acidity characteristics. Group VI had limited processing potential and should be used cautiously in breeding. The comprehensive evaluation results showed that the top five germplasm resources in terms of score were W119, 61, 82, 83, and W144. This study enriched the high-quality processed tomato germplasm resources and provided parental resources for quality breeding of processed tomatoes. Full article

Drought and salt stresses are major abiotic factors limiting maize yield. Lignin, a key cell wall component, plays a crucial role in boosting plant stress resistance. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme at the late stage of lignin biosynthesis; however, a systematic study of its functions in abiotic stress responses and its potential for genetic improvement in maize remains lacking. In this study, we conducted the first comprehensive, multi-dimensional analysis of the maize ZmCAD gene family, including gene identification, evolutionary relationships, protein interaction networks, and stress-responsive expression patterns. We identified 9 ZmCAD members that showed significant functional divergence in evolution, structure, and expression patterns. Expression analysis revealed complex, tissue-specific responses of ZmCAD genes to drought and salt stress, with ZmCAD6 strongly induced by drought. Importantly, through haplotype analysis of 157 waxy maize inbred lines, we successfully identified an elite haplotype (H3) of ZmCAD6 that is significantly associated with improved drought tolerance in maize. This study not only clarifies the functional differentiation mechanisms of the ZmCAD gene family but also provides the identified elite ZmCAD6-H3 haplotype as a valuable genetic resource and precise target for molecular breeding aimed at enhancing drought tolerance in maize. Full article

The mung bean (Vigna radiata) is rich in nutrients and bioactive compounds and is valuable for its antioxidant content in functional food development. However, mung bean seed coats are discarded or used as a low-value feed owing to their coarse texture. Here, 12 homozygous mung bean lines with different seed coat colors were selected from six recombinant inbred lines. The seed coats and cotyledons were separated and quantitatively analyzed for protein, starch, dietary fiber, polyphenols, flavonoids, vitexin, isovitexin, and antioxidant activities using standard chemical assays and HPLC, followed by statistical analysis and principal component analysis. The cotyledons contained more protein (26.97–28.34%) and starch (50.40–56.25%), whereas the seed coat contained more dietary fiber (74.17–79.93 g/100 g) and bioactive compounds. Polyphenolic compounds were significantly higher in the seed coat than in the cotyledons (p < 0.05) and were positively correlated with seed coat darkness, indicating that the black mung bean had higher bioactive functions. This study provides evidence for mung bean variety improvement and functional food development. Full article

Leaf inclination angle (LIA) and leaf area index (LAI) are important components of crop population canopy structure, which affect population photosynthetic production via altering canopy light interception and transmittance, and gas diffusion. In this study, we used a genetically diverse maize population of 378 inbred lines as materials to detect significantly associated SNPs with LIA and LAI using the mixed linear model (MLM) of genome-wide association study (GWAS). A total of 21 SNPs associated with LIA explain 6.07–10.86% of the phenotypic variation, containing two major-effect SNPs over 10%; 38 SNPs associated with LAI explain 2.91–10.36% of the phenotypic variation, containing one major-effect SNP. One candidate gene, GLCT1, significantly associated with LIA was identified, which might involve cell-wall biosynthesis. In addition, a cascade of SNPs significantly associated with LAI was identified in a single environment, and a candidate gene encoding the bHLH144 transcription factor was found. The results provide a theoretical basis for the selection of maize inbred lines with ideal canopy architecture and further investigation of the genetic mechanism of LIA and LAI. Full article

