Salt tolerance during germination is a complex trait involving coordinated regulation of multiple developmental processes, yet its shared genetic architecture remains largely unknown. Here, we integrated genome-wide association study (GWAS) and multi-trait GWAS (MTAG) to dissect the pleiotropic basis of salt tolerance in 355 upland cotton accessions by using 2.52 million high-quality SNPs. A total of 517 and 534 significantly associated SNPs were identified by GWAS and MTAG, respectively, revealing 79 salt-tolerance-related QTLs. A major locus, qRST-D08-8, was refined to a 73.8 kb interval containing 12 candidate genes, among which GhWRKY21-D08 (Ghir_D08G020650) was supported by expression profiling and functional assays. Virus-induced gene silencing (VIGS) indicated that GhWRKY21-D08 enhances salt tolerance in cotton by increasing antioxidant enzyme activities to scavenge reactive oxygen species (ROS). Notably, a cis-regulatory SNP (-718 C/A) in the promoter region significantly altered transcriptional activity, linking regulatory variation to phenotypic divergence. Population genetic analyses suggest that the favorable haplotype (Hap1) has undergone recent positive selection during breeding without compromising yield-related traits. These findings highlight the role of cis-regulatory variation in shaping adaptive traits and provide a valuable target for molecular breeding of salt-tolerant cotton.

Improving lint percentage (LP) through genetic breeding is crucial for stabilizing cotton fiber yield. To dissect the genetic basis of LP, a recombinant inbred line (RIL) population consisting of 300 lines were derived from a cross between the high-LP cultivar ‘CRI50’ and the low-LP standard line ‘TM-1’. Multi-environment phenotypic investigations revealed that LP showed a continuous distribution with high heritability (H²=81.65%), indicating complex genetic control with strong genetic determination. Bulked segregant RNA-seq (BSR-seq) analysis of extreme LP pools identified a major quantitative trait locus (QTL), qLP-D03-1, on chromosome D03. Further GWAS and QTL hotspot analysis narrowed the candidate region to approximately 250 kb on chromosome D03. Within this region, GhLPA1 (Ghicr24_D03G124100), encoding a ribosomal protein with extraribosomal functions, was identified as the key candidate gene, and its function was confirmed by virus-induced gene silencing (VIGS) analysis. Haplotype analysis showed that the ‘CRI50’-type allele (Hap1) conferred significantly higher LP than the ‘TM-1’-type allele (Hap2). Furthermore, a kompetitive allele-specific PCR (KASP) marker developed from a functional SNP in the 3′ untranslated region (UTR) of GhLPA1 effectively differentiated genotypes with contrasting LP, which providing a valuable marker for marker-assisted selection (MAS) in cotton breeding.

Efficient genetic transformation technologies are crucial for exploring plant gene functions and promoting molecular breeding. However, the widely used genetic transformation technology mediated by Agrobacterium tumefaciens is time-consuming and genotype-dependent, which limits the high-throughput functional characterization of cotton genes. The transformation system mediated by Agrobacterium rhizogenes (ARM) presents a rapid and effective alternative, but previous ARM techniques in cotton suffered from low efficiency and complicated operation. Here, we optimized the traditional ARM method suitable for nonsterile environments. The two-step ARM technology we used effectively enhanced the transformation efficiency within the upland cotton. The entire process only takes one month, and this system is applicable to various upland cotton varieties, with a maximum transformation efficiency of up to 100%. Results have shown that the ARM method only produces transgenic roots rather than whole transgenic plants. The obtained transgenic hairy roots can be employed to endogenous gene silencing and gene overexpression, enabling subcellular localization analysis and in-depth exploration of gene functions. In summary, we have first described a rapid, universal, efficient, and nonsterile ARM system in cotton, offering a reliable foundation for the cotton gene functional study and the advancement of genetic improvement breeding.

Peptide hormones are essential signaling molecules in plants, playing critical roles in regulating growth and development, stress responses, and crop genetic improvement. However, the full extent of their functions, functional redundancy among different peptide hormones, signaling mechanisms between ligand and receptor pathways, and peptide hormones-mediated regulation of plant development and environmental adaptability are still not fully understood. In this study, recent advances in understanding the formation and functions of plant peptide hormones, distinguishing between non-secretory and secretory peptides and their respective physiological roles are reviewed. These peptide hormones interact intricately with receptor kinases to regulate multiple signal transduction pathways. Plant peptide hormones are involved in cell proliferation and differentiation within both shoot apical and root apical meristems, as well as in the development of various organs. They also play a central role in plant reproduction, particularly in coordinating male-female gametophyte interactions for successful fertilization. Furthermore, plant peptide hormones contribute to abiotic stress responses and immune responses against biotic stresses. An overview of the multifaceted roles of plant peptide hormones in growth, development, and environmental adaptability, emphasizing their importance in plant biology are presented. Understanding the complex functions of these peptide hormones lays the foundation for developing strategies to enhance crop resilience and productivity.

