Search Results (118)

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

Potato early blight (EB), caused by Alternaria, is an economically devastating fungal disease affecting global potato production. Using a hybrid population derived from distantly related varieties, we combined resistance evaluation, histological analysis, Bulked Segregant Analysis sequencing, RNA sequencing and molecular dynamics simulation, which successfully identified key candidate resistance genes. Genetic mapping localized three major resistance-associated regions on chromosome 8 spanning positions 25.07–29.20 Mb, 38.05–38.80 Mb, and 39.40–40.78 Mb. Through candidate gene analysis, we identified CND41, encoding an aspartic protease, as the prime candidate. This gene exhibited significantly higher basal expression levels and stronger pathogen-induced upregulation in resistant genotypes. Molecular dynamics simulations further identified six crucial non-synonymous mutations in the TAXI-N domain that likely contribute to enhanced resistance by destabilizing the susceptibility-associated protein conformation. Transient overexpression of CND41 provided functional evidence supporting its likely involvement in early blight resistance (EBR). These findings contribute valuable genetic resources and a strong candidate gene for molecular breeding toward EBR potato varieties. Full article

The first female flower node (FFFN) is a crucial trait affecting earliness and yield in bitter gourd (Momordica charantia L.). To identify the genetic locus and candidate gene controlling FFFN, we performed phenotypic and genetic analyses using two parental lines, ‘M144’ (average FFFN: 6.3 ± 2.0) and ‘K55’ (average FFFN: 22.0 ± 4.5), along with their F₁ hybrid and an F₂ population consisting of 317 individuals. The results show that the low FFFN trait was incompletely dominant over the high FFFN trait. Using BSA-seq, we mapped a FFFN locus to an interval of 18.8–22.5 Mb on chromosome 4. Fine mapping with KASP markers narrowed the McFFFN4.1 to a 73.05 kb interval between markers 25QP334 and 26QP20, which contained seven predicted genes. Transcriptome analysis revealed that only Moc04g29650, which is annotated as cytochrome b-c1 complex subunit Rieske, was differentially expressed between the parents within this mapping interval. Sequence comparison identified a single SNP (C > A) in the promoter region of Moc04g29650, which was located within a putative YAB1/FIL-binding motif. Given the known role of FILAMENTOUS FLOWER (FIL) in regulating floral transition in Arabidopsis thaliana, Moc04g29650 is proposed as the most likely candidate gene for McFFFN4.1. The KASP marker 26QP20, located near Moc04g29650, showed the strongest association with FFFN in the F₂ population, with a maximum LOD score of 5.45, and thus represents a valuable tool for marker-assisted selection (MAS) breeding in bitter gourd. This study lays a foundation for cloning McFFFN4.1 and genetically improving early maturity in bitter gourd. Full article

Cucumber (Cucumis sativus L.) is a globally significant vegetable crop, and its fruit quality remains a major focus of research. The hollow-heart trait, characterized by internal cracks or cavities, severely compromises both the commercial value and edible quality of cucumber fruit. In this study, a six-generation segregating population (P₁, P₂, F₁, F₂, BC₁P₁, BC₁P₂) was developed from the parental lines “JZ6-1-2” and “D0432-3-4”. BSA-seq was employed to map candidate genomic regions associated with the hollow-heart trait to chromosomes 2, 3, and 7. Subsequently, a major QTL for the trait was delineated on chromosome 7, spanning a region containing 98 genes. Comparative RNA-seq between the parental lines identified 2141 differentially expressed genes. The integration of QTL mapping and RNA-seq data revealed 11 candidate genes residing within the key QTL interval. Through further validation via qRT-PCR, gene sequence comparison, and gene annotation, Csa7G039280 was identified as a promising candidate gene regulating hollow-heart formation, potentially via the lignin biosynthesis pathway. The identification of these candidate regions and genes provides critical information for molecular breeding aimed at developing non-hollow-heart cucumber varieties, thereby enhancing the understanding of the genetic regulatory mechanisms underlying this economically important trait. Full article

