Search Results (272)

Polyamines, a class of low-molecular-weight nitrogen-containing bases with high biological activity, are ubiquitous in organisms and play protective roles in plants under stress. Polyamine oxidase (PAO), a typical flavoprotein characterized as a glycoprotein, is a key enzyme in polyamine catabolism that directly mediates polyamine breakdown and maintains intracellular polyamine homeostasis. However, the specific functions of PAOs in cotton fiber development remain largely unclear. In this study, we identified 23 GhPAO genes from the upland cotton (Gossypium hirsutum L.) genome via comprehensive bioinformatics approaches. We systematically analyzed their physicochemical properties, phylogenetic relationships, gene structures, chromosomal locations, conserved motifs, cis-acting elements, and expression patterns. Quantitative real-time PCR (qPCR) analysis confirmed that GhPAO10 and GhPAO21 exhibited the most pronounced transcript accumulation during both fiber development and stress response processes. Further yeast one-hybrid (Y1H) and dual-luciferase reporter assays indicated that the GhPAO21 promoter was directly regulated by the transcription factor GhTGA1. Our findings provide a foundation for elucidating the functional roles of the PAO gene family in upland cotton and underscore potential candidate genes associated with fiber development and stress responses. Full article

Nitrogen (N) is a key nutrient for upland rice (Oryza sativa L.), and plant growth-promoting rhizobacteria (PGPR) have been investigated as a sustainable strategy to improve plant nutrition and crop performance. This study evaluated the effects of N topdressing and PGPR inoculation on leaf chlorophyll index (LCI), leaf nutrient concentrations, and yield components in upland rice. A field experiment was conducted in a randomized block design (4 × 6 factorial) with four N rates (0, 40, 80, and 120 kg ha⁻¹) and five PGPR strains (Azospirillum brasilense, Nitrospirillum amazonense, Bacillus subtilis, Priestia aryabhattai, and Methylobacterium symbioticum), plus a non-inoculated control. No significant interaction between N rates and PGPR inoculation was observed. Nitrogen increased leaf phosphorus (P), potassium (K), and magnesium (Mg) concentrations and panicle number; however, it also increased unfilled grains, reduced grain weight, and did not affect grain yield. Azospirillum brasilense increased LCI by 25.7%. Bacillus subtilis and A. brasilense increased leaf N, K, Mg, copper (Cu) and manganese (Mn) concentrations. Azospirillum brasilense, B. subtilis, N. amazonense, and P. aryabhattai reduced unfilled grains, increased grain weight and grain yield by up to 10.7%, whereas M. symbioticum did not differ from the control in grain yield. Under the conditions of this study, nitrogen was not limiting for grain yield, and all strains, except M. symbioticum, were associated with increases in grain yield and changes in plant nutritional status. Full article

Acibenzolar-S-methyl (ASM), a salicylic acid (SA) analog, and jasmonic acid (JA) are chemical inducers of plant defenses, yet crosstalk between SA- and JA-associated pathways may result in antagonistic outcomes. Here, we assessed how ASM and JA, applied alone or in combination, are associated with rice blast severity and defense-related responses in an upland rice cultivar. Plants of rice (Oryza sativa L., cv. Primavera) were treated with JA, ASM or JA + ASM and subsequently challenged with Magnaporthe oryzae. ASM treatment was associated with reduced leaf blast severity (LBS), whereas JA treatment was associated with increased LBS. Antagonistic outcomes were observed in the combined treatment: LBS in JA + ASM plants was higher than in ASM-treated plants but lower than in JA-treated plants. Lipoxygenase (LOX) activity was induced by JA and positively correlated with LBS, indicating that higher LOX activity aligned with greater susceptibility under the tested conditions. In contrast, ASM-treated plants showed higher peroxidase (POX) activity, which was associated with lower LBS. Disease outcomes were also linked to secondary defense metabolism and phenylpropanoid-related components, including phenylalanine ammonia-lyase (PAL), salicylic acid (SA) and phenolic compounds (PC). Overall, these results provide an integrated biochemical profile of how ASM, JA and their combination are associated with contrasting blast outcomes in upland rice, consistent with antagonistic interactions between JA- and SA-associated defense responses. These findings may inform the use of defense inducers and the interpretation of defense markers in upland rice systems where blast management is a major constraint. Full article