Among different abiotic stress salinity is a key factor limiting the growth and productivity of faba bean (Vicia faba L.) plants. In recent years, nanotechnology has been applied to mitigate the harmful effects of salt stress on various plant species. Nanoparticles are compounds with one or more dimensions between 1 and 100 nanometers and differs from their bulk material counterparts. Previous studies have shown that nanoparticles including Selenium can be applied to mitigate the harmful effects on various plant species. Therefore, the present study aims to evaluate the efficacy of Selenium nanoparticles (SeNPs) in mitigating salinity stress in faba bean. To investigate this, we exposed faba beans plants with three different salt concentrations (0 mM, 40 mM, and 80 mM of NaCl) then treated it with foliar sprays of SeNPs at three varying concentrations (0 ppm, 5 ppm, and 10 ppm). Under salinity stress the faba beans plants were observed to be significantly impaired in plant growth and photosynthetic activity. Furthermore, increased levels of malondialdehyde (MDA) in faba beans exposed to salinity indicated significant cellular damage. However, the application of SeNPs under salinity conditions enhanced plant height and chlorophyll content compared to the control. SeNPs also boosted the activity of key antioxidant defense enzymes, including catalase (CAT), ascorbic peroxidase (APX), and polyphenol oxidase (PPO). In addition, they decreased MDA levels and increased proline and phenol concentrations. These findings suggest that SeNPs improved plant health and vitality by mitigating oxidative stress caused by salt. In conclusion, applying SeNPs spray effectively reduced the harmful effects of salt stress on faba bean plants.

Fibrillins (FBNs) are indispensable for plant growth and development, orchestrating multiple physiological processes. However, the precise functional role of FBNs in cotton fiber development remains uncharacterized. This study reports a genome-wide characterization of the FBN gene family in cotton. A total of 28 GhFBN genes were identified in upland cotton, with systematic analyses of their phylogenetic relationships, protein motifs, gene structures, and hormone-responsive cis-regulatory elements. Expression profiling of GhFBN1A during fiber development revealed stage-specific activity across the developmental continuum. Transcriptomic analyses following hormone treatments demonstrated upregulation of GhFBN family members, implicating their involvement in hormone-mediated regulatory networks governing fiber cell development. Collectively, this work presents a detailed molecular characterization of cotton GhFBNs and establishes a theoretical foundation for exploring their potential applications in cotton breeding programs aimed at improving fiber quality.

The length of fruit branches significantly influences plant architecture in upland cotton (Gossypium hirsutum L.), which is crucial for optimizing fiber yield and quality. In this study, a comprehensive genome-wide association study was conducted based on whole-genome resequencing data that identified 249 significant SNPs associated with fruit branch length (FBL), forming 79 distinct quantitative trait loci (QTL) regions. Notably, stable QTL regions qFBL-A10-4 and qFBL-D03-17 were identified, harboring key candidate genes such as Ghir_A10G014390 and Ghir_D03G011390. Superior haplotypes of these genes significantly enhance FBL, fiber yield, and quality, offering valuable targets for cotton breeding programs focused on optimizing plant architecture and productivity.

Cotton (Gossypium spp.), an economically and strategically significant crop in China, faces challenges such as rising cultivation costs and conflicts between grain and cotton cultivation. These challenges underscore the need for enhancing yields per unit area. In response, this study employs deep learning techniques, combined with high-throughput angle detection, to conduct genome-wide association studies (GWAS) on 355 upland cotton accessions, identify key SNPs and candidate genes for plant architecture by fruit branch angle (FBA) influences planting density, yield, and mechanized harvesting. A convolutional neural network (CNN)-based software was developed for rapid and accurate branch angle detection, showing high correlation with both AutoCAD and manual measurements. Significant phenotypic variation in FBA was observed across various cotton planting regions, with the Northwest Inland Region (NIR) exhibiting notably smaller angles. In total, 107 significant Single Nucleotide Polymorphisms (SNPs) were detected across 45 quantitative trait loci (QTL), and three potential candidate genes (Ghir_A11G034910, Ghir_D05G007790, and Ghir_D05G031350) were identified, providing insights into the genetic basis of FBA and presenting valuable genetic resources for cotton breeding programs.