Shoot branching, as an important architectural trait, influences the number of flower heads and the pattern of flowering in sunflowers (Helianthus annuus L.). However, the main genetic factors leading to extensive branching throughout the plant were not clearly understood. In this study, we analyzed branching inheritance and identified a significant locus using an F₂ population (n = 660) from a cross between the non-branched line 150A and the highly branched line PT326. The branching phenotypes varied from having no branches to complete plant branching, with segregation fitting a 3:1 ratio (χ² = 2.916, p > 0.05), suggesting that a single major gene controls this trait, with the non-branched phenotype being dominant. Using bulked segregant analysis (BSA) and whole-genome resequencing, a strong and consistent signal was identified on chromosome 10 across three separate statistical analyses, pinpointing a primary candidate interval of approximately 3.40 Mb, named qBr10. Through the use of 10 developed Kompetitive Allele-Specific PCR (KASP) markers and recombinant screening, qBr10 was restricted to a 388.5 kb (Chr10:13,422,378–13,780,875). Analysis of this interval identified 21 genes, among which WRKY21 and MTB3 were prioritized as candidate genes for further functional validation. Our findings identified qBr10 as a strong candidate for cloning and offer closely associated markers to aid in marker-assisted improvement of branching and capitulum number in sunflower breeding. Full article

Salt stress represents a significant abiotic stress factor that adversely affects plant growth and development. It directly inhibits both vegetative and reproductive growth, resulting in substantial reductions in crop yield and quality. Consequently, the identification of salt tolerance genes and the elucidation of their underlying molecular mechanisms are crucial for improving crop salt tolerance and ensuring agricultural productivity. To investigate the molecular basis underlying differential salt tolerance between Zheng58 and PH4CV, we employed pooled sequencing (BSA-seq) using extreme phenotypic individuals from their F₂ population and conducted a comparative transcriptome analysis at the seedling stage of the two genotypes. Phenotypic, physiological, biochemical, and ion content analyses revealed that Zheng58 exhibited significantly superior performance compared to PH4CV under salt stress conditions. BSA-seq analysis identified six genomic regions associated with salt tolerance, encompassing a total of 391 genes. Functional annotation enabled the screening of 151 candidate genes potentially involved in salt stress responses. Transcriptome profiling indicated that differentially expressed genes were significantly enriched in biological processes, particularly plant hormone signal transduction and MAPK signaling pathways. Integrating BSA-seq and transcriptome data, key candidate gene ZmACC2 (Zm00001eb419400) was identified as potentially involved in the regulation of salt tolerance in maize. This gene may modulate Na⁺/K⁺/Ca²⁺ homeostasis and reactive oxygen species metabolism through defense responses mediated by ethylene (ETH) and hydrogen peroxide, as well as through ion homeostasis regulatory pathways. This study provides valuable candidate genes and a theoretical foundation for further dissection of the molecular mechanisms governing salt tolerance in maize. Full article

Fruit branch length in cotton is a key trait influencing plant architecture and suitability for mechanisation; elucidating its molecular regulatory mechanisms is crucial for breeding varieties with desirable plant architecture. In this study, an F₂ segregating population was established using the long-fruit-branch upland cotton line L16 and the short-fruit-branch line S14 as parents. By integrating morphological, cytological, and omics approaches, we systematically analysed the underlying mechanisms of variation in fruit branch length. Phenotypic analysis indicated that the inter-node elongation rate of the first fruit branch in L16 was significantly higher than that in S14. Tissue section observations revealed that the length of cortical parenchyma cells in L16 was significantly greater than that in S14, suggesting that the difference in fruit branch length primarily stems from variations in the extent of cortical parenchyma cell elongation. BSA-Seq analysis identified five QTL regions significantly associated with fruit branch length, encompassing 82 coding genes. Further RNA-Seq analysis of the fruit branch initiation stage (T0) and rapid elongation stage (T1) identified 3106 differentially expressed genes common to both stages. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in pathways related to plant hormone signalling, the cytoskeleton, and microtubule organisation. By integrating BSA-Seq and RNA-Seq data, three candidate genes were screened that simultaneously harboured non-synonymous mutations and were significantly highly expressed in the short fruit branch line S14. Combined with bioinformatics analysis, GH_D02G0744 was predicted to be the most likely key candidate gene regulating cotton fruit branch length. This study provides important genetic resources to elucidate the molecular regulatory mechanisms of cotton fruit branch length and lays a theoretical foundation for molecular breeding to improve cotton plant architecture. Full article