Plant nutrient content is spatially and temporally dynamic, exposing insect herbivores to substantial nutritional variability. Such variability can constrain insects to feeding on sub-optimal diets, but it can also allow them to regulate their intake towards an optimal nutrient balance. Nutrient regulation is important in pest management, as the nutritional state of insects may alter their susceptibility to insecticides. Diet macronutrient balance has been shown to significantly affect the susceptibility of Helicoverpa zea larvae to endotoxins produced by transgenic crops containing Bacillus thurigiensis (Bt) genes. However, this was demonstrated using a highly inbred laboratory strain, limiting extrapolation to field populations. Here, we test the impact of field-relevant macronutrient variability on the efficacy of two Bt toxins across three field populations to increase the relevance to resistance monitoring and management. While differences in susceptibility were limited across populations, dietary effects were highly population specific. The Bt toxin that was most affected by diet and the diet that supported optimal survival and performance varied across populations. These findings indicate that nutrition can strongly influence Bt susceptibility, but these effects are influenced by population-level differences. To accurately assess Bt susceptibility in the field, bioassay diets should be tailored to the nutritional ecology of local populations. Full article

Low temperature during early spring severely impairs maize germination, leading to significant yield losses. To elucidate the mechanisms underlying cold tolerance at the germination stage, we compared two cold-tolerant maize inbred lines (AM and CM) with a cold-sensitive line (BM) under control (25 °C) and chilling (6 °C) conditions. Phenotypic observations showed that AM and CM maintained high germination rates and exhibited enhanced coleoptile elongation under cold stress, whereas BM displayed substantial growth inhibition. Cold-tolerant lines accumulated less malondialdehyde and showed markedly higher SOD and POD activities, indicating a stronger antioxidant defense. Transcriptome profiling revealed that cold tolerance is associated with a more robust transcriptional response in AM and CM, characterized by significant activation of the phenylpropanoid and flavonoid biosynthesis pathways. Among the differentially expressed genes, the class III peroxidase gene ZmPER5 was strongly upregulated in AM and CM but only weakly induced in BM, suggesting its central role in reinforcing the cell wall structure and enhancing ROS-scavenging capacity under chilling conditions. Other lignin- and flavonoid-related genes, including ZmHCT4 and ZmCYP75, also exhibited genotype-specific induction patterns consistent with cold tolerance. qRT-PCR validation confirmed the RNA-seq expression trends. These results demonstrate that maize cold tolerance during germination relies on the coordinated enhancement of antioxidant enzyme activity, activation of phenylpropanoid-derived lignin biosynthesis, and accumulation of protective flavonoids. The identified candidate genes, especially ZmPER5, provide valuable targets for improving cold tolerance in maize breeding. Full article

Wheat (Triticum aestivum L.) is one of the most important staple crops in the world. Iron (Fe) plays a vital role in the growth and development of wheat as an essential nutrient. Meanwhile, Fe is closely associated with human health, as Fe deficiency anemia can cause fatigue, weakness, heart problems, and so on. In this study, quantitative trait loci (QTLs) for grain Fe content (GFeC) were detected in two populations: a recombinant inbred line (RIL) population with 175 lines derived from a cross between Avocet and Huites (AH population) genotyped with diversity array technology (DArT) and a natural population of 243 varieties (CH population) genotyped by using the 660K single-nucleotide polymorphism (SNP). Three stable QTLs (QGFe.haust-AH-5B, QGFe.haust-AH-6A, and QGFe.haust-AH-7A.2) were identified through QTL mapping with phenotypic variations of 11.55–13.63%, 3.58–9.89%, and 4.81–11.12% in the AH population in four environments. Genetic effects of QGFe.haust-AH-5B, QGFe.haust-AH-6A, and QGFe.haust-AH-7A.2 were shown to significantly increase GFeC by 8.11%, 14.05%, and 5.25%, respectively. One hundred and thirty-three significant SNPs were identified (p < 0.001) through a genome-wide association study (GWAS) for GFeC on chromosomes 1B, 2B, 3A, 3B, 5D, and 7A with phenotypic variations of 5.26–9.88% in the CH population. A novel locus was co-located within the physical interval 689.86 Mb-690.01 Mb in five environments through QTL mapping and GWAS, with one high-confidence gene, TraesCS7A02G499500, which was temporarily designated as TaqFe-7A, involved in GFeC regulation. A Kompetitive allele-specific PCR, KAFe-7A-2, was developed, which was validated in 181 natural populations. Genetic effect analysis revealed that favorable haplotype AA significantly increased GFeC by 4.64% compared to an unfavorable haplotype (p < 0.05). Therefore, this study provides the theoretical basis for cloning the GFeC gene and nutritional fortification breeding. Full article