Nitrogen is an essential macronutrient for plant growth, photosynthesis, and grain yield. However, the nitrogen use efficiency (NUE) of crops remains relatively low, leading to nitrogen losses and environmental concerns. This is particularly important in upland rice because it is a high nitrogen user, but research of its NUE is limited. This literature review explored the contributions of leaf morphology, specifically leaf size and leaf angle, to nitrogen utilization efficiency in upland rice under varying rates of nitrogen fertilization. It also evaluated sustainable nitrogen management practices across diverse cropping systems. Findings reveal that nitrogen fertilization significantly influences leaf development, canopy structure, and nitrogen remobilization, all of which directly affect photosynthetic efficiency and yield. Breeding strategies focusing on moderate leaf size and erect leaf angles improve the nitrogen uptake and use by rice. In addition, sustainable farming practices, including precision nitrogen management, conservation agriculture, and intercropping with legumes, are effective in enhancing NUE and reducing nitrogen losses across various rice production systems. Future research should focus on identifying the thresholds of nitrogen rates that optimize leaf morphology across diverse upland rice genotypes and unravel the genetic and physiological mechanisms linking nitrogen application to leaf development. 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

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs with superior fiber quality. Xinjiang is one of the major cotton-producing regions in China, and breeding high-quality early-maturing upland cotton adapted to local ecological conditions is essential for improving cotton yield and quality. However, the genetic relationship and differentiation between the two types of cotton germplasm remain unclear, which hinders the efficient utilization of germplasm resources in breeding. Therefore, this study aimed to clarify the genetic diversity and differentiation between the two germplasm types and identify key candidate loci related to early maturity and fiber quality, providing support for cotton breeding. Results: Here, we used a 40K Single Nucleotide Polymorphism chip to genotype core cotton germplasm in northern Xinjiang, and analyzed their population structure, genetic diversity and functional SNP loci associated with early maturity and fiber quality. The tested materials were clearly divided into two subgroups (ILs and early-maturing lines). Genetic diversity analysis revealed a significantly narrow genetic basis in the early-maturing subgroup, while the IL subgroup had higher genetic diversity. Specifically, the early-maturing subgroup showed lower nucleotide diversity and polymorphism information content compared with the IL subgroup, indicating that the genetic variation of early-maturing cotton germplasm in northern Xinjiang is relatively limited. A total of 25 non-synonymous SNPs were identified, among which the c.A613G:p.T205A mutation in GH_D09G1484 (mRNA-decapping enzyme 1, DCP1) was a characteristic variation of early-maturing cotton, and a possible non-synonymous mutation in GH_A09G2400 (Heat shock transcription factor A6b, HSFA6B) was associated with fiber development. These two candidate genes were annotated to be involved in plant growth and development, further supporting their potential roles in regulating cotton early maturity and fiber quality. Conclusions: This study clarified the genetic differentiation between the two types of germplasms and identified key candidate loci for early maturity and fiber quality, providing precise molecular markers and theoretical support for breeding high-quality early-maturing upland cotton adapted to Xinjiang’s ecological conditions. The results also highlight the value of Gossypium hirsutum–Gossypium barbadense introgression lines in enriching the genetic basis of early-maturing cotton, which can be further utilized to solve the core breeding contradiction in the Xinjiang cotton region. Full article

Cotton, a globally vital cash crop, is severely constrained by V. dahliae. Lignin, a core structural component of plant cell walls, plays a crucial role in physical defense, with its biosynthesis regulated by hydroxycinnamoyltransferase (HCT)—a key enzyme in the phenylpropanoid pathway. However, the HCT gene family in upland cotton (Gossypium hirsutum) and its role in resistance to V. dahliae remain poorly understood. In this study, we performed a genome-wide identification of the HCT gene family in G. hirsutum, identifying 74 GhHCT genes that were classified into five evolutionary subfamilies. Bioinformatics analysis revealed that GhHCT proteins exhibit conserved functional domains but diverse gene structures, with promoter regions enriched in hormone-responsive and stress-responsive cis-acting elements. Expression profiling revealed that multiple GhHCT genes were significantly induced in response to V. dahliae infection. Three genes, GhHCT2, GhHCT35, and GhHCT47, showed significantly higher expression levels in resistant cultivars than in susceptible cultivars during early infection stages, suggesting pivotal roles in defense. These three candidate genes, which contain MeJA/SA-responsive elements in their promoters, may enhance resistance by regulating lignin synthesis to strengthen the cell wall barrier. In summary, this study provides the first comprehensive characterization of the HCT gene family in upland cotton. It identifies key candidates for improving resistance to V. dahliae, offering valuable genetic resources for molecular breeding. Full article