Objectives: Peduncle length (PL) is a critical agronomic trait in sorghum [Sorghum bicolor (L.) Moench], influencing mechanical harvesting efficiency. Exploration of the PL genetic mechanism and the PL major genes of sorghum can provide a reference for breeding of sorghum suitable for mechanization and PL genetic research of other graminaceous crops. Methods: Here, we conducted genetic analysis, transcriptome analysis, and candidate major gene screening of PL using long-peduncle (KY133B) and short-peduncle (KY123B) parents, as well as their constructed F2 segregated populations. Results: Genetic analysis revealed that PL trait may be controlled by two major genes with additive-dominant effects, showing a heritability of 69.638%. At the early stage of sorghum peduncle elongation, the young panicle of the parents was sampled and performed transcriptome analysis. DEGs 3603 genes were obtained. With the short peduncle parent (F) as the control, 2204 upregulated genes and 1399 downregulated genes were expressed in the long peduncle parent (M). We compared the 1161 genes obtained by BSA-seq from the laboratory in the early stage with the DEGs obtained by RNA-seq, and obtained 148 co-localized genes. Through the high DEGs screening criteria (|Log₂FC(M/F)| ≥ 5, p < 0.0001), we further identified 36 genes with highly significant expression differences between parents. Functional annotation identified four candidate major genes strongly associated with PL: LOC8056900 (MIZU-KUSSEI 1), LOC8065075 (ethylene-responsive transcription factor WIN1), LOC8083493 (GDSL esterase/lipase), and LOC8085367 (auxin-responsive protein IAA21). qPCR validated their expression trends, corroborating RNA-seq results. Conclusions: The comprehensive information presented here provides a reference for understanding the PL mechanism of sorghum and provides some important candidate major genes related to PL. This study laid the foundation for subsequent gene functional verification and mechanism analysis of sorghum peduncle length major genes. Full article

Fusarium ear rot (FER), caused by Fusarium verticillioides, is a devastating disease that substantially reduces maize yield and compromises kernel quality. To investigate the genetic and molecular basis of resistance, an F₂ population derived from a cross between the resistant inbred line 3IBZ2 and the susceptible inbred line KW5G321 was analysed. By integrating bulked segregant analysis sequencing (BSA-Seq) with RNA sequencing (RNA-Seq), a major quantitative trait locus (QTL), designated qFER4, was identified on chromosome 4. Genetic analysis further demonstrated that qFER4 confers resistance through partial dominance. Transcriptome profiling of the resistant line revealed 7684 and 7906 differentially expressed genes (DEGs) at 36 and 72 h post inoculation (hpi), respectively. These DEGs were significantly enriched in defence-related biological processes and pathways, including phenylpropanoid biosynthesis, jasmonic acid signalling, MAPK cascades, and plant-pathogen interactions. By combining QTL mapping with transcriptome analyses, four candidate genes within the qFER4 interval were screened. Sequence analysis identified extensive structural variations in the promoter and coding regions of Zm00001d053393, including a premature stop codon predicted to lead to a gain-of-function mutation. In contrast, the other three genes exhibited only minor promoter polymorphisms with identical coding sequences between the parental lines. Overall, this study identifies a novel major-effect QTL and candidate gene associated with FER resistance, providing a foundation for gene function and a valuable genetic resource for breeding FER-resistant maize varieties. Full article