Pericarp characteristics are key factors determining the eating quality of fresh-eating maize. This study aimed to elucidate the genetic basis of traits such as pericarp thickness, break force, and brittleness in fresh-eating maize, identify key genes regulating these traits, and provide a theoretical foundation for improving mouthfeel quality through molecular marker-assisted breeding. Using 196 fresh-eating maize inbred lines with diverse genetic backgrounds, pericarp-related traits were phenotypically measured using a texture analyzer. Genotyping was performed using the GenoBaits Maize 45K Panel chip (MolBreeding, Shijiazhuang City, China). Genome-wide association studies (GWAS) were conducted to identify significantly associated SNP loci, and candidate genes were screened for functional annotation. Phenotypic analysis revealed a significant positive correlation between pericarp thickness and break force, and a significant negative correlation between break force and brittleness. GWAS detected 21, 2, and 1 stable SNPs significantly associated with pericarp thickness, break force, and brittleness, respectively. A total of 47 candidate genes for pericarp thickness, 7 for break force, and 4 for brittleness were identified. Functional annotation indicated that the candidate gene Zm00001eb314860 (ZmbZIP130), annotated as a member of the bZIP transcription factor family, may function as a pleiotropic gene involved in regulating pericarp-related traits. These findings demonstrate that pericarp traits in fresh-eating maize are controlled by multiple genes. The significant loci and candidate genes identified in this study lay a foundation for further elucidating the molecular mechanisms underlying pericarp quality formation and for molecular breeding. Full article

Sweet corn is widely cultivated and valued for its palatability and nutritional quality, with kernels accumulating substantial carotenoids, which serve as essential antioxidants and vitamin A precursors. This study elucidated the genetic basis of carotenoid variation in sweet corn kernels by integrating quantitative trait loci (QTL) mapping with a candidate region association study. Seven carotenoid-related traits were quantified in a recombinant inbred line (RIL) population and its parental lines. QTL mapping based on a high-density genotyping-by-target sequencing (GBTS) map and BLUE values across two environments identified 15 loci on chromosomes 5, 6, 7, 8, and 9, explaining 3.83–17.25% of the phenotypic variance. Notably, chromosome 6 harbored a cluster of major-effect QTLs regulating β-cryptoxanthin, zeaxanthin, lutein, total carotenoids, and provitamin A contents. A regional association study within these linkage-defined intervals detected 71 significant SNPs (Bonferroni p < 1/n) and identified Zm00001d036238, encoding a GDSL esterase/lipase, as a strong candidate gene associated with β-cryptoxanthin accumulation. This gene exhibited kernel-specific expression in the endosperm and harbored a downstream cis-variant (Chr6: 78,466,427) correlated with increased carotenoid content. Allelic effect analysis indicated that the A/A genotype conferred markedly higher β-cryptoxanthin levels than other genotypes. Collectively, these findings provide valuable genetic resources for marker-assisted selection and biofortification breeding to enhance the nutritional quality of sweet corn. Full article