The Cyrtodactylus chauquangensis species group is a large limestone karst radiation of bent-toed geckos with at least 28 nominal species and has a broad distribution range with seven species found in northwestern Thailand, five in south-central China, five in northern Laos and 11 in northern Vietnam. To trace the biogeographic pattern of this group, we reconstruct its phylogenetic relationships and evolutionary history using three mitochondrial genes and four nuclear genes. Our results show that the C. chauquangensis species group is monophyletic, which can be divided into at least seven subclades. In terms of biogeography, the group might have originated from the Northwest Uplands of the Indochina region, including northern Laos and part of northwestern Vietnam, during the early Miocene and subsequently dispersed into northwestern Thailand. It later colonized the northern Annamites, Northeast Lowland, Northeast Uplands, and South-central China. A majority of lineages within this group likely diverged during the Miocene epoch when the East Asian monsoon was developed and increased precipitation in the region. The changing climate might have promoted plant diversity and provided suitable habitats and food resources for members of the C. chauquangensis group. In addition, the elevated rate of precipitation probably accelerated the dissolution of the limestone substrate and profoundly influenced the development of the karst region. The results of our study further highlight the importance of this unique period of time in shaping evolutionary histories of many different taxonomic groups in the region. Full article

Gibberellins (GAs) play a crucial regulatory role in the growth and development of cotton (Gossypium hirsutum L.). Through bioinformatics analyses, we identified a total of 39 GA2ox genes (encoding gibberellin 2-oxidases) in the cotton genome, designated GhGA2ox1 to GhGA2ox39. Based on phylogenetic analysis, these genes were classified into five groups. We further examined their gene structures, conserved motifs, and chromosomal distributions, revealing that members within the same group shared similar structural and motif organizations. Collinearity and cis-element analyses provided important insights into the evolutionary history and regulatory potential of the GA2ox gene family in cotton. Notably, using nucleotide diversity (π) and population differentiation (F_ST) analyses across the entire family, we screened and identified nine candidate genes that underwent strong artificial selection during cotton domestication and improvement. Further haplotype-phenotype association analysis identified GH_D09G0919 (GhGA2ox31) as a key regulator of Plant Height (PH). To validate their regulatory roles, we analyzed the genotype distribution in accessions with extreme phenotypes. The results revealed divergent selection histories for these two loci: the favorable allele of GH_D01G0720 (GhGA2ox23) was already fixed in the tested population, whereas GH_D09G0919 maintained significant natural variation. Specifically, the Hap2 allele of GH_D09G0919 was significantly enriched in the shortest accessions compared to the tallest ones. Importantly, quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed that the Hap2 allele drives significantly higher gene expression in leaves, suggesting that enhanced GA catabolism underlies the compact phenotype. Additionally, transcriptomic profiling revealed the tissue-specific expression patterns of candidate genes, implying their functional roles in development. Furthermore, functional validation using the Arabidopsis mutant of the homologous gene (AtGA2ox8) confirmed its conserved role in regulating plant height, as the mutant exhibited a distinct short-stature phenotype. These results uncover valuable genetic resources for molecular breeding to shape compact cotton architecture. Collectively, this study aims to analyze the evolutionary patterns of the cotton GA2ox gene family and to identify key genes that regulate plant height under artificial selection, providing theoretical support for molecular breeding of compact plant types. Full article