Branch number is an important agronomic trait that determines the number of siliques per plant and yield in rapeseed (Brassica napus). However, the complex genetic and molecular mechanisms regulating the formation of branch number in rapeseed remain unclear. In a previous study, we isolated an EMS-induced multi-branching mutant (mbm1). Here, agronomic trait analysis showed that the mbm1 mutant produced more effective primary branches, total silique number, and yield per plant compared with the wild type. Genetic analysis indicated that the multi-branching trait of the mbm1 mutant is controlled by incompletely dominant gene(s) and follows nuclear inheritance. As a result of combined BSA-seq-based mapping and RNA-seq profiling, two candidate genes, BnaC03G0462000ZS (BnaC03.GAE6) and BnaC03G0491900ZS (BnaC03.MEE14), were identified based on sequence variation and expression differences. KASP marker analysis confirmed that there are significant associations between these two gene loci and the multi-branching trait. Hybrid progeny derived from crosses between the mbm1 mutant and commercial cultivars L329 and ZS11 showed significantly improved yield due to increased effective branch number. Together, these results provide important genetic resources and a theoretical foundation for further elucidating the genetic regulatory network of branching in rapeseed and for developing high-yielding rapeseed varieties with ideal plant architecture. Full article

Background/Objectives: Sweetness is a key determinant of the eating quality of sweet corn, primarily governed by the soluble sugar content in kernels. The soluble sugar content decreases rapidly during the postharvest shelf life, which directly affects the flavor and quality. Relatively few studies have been conducted on the shelf life of sweet corn. Methods: An F₆ recombinant inbred line (RIL) population was constructed from two super sweet inbred lines with contrasting soluble sugar degradation rates: D174 (low degradation rate) and D179 (high degradation rate). Extreme phenotype pools were established using soluble sugar content as the target trait. Based on bulked segregant analysis sequencing, we identified chromosomal segments associated with postharvest soluble sugar reduction in sweet corn, annotated the gene information within these segments, and analyzed the functions of the annotated genes using the Gene Ontology and Genomes databases. Results: Results revealed three associated regions located at 44,205,775–45,290,843 bp on chromosome 4, 6,250,656–6,744,665 bp on chromosome 2, and 135,428,709–136,732,132 bp on chromosome 10. This interval contained 195 genes. Integrated analysis of gene expression, gene annotations, and quantitative real-time PCR indicated that Zm00001eb069070, which is highly expressed in kernels with a prolonged shelf life, might be a key candidate gene regulating soluble sugar degradation in sweet corn. Conclusions: This study provides valuable genetic resources for the improvement of favorable agronomic traits and the advancement of molecular breeding strategies for sweet corn. Full article

Background: Starch accumulation contributes substantially to maize grain yield and quality. Starch synthase III (SSIII) is a key component of the starch biosynthetic enzyme complex. However, its regulatory role in starch accumulation in maize endosperm remains incompletely understood. Methods: The du1-2018 mutant arose spontaneously during a conventional maize breeding program. Phenotypic characterization, storage compound contents, and starch structure were compared between the mutant and wild-type lines. BSA-seq, genetic linkage analysis, and transcriptomic analysis were employed to identify the candidate gene responsible for the mutant phenotype. Transcriptome sequencing was performed on developing kernels to evaluate the genome-wide effects of the du1-2018 mutation. Results: The du1-2018 mutant exhibited dull, glassy, and mildly shrunken kernels, with decreased starch levels and elevated soluble sugar and protein contents. The du1-2018 mutation disrupted starch accumulation, resulting in smaller, irregularly shaped starch granules and significant changes in starch composition and fine structure. This mutation was identified as a severe loss-of-function allele of the dull1 (du1) gene, evidenced by almost undetectable Du1 transcripts in developing kernels. Notably, transcriptomic analysis revealed that a substantial proportion of differentially expressed genes (DEGs) were involved in amino acid and protein metabolism. Conclusions: The novel du1 allelic variant, du1-2018, disrupts starch biosynthesis in maize endosperm, leading to reduced starch accumulation, altered starch structure, and transcriptional changes in nitrogen-related metabolic pathways. Our results provide new insights into the regulatory mechanisms underlying SSIII function in starch synthesis and endosperm development, and suggest potential links to carbon/nitrogen balance, with implications for future genetic improvement of maize grain quality. Full article