Salt stress represents a significant abiotic factor that constrains maize growth. Epigenetic modifications play a crucial role in enabling plants to respond effectively to such stresses. Among these alterations, m⁶A methylation, which is the most common post-transcriptional modification of eukaryotic mRNA, shows dynamic variations that are closely linked to stress responses. In this study, we conducted a transcriptome-wide m⁶A methylation analysis on maize roots from the inbred line PH4CV, following treatment with 180 mM NaCl. The results identified 1309 differentially m⁶A methylated peaks (DMPs) and 2761 differentially expressed genes (DEGs) under salt stress conditions. Association analysis revealed that 179 DEGs contain DMPs. Key pathways involved in stress responses, including Ca²⁺ signaling transduction and ABA signaling, as well as ion homeostasis regulation (involving AKT, HKT, and other families) and the reactive oxygen species scavenging system (including POD, SOD, and CAT), play crucial roles in coping with salt stress. Furthermore, we identified a total of 26 m⁶A-related genes, comprising 7 eraser genes, 10 reader genes, and 9 writer genes. Notably, several key salt-responsive genes, such as RBOHB, AKT1, HKT1, and POD12, are correlated with m⁶A modification. This study provides a comprehensive map of m⁶A methylation dynamics in maize roots under salt stress, laying a foundational resource for future investigations into the epigenetic regulation of salt tolerance in maize. Full article

Liquid chromatography–mass spectrometry analysis of Pseudomonas chlororaphis subsp. phenazini S1Bt23 extracts detected phenazine-1-carboxylic acid (PCA) and 2-hydroxyphenazine (2-OH-PHZ) as the main phenazine derivatives. We investigated their relative contributions to the antagonistic activity of strain S1Bt23 against Pythium arrhenomanes, a root rot pathogen of corn. CRISPR-Cas9 knockouts were carried out on the phzF gene, required for PCA synthesis, and the phzO gene, which is involved in converting PCA to 2-OH-PHZ. Deletion of the phzF gene abrogated the production of PCA and 2-OH-PHZ, and the ΔphzF mutant lost the antagonism against Pythium arrhenomanes. In contrast, deletion of the phzO gene created a 2-OH-PHZ-negative mutant with intact antagonistic ability. Concordantly, S1Bt23 wild type and the ΔphzO mutant, but not the ΔphzF mutant, significantly bioprotected corn seeds of a susceptible inbred variety, CO441, from P. arrhenomanes. At equimolar amounts of 75 nM, synthetic PCA inhibited Pythium growth, whereas 2-OH-PHZ did not. This highlights the critical contribution of PCA to the biocontrol activity of strain S1Bt23 against P. arrhenomanes. Unexpectedly, deletion of phzO did not result in additional PCA accumulation. This suggests that the conversion of PCA to 2-OH-PHZ by S1Bt23 is a potential protective mechanism against the overproduction of lethal cellular doses. This study paves the way for bioengineering strain S1Bt23 into a more effective biopesticide. Full article

Nitrogen (N) is essential for maize (Zea mays L.) productivity, yet its acquisition is limited by the low N uptake efficiency of current varieties. Root cortical aerenchyma (RCA) formation provides a carbon-saving strategy that enhances soil exploration and N acquisition by reducing the metabolic cost of root tissue. However, the genetic basis of RCA formation remains poorly characterized. This study employed an association panel of 295 maize inbred lines to dissect the genetic architecture of RCA formation under low nitrogen (LN) stress. Phenotypic analysis demonstrated that LN stress significantly induced RCA area (RCAA) and proportion (RCAP), with responses ranging from −0.31 to 1.16 mm² for RCAA and −11.34% to 40.18% for RCAP. The non-stiff stalk (NSS) subpopulation exhibited 29.19% higher RCAA under LN than the stiff stalk subgroup. Genome-wide association analysis detected a total of 560 significant SNPs and 810 candidate genes associated with RCA-related traits. Transcriptomic profiling further identified 537 differentially expressed genes between inbred lines with contrasting RCA phenotypes. Integrated GWAS and transcriptomic analysis pinpointed 12 co-localized candidates, subsequently refined to four core genes (GRMZM2G033570, GRMZM2G052422, GRMZM2G080603, and GRMZM2G472266), which were implicated in ethylene signaling and stress-responsive root development. Favorable haplotypes of three genes were predominantly distributed in the NSS (25.64–56.00%) and tropical/subtropical (20.51–46.67%) subpopulations. These findings elucidate the genetic basis of LN-responsive RCA formation and provide fundamental resources for marker-assisted breeding of N-efficient maize. Full article