Cotton is one of the most significant economic crops cultivated worldwide. Cottonseed is a strategic reservoir of high-quality plant protein and an underexploited resource for the food and feed industries. To quantify nutritional diversity and identify superior germplasm, we evaluated 312 upland cotton (Gossypium hirsutum L.) accessions over two consecutive growing seasons and characterized 30 agronomic and nutritional traits. Protein content varied widely (29.6–48.8%), with a coefficient of variation of 7.5–11.7% and a two-year mean of 37.0%. Glutamic acid (Glu; 154.0 mg/g) and aspartic acid (Asp; 90.7 mg/g) were the most abundant amino acids, and lysine and arginine were relatively high among essential amino acids. Correlation analysis based on genotype best linear unbiased estimates (BLUEs) showed that most nutritional traits were positively or neutrally associated with key yield-related traits, particularly lint percentage (LP) (e.g., protein vs. LP: r = 0.18, p < 0.01), indicating the feasibility of simultaneous improvement in seed nutritional quality and lint yield potential. Using 29 core traits with complete two-year data, we developed an integrated evaluation framework combining principal component analysis (PCA), grey relational analysis (GRA), TOPSIS, and the analytic hierarchy process (AHP) to rank accessions comprehensively. This framework identified 10 elite germplasm lines with high protein content and favorable yield potential, exemplified by “Xinluzhong 34” (Rank 1; phenotypic comprehensive value, P_i = 0.733). These results provide a quantitative foundation for value-added cottonseed utilization and support breeding strategies aimed at developing cultivars with both high yield and enhanced nutritional quality. Full article

Cotton (Gossypium spp.) is the most important fiber crop for the textile industry globally. Abiotic stresses, including drought, have become prevalent in affecting cotton production worldwide. There is a shortage of studies on the use of biochar as a soil amendment in the semi-arid and arid Southwest and West U.S. Cotton Belt to alleviate drought stress. This study was conducted to examine the effects of biochar at four application rates (0, 6.25, 12.5, and 25.0 t ha⁻¹) on cotton yield and yield components using six tetraploid cotton genotypes, including one Pima (G. barbadense L.) and five Upland cottons (G. hirsutum L.), under well-watered (WW) and drought stress (DS) conditions in an arid region of New Mexico, USA. The six cotton genotypes consistently showed that DS at the flowering stage significantly decreased boll number (BN), boll weight (BW), and lint percentage (LP), and thereby seed cotton weight (SCW) per plant and lint weight (LW) per plant. However, Pima DP 359 RF had the lowest reduction (23–33%) in BN, SCW, and LW due to drought, while DP 2020 B3XF was the most sensitive to drought, with a 45–48% reduction in the traits. Under DS conditions, biochar at the rate of 12.5 t ha⁻¹ had the highest SCW and LW, and the lowest reduction in BN, BW, SCW, and LW due to drought, which was significantly different from the non-biochar control, and no genotype × biochar interaction was detected. However, biochar had no positive effects on cotton productivity under non-drought conditions. This study has demonstrated the positive effects of biochar on cotton yield and yield components in alleviating drought stress, laying the foundation for more follow-up studies toward its utility in cotton production in semi-arid and arid areas. Full article

Cotton is an important cash crop globally. Cotton fiber is the main economic product of cotton plants. Phosphorus, as one of the essential nutrients, plays an important role in plant growth and development. However, few studies focus on phosphorus regulating fiber elongation. In this study, we used the cotton ovule culture system in vitro to explore the effects of various phosphorus levels on fiber and ovule growth, and screened for phosphorus-responsive factor, as well as revealed its action mechanism. The results indicated that fiber elongation was more sensitive than ovule growth to phosphorus deficiency. GhPHR1, a homolog of phosphate starvation response 1 (PHR1) in upland cotton, was significantly upregulated in fibers and ovules under phosphorus-deficient conditions. GhPHR1 directly binds to the promoter of the glucosylceramide synthase gene in cotton (GhGCS1) and positively regulates its expression. Overexpressing GhGCS1 enhanced phosphorus uptake and transport in cotton, increased phosphorus content in fiber cells, and promoted fiber cell elongation. Conversely, downregulating GhGCS1 reduced phosphorus content in fiber cells and suppressed fiber elongation. These findings demonstrate the importance of the GhPHR1-GhGCS1 molecular module in regulating fiber cell elongation and elucidate the molecular mechanism by which phosphorus influences fiber elongation. Full article