Serine hydroxymethyltransferase (SHMT) is an important conserved protein involved in one-carbon metabolism pathways, essential for plant growth and environmental adaptation. Despite its significance, the SHMT gene family in Gossypium hirsutum, a globally major economic crop for textile materials and strategic resources, has not been systematically identified and studied. In this research, 20 GhSHMT genes were identified and analyzed. They were systematically categorized into four groups based on evolutionary analysis. Collinearity analysis suggested the significant role of whole-genome or segmental duplication events in the gene family expanding. Examination of promoter elements indicated the potential participation of GhSHMTs in abiotic stress, and further transcriptome expression analysis demonstrated that GhSHMT11s responded to salt stress treatment. GhSHMT11s were localized in mitochondria and could form homo-complex. Silencing GhSHMT11s using VIGS system resulted in increased accumulation of reactive oxygen species and a significant decrease in net photosynthetic rate in cotton leaves, consequently leading to a notable reduction in biomass. Heterologous overexpression of GhSHMT11-A in Arabidopsis led to improved salt tolerance by decreasing the reactive oxygen species accumulation. This study provided valuable insights into the functional role of the GhSHMT gene family and identified a potential positive candidate gene for molecular breeding of salt tolerance in cotton.

BACKGROUND:Monoacylglycerol lipase (MAGL) genes belong to the alpha/beta hydrolase superfamily, catalyze the terminal step of triglyceride (TAG) hydrolysis, converting monoacylglycerol (MAG) into free fatty acids and glycerol.RESULTS:In this study, 30 MAGL genes in upland cotton have been identified, which have been classified into eight subgroups. The duplication of GhMAGL genes in upland cotton was predominantly influenced by segmental duplication events, as revealed through synteny analysis. Furthermore, all GhMAGL genes were found to contain light-responsive elements. Through comprehensive association and haplotype analyses using resequencing data from 355 cotton accessions, GhMAGL3 and GhMAGL6 were detected as key genes related to lipid hydrolysis processes, suggesting a negative regulatory effect.CONCLUSIONS:In summary, MAGL has never been studied in upland cotton previously. This study provides the genetic mechanism foundation for the discover of new genes involved in lipid metabolism to improve cottonseed oil content, which will provide a strategic avenue for marker-assisted breeding aimed at incorporating desirable traits into cultivated cotton varieties.

Cotton is essential for the textile industry as a primary source of natural fibers. However, environmental factors like drought present significant challenges to its cultivation, adversely affecting both production levels and fiber quality. Enhancing cotton’s drought resilience has the potential to reduce yield losses and support the growth of cotton farming. In this study, the cotton calcium-dependent protein kinase GhCDPK16 was characterized, and the transcription level of GhCDPK16 was significantly upregulated under drought and various stress-related hormone treatments. Physiological analyses revealed that the overexpression of GhCDPK16 improved drought stress resistance in Arabidopsis by enhancing osmotic adjustment capacity and boosting antioxidant enzyme activities. In contrast, silencing GhCDPK16 in cotton resulted in increased dehydration compared with the control. Furthermore, reduced antioxidant enzyme activities and downregulation of ABA-related genes were observed in GhCDPK16-silenced plants. These findings not only enhanced our understanding of the biological functions of GhCDPK16 and the mechanisms underlying drought stress resistance but also underscored the considerable potential of GhCDPK16 in improving drought resilience in cotton.

Transcription Factors (TFs) are key regulators of how plants grow and develop. Among the diverse TF families, the Glabrous-enhancer binding protein (GeBP) family plays a key role in trichome initiation and leaf development. The specific roles of GeBP TFs in plants remain largely unexplored, although GeBP transcription factors play important roles in plants. This study identified 16 GhGeBP genes in Gossypium hirsutum, ranging from 534 bp (GhGeBP14) to 1560 bp (GhGeBP2). Phylogenetic analysis grouped 16 GhGeBP genes clustered into three subgroups, unevenly distributed across 14 chromosomes. Analysis of the cis-acting elements revealed 408 motifs in the 2 kb upstream regions of the promoters, including stress-responsive, phytohormone-responsive, and light-responsive elements. Tissue-specific expression analysis showed 8 GhGeBP genes were highly expressed across all tissues, while GhGeBP4 and GhGeBP12 were down-regulated under conditions of drought, salt, cold, and heat stress. A genome-wide association study (GWAS) identified GhGeBP4 was associated with fiber micronaire (FM) and fiber strength (FS), while GhGeBP9 was linked to the node of the first fruiting branch (NFFB) and flowering time (FT). Haplotype analysis revealed that GhGeBP4-HAP2 exhibited higher fiber quality traits, while GhGeBP9-HAP2 was associated with early maturity. The results of this study offer significant insights that are worthy of further investigation into the role of the GhGeBP gene family in G. hirsutum and promising targets for marker-assisted selection strategies in cotton breeding programs, particularly for improving fiber quality and early maturity traits.