Thousand-seed weight (TSW) is a critical determinant of yield in rapeseed (Brassica napus L.). Developing germplasm with high TSW is therefore a key strategy in high-yield rapeseed breeding. However, the genetic and molecular mechanisms underlying TSW in rapeseed remain poorly understood. In our earlier work, we identified a mutant, designated GRG177, which exhibits a remarkably high TSW exceeding 7 g. To unravel the mechanisms driving this elevated TSW, we conducted a comprehensive analysis of GRG177, integrating morphological, genetic, developmental, anatomical, and physiological approaches. Compared with the control germplasm GRD328 (TSW ≈ 3.5 g), GRG177 displayed a significant increase in seed weight and seed volume, larger silique surface area, and higher yield per plant. However, it also showed a notable reduction in both silique number per plant and seed number per silique. Genetic analysis of a segregating population revealed that the high-TSW trait in GRG177 is governed by two pairs of dominant epistatic major genes plus polygenes. Endogenous hormone analysis revealed significantly higher zeatin riboside (ZR) content in the early stage of seed development in GRG177, whereas indole-3-acetic acid (IAA) and abscisic acid (ABA) levels were significantly up-regulated in the late stage of seed development. Anatomical observation using paraffin sections further confirmed that enhanced cell division activity in the early stage and improved cell expansion capacity in the later stage underpin the formation of high TSW. Furthermore, BSA-seq was utilized to map four TSW-related Quantitative Trait Loci (QTLs) and screen 13 candidate genes involved in IAA, ZR, and ABA signaling pathways. In conclusion, these findings provide novel insights into the regulatory mechanisms governing high-TSW formation in rapeseed and present valuable genetic resources for high-yield breeding. Full article

In cabbage, epidermal wax plays a key role in adaptation to abiotic and biotic stresses. The glossy green cabbage variety, which has less wax, is becoming increasingly popular on the market. In this study, the highly inbred waxy cabbage HQ2-1 and the glossy green cabbage Y2-1 were sampled for fine mapping and transcriptomics analysis. In the glossy green leaf cabbage, inheritance follows a simple dominant pattern. BSA-seq and interval targeted sequencing technology identified BoCER1 as the candidate gene controlling the leaf wax trait in Brassica oleracea. Downregulated genes in the α-linolenic acid metabolic pathway and upregulated genes in the wax synthesis pathway in HQ2-1 collectively promote wax formation in HQ2-1 leaves. Cold stress induced the upregulation of α-linolenic acid metabolic pathway genes in HQ2-1, and we speculate that the upregulation of these genes may promote jasmonic acid accumulation. Our study lays a solid foundation for further understanding the regulatory mechanism of leaf wax formation in cabbage and for the translational application of breeding new glossy cabbage varieties. Full article

The excessively concentrated ripening period of mulberries causes seasonal surplus. Fruit mulberry (Morus spp.) exhibits the unique trait of “simultaneous flowering and leaf flushing”, rendering budburst timing closely correlated with fruit ripening time. Thus, deciphering the molecular mechanism underlying winter bud dormancy maintenance in fruit mulberry is urgently needed. Herein, an F₁ hybrid population comprising 337 individuals, derived from Morus wittiorum (♀) and ‘322’ (♂), was utilized as research material. Through Bulked Segregant Analysis Sequencing (BSA-Seq), we successfully mapped a dormancy-associated QTL interval designated as LB (Late Burst), spanning 9,990,001–11,990,000 bp on Chromosome 13. Integrating Weighted Gene Co-expression Network Analysis (WGCNA) results, MaSVP was identified as a candidate gene within this interval. Virus-induced gene silencing (VIGS) of MaSVP in winter buds of Morus wittiorum significantly accelerated budburst compared to the control, demonstrating that MaSVP represses winter bud dormancy release and plays a crucial role in regulating dormancy maintenance in fruit mulberry. Dynamic expression profiling of dormancy-related genes revealed that the transcript levels of MaSVP, MaSAPK3, MaCASL2, and MaPYR8 were significantly downregulated (Tukey’s test, p < 0.05) as budburst approached, whereas those of MaFT and MaGA20ox1-D were significantly upregulated (Tukey’s test, p < 0.05). These results indicate that winter bud dormancy maintenance in Morus wittiorum is associated with abscisic acid (ABA) and gibberellin (GA) metabolism. Collectively, this study provides critical insights into the biological basis of winter bud dormancy maintenance in fruit mulberry and offers valuable genetic resources for breeding late-maturing cultivars. Full article