Drought is a major problem affecting upland rice growth worldwide, including in northeast Thailand, with insufficient irrigation, where drought stress leads to reduced yields and may affect the functional compound content of rice grains. This research aimed to study the efficacy of arbuscular mycorrhizal fungi (AMF) Rhizophagus variabilis KS-02 and endophytic fungi (EPF) Trichoderma zelobreve PBMP16 on promoting the growth and accumulation of functional substances in upland black rice under drought conditions. Factorial experiments in a randomized complete block design (RCBD) were conducted by cultivating rice inoculated with AMF and EPF as well as co-inoculated with AMF+EPF under three watering conditions: 100% field capacity (FC), 66% FC, and 33% FC. The results show that both AMF, EPF improved some plant growth parameters and physiological performance under both well-watered and water-limited conditions. Inoculating plants with fungi increased the production of enzymes APX, CAT, and GR, as well as proline, which helps plants tolerate water deficit stress. Functional grain quality, including phenolic compounds, anthocyanins, and antioxidant activity, was also increased by fungal inoculation. While co-inoculation provided advantages for certain parameters, particularly antioxidant activity and biomass, single inoculation with AMF or EPF was equally effective or superior for specific traits depending on the level of water stress. Overall, this report shows that both AMF and EPF contribute to improving the productivity and functional quality of upland black rice under drought conditions, with treatment effects varying according to fungal type and water availability. Full article

Shanlan upland rice is a unique genetic resource from the mountainous regions of Hainan, China, yet its genetic diversity and agronomic potential remain poorly characterized. This study systematically evaluated 114 Shanlan upland rice landraces using phenotypic assessment and 38 genome-wide Insertion/Deletion (InDel) markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, and yield components. The molecular analysis revealed a moderate level of genetic diversity (average PIC = 0.43) and consistently grouped the landraces into three distinct genetic subpopulations. To facilitate efficient germplasm management, we developed a DNA fingerprinting system using a reduced set of 19 core InDel markers, which was integrated with a phenotypic QR code database. Furthermore, a network-based strategy identified a core collection of 54 accessions, streamlining the resource for future breeding and conservation efforts. These findings provide a robust molecular framework for the conservation and genetic improvement of Shanlan upland rice. Full article

Background: Sucrose metabolism plays a crucial role in plant responses to abiotic stresses such as drought and high temperatures, significantly influencing plant growth and yield formation. In higher plants, the second step in sucrose bioconversion involves sucrose phosphate phosphatase (SPP) hydrolyzing sucrose-6-phosphate to form sucrose. This study determined the number of SPP gene family members in upland cotton (Gossypium hirsutum), systematically analyzed their fundamental characteristics, physicochemical properties, phylogenetic relationships, chromosomal localization, and expression patterns across different tissues and under various abiotic stresses. Methods: The SPP gene family in hirsutum was identified using Hidden Markov Models (HMMER) and the NCBI Conserved Domain Database (NCBI CDD), and its physico-chemical properties were analyzed via the SOPMA online analysis website. Phylogenetic relationships were determined using MEGA 12.0 software. Promoter regions were analyzed with PlantCARE, sequence patterns were identified via MEME, and transcriptome data were downloaded from the CottonMD database. Results: This study identified four members of the hirsutum SPP gene family, with amino acid lengths ranging from 335 to 1015, molecular weights between 38.38 and 113.28 kDa, and theoretical isoelectric points (pI) between 5.39 and 6.33. These genes are localized across four chromosomes. The SPP gene family in hirsutum exhibits closer phylo-genetic relationships with SPP genes in Arabidopsis thaliana and Chenopodium quinoa. Their promoter regions are rich in cis-elements associated with multiple abiotic stress resistance functions, and their expression patterns vary across different tissues and under different abiotic stress conditions. Conclusions: The GhSPP gene may play an important role in the growth and development of upland cotton and its responses to salt stress and drought. Therefore, it could be considered as a candidate gene for future functional analysis of cotton resistance to salt and drought stress. Full article