BACKGROUND:Cotton serves as a primary source of natural fibers crucial for the textile industry. However, environmental elements such as drought have posed challenges to cotton cultivation, resulting in adverse impacts on both production and fiber quality. Improving cotton's resilience to drought could mitigate yield losses and foster the expansion of cotton farming. Rab7 protein, widely present in organisms, controls the degradation and recycling of cargo, and has a potential role in biotic and abiotic tolerance. However, comprehensive exploration of the Rab7 gene family in Gossypium remains scarce. RESULTS:Herein, we identified a total of 10, 10, 20, and 20 Rab7 genes through genome-wide analysis in Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. Collinearity analysis unveiled the pivotal role of whole genome or segmental duplication events in the expansion of GhRab7s. Study of gene architecture, conserved protein motifs, and domains suggested the conservation of structure and function throughout evolution. Exploration of cis-regulatory elements revealed the responsiveness of GhRab7 genes to abiotic stress, corroborated by transcriptome analysis under diverse environmental stresses. Notably, the greatly induced expression of GhRab7B3-A under drought treatment prompted us to investigate its function through virus-induced gene silencing (VIGS) assays. Silencing GhRab7B3-A led to exacerbated dehydration and wilting compared with the control. Additionally, inhibition of stomatal closure, antioxidant enzyme activities and expression patterns of genes responsive to abiotic stress were observed in GhRab7B3-A silenced plants. CONCLUSIONS:This study sheds light on Rab7 members in cotton, identifies a gene linked to drought stress, and paves the way for additional investigation of Rab7 genes associated with drought stress tolerance.

The SAUR (small auxin-up RNA) family constitutes a category of genes that promptly respond to the hormone auxin and play a pivotal role in diverse biological processes encompassing plant growth and the response to abiotic stress. Santalum album L., a semi-parasitic evergreen tree, is renowned for its economically valuable essential oils, positioning it among the most prized tree species. In this study, a meticulous identification and comprehensive analysis of 43 SAUR genes was conducted within S. album. Based on phylogenetic relationships, the SaSAUR genes were systematically categorized into five groups. A collinearity analysis revealed intriguing insights, disclosing 14 segmental duplications and 9 tandem duplications within the SaSAUR genes, emphasizing the pivotal role of duplication in the expansion of this gene family. Noteworthy variations in the expression levels of SaSAUR genes were observed by delving into the SaSAUR transcriptome data from various tissues, including leaves, roots, and heartwood, as well as under salt-stress conditions. Notably, SaSAUR08 and SaSAUR13 were significantly upregulated in heartwood compared with roots and leaves, while SaSAUR18 was markedly more expressed in roots compared with heartwood and leaves. Furthermore, SaSAUR27 and SaSAUR28 were found to respond closely to salt stress, hinting at their potential involvement in the salt-stress response mechanism. This research offers a comprehensive investigation of SAUR genes in S. album and establishes a foundation for future exploration of the SAUR gene family, particularly its relation to growth and salt-stress responses.

本实验基于多重PCR与膜芯片核酸杂交技术,旨在构建同时检测饲料及原料中6种致病微生物的检测方法,并对方法的特异性、检出限及适用性进行了验证.结果表明:该方法具有良好重复性、再现性和特异性,综合检出限为培养前1～5 CFU/mL(核酸样本为0.01 ng/μL),可实现对沙门氏菌、大肠埃希氏菌O157∶H7、金黄色葡萄球菌、志贺氏菌、单核细胞增生李斯特氏菌、副溶血性弧菌等6种致病微生物的高通量检测,检测结果与标准方法一致.多重PCR 膜芯片技术可成为饲料及原料中微生物污染快速、高通量筛查新的技术手段.

EDITORIAL article Front. Plant Sci., 20 July 2023Sec. Plant Abiotic Stress Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1246964

Storage proteins are essential for seed germination and seedling growth, as they provide an indispensable nitrogen source and energy. Our previous report highlighted the defective endosperm development in the serine hydroxymethyltransferase 4 (OsSHMT4) gene mutant, floury endosperm20-1 (flo20-1). However, the alterations in storage protein content and distribution within the flo20-1 endosperm remained unclear. Here, the immunocytochemistry analyses revealed a deficiency in storage protein accumulation in flo20-1. Electron microscopic observation uncovered abnormal morphological structures in protein bodies (PBI and PBII) in flo20-1. Immunofluorescence labeling demonstrated that aberrant prolamin composition could lead to the subsequent formation and deposition of atypical structures in protein body I (PBI), and decreased levels of glutelins and globulin resulted in protein body II (PBII) malformation. Further RNA-seq data combined with qRT-PCR results indicated that altered transcription levels of storage protein structural genes were responsible for the abnormal synthesis and accumulation of storage protein, which further led to non-concentric ring structural PBIs and amorphous PBIIs. Collectively, our findings further underscored that OsSHMT4 is required for the synthesis and accumulation of storage proteins and storage organelle formation in endosperm cells.

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) mainly promoted the assembly of the SNARE complex to drive the final membrane fusion step of membrane transport. Previous research on R-SNAREs has mainly focused on development and growth and has rarely been involved in abiotic stress, especially in cotton. Here, we performed a comprehensive analysis of R-SNARE genes in upland cotton. In total, 51 Gh-R-SNARE genes across six phylogenetic groups were unevenly distributed on 21 chromosomes. Cis elements related to plant growth and response to abiotic stress responses were found in the promoter region of Gh-R-SNAREs. Nine Gh-R-SNARE genes were obviously upregulated under drought stress conditions by RNA-seq and qRT–PCR analysis. Among them, GhVAMP72l might be the key candidate gene contributing to drought stress tolerance in cotton by virus-induced gene silencing (VIGS) assay. These results provide valuable insights for the functional analysis of cotton R-SNAREs in response to drought stress and highlight potential beneficial genes for genetic improvement and breeding in cotton.

[目的]对棉花GA20ox基因GhGA20ox6进行克隆和初步的功能验证,分析其对棉花株高的影响.[方法]通过分子克隆的方法,在陆地棉标准系TM-1的茎中成功获得GhGA20ox6基因;利用进化树分析、氨基酸序列比对明确其与拟南芥、水稻中同源基因的进化关系;利用实时定量聚合酶链式反应分析GhGA20ox6在TM-1中的组织特异性表达;利用亚细胞定位分析其在细胞中的定位,并在拟南芥中进行了功能分析.[结果]GhGA20ox6的开放阅读框长度为1155 bp,编码384个氨基酸残基,编码产物的分子质量为43.32 ku,预测的等电点为6.37.进化树分析显示GhGA20ox6与水稻绿色革命基因sd1(OsGA20ox2)的相似性最高.组织特异性表达分析发现,GhGA20ox6在TM-1茎中的表达量高于其在其他器官中的表达量.在烟草表皮细胞的亚细胞定位分析发现,GhGA20ox6蛋白定位在细胞膜.在拟南芥中过表达GhGA20ox6能显著促使赤霉素不敏感矮化基因GID1(gibberellin insensitive dwarf1)表达量上升,转基因拟南芥的株高增加、抽薹提前.[结论]通过对GhGA20ox6的克隆和功能分析,推测它可能与棉花体内的赤霉素合成相关,进而影响棉花株高.这些结果为进一步在分子水平验证GhGA20ox6在棉花生长发育中的生物学功能奠定基础.

In the process of growth and development, cotton exhibits premature senescence under various abiotic stresses, impairing yield and fiber quality. NAC (NAM, ATAF1,2, and CUC2) protein widely distributed in land plants, play the critical role in responding to abiotic stress and regulating leaf senescence. We have identified and functional analyzed a NAM domain gene GhNAC82 in upland cotton, it was located on the A11 chromosome 4,921,702 to 4,922,748 bp, only containing one exon. The spatio-temporal expression pattern analysis revealed that it was highly expressed in root, torus, ovule and fiber development stage. The results of qRT-PCR validated that GhNAC82 negatively regulated by salt stress, drought stress, H2O2 stress, IAA treatment, and ethylene treatment, positively regulated by the ABA and MeJA treatment. Moreover, heterologous overexpression of GhNAC82 results in leaf premature senescence and delays root system development in Arabidopsis thaliana. The phenotype of delayed-senescence was performed after silencing GhNAC82 by VIGS in premature cotton. Taken together, GhNAC82 was involved in different abiotic stress pathways and play important roles in negatively regulating leaf premature senescence.