Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application

Identification of AGO2 and PLEC genes polymorphisms in Hu sheep and their relationship with body size traits

The body size traits are major traits in livestock, which intuitively displays the development of the animal's bones and muscles. This study used PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR) to analyze the Single-nucleotide polymorphism and expression characteristics of Argonaute RISC catalytic component 2 (AGO2) and Plectin (PLEC) genes in Hu sheep. Two intron mutations were found in Hu sheep, which were AGO2 g.51700 A > C and PLEC g.23157 C > T, respectively. Through association analysis of two mutation sites and body size traits, it was found that AGO2 g.51700 A > C mainly affects the chest and cannon circumference of Hu sheep of while PLEC g.23157 C mainly affects body height and body length. The combined genotypes of AGO2 and PLEC genes with body size traits showed SNPs at the AGO2 g.51700 A > C and PLEC g.23157 C > T loci significantly improved the body size traits of Hu sheep. In addition, the AGO2 gene has the highest expression levels in the heart, rumen, and tail fat, and the PLEC gene is highly expressed in the heart. These two loci can provide new research ideas for improving the body size traits of Hu sheep.

Investigating the ecological implications of nanomaterials: Unveiling plants' notable responses to nano-pollution

The rapid advancement of nanotechnology has led to unprecedented innovations; however, it is crucial to analyze its environmental impacts carefully. This review thoroughly examines the complex relationship between plants and nanomaterials, highlighting their significant impact on ecological sustainability and ecosystem well-being. This study investigated the response of plants to nano-pollution stress, revealing the complex regulation of defense-related genes and proteins, and highlighting the sophisticated defense mechanisms in nature. Phytohormones play a crucial role in the complex molecular communication network that regulates plant responses to exposure to nanomaterials. The interaction between plants and nano-pollution influences plants' complex defense strategies. This reveals the interconnectedness of systems of nature. Nevertheless, these findings have implications beyond the plant domain. The incorporation of hyperaccumulator plants into pollution mitigation strategies has the potential to create more environmentally sustainable urban landscapes and improve overall environmental resilience. By utilizing these exceptional plants, we can create a future in which cities serve as centers of both innovation and ecological balance. Further investigation is necessary to explore the long-term presence of nanoparticles in the environment, their ability to induce genetic changes in plants over multiple generations, and their overall impact on ecosystems. In conclusion, this review summarizes significant scientific discoveries with broad implications beyond the confines of laboratories. This highlights the importance of understanding the interactions between plants and nanomaterials within the wider scope of environmental health. By considering these insights, we initiated a path towards the responsible utilization of nanomaterials, environmentally friendly management of pollution, and interdisciplinary exploration. We have the responsibility to balance scientific advancement and environmental preservation to create a sustainable future that combines nature's wisdom with human innovation.

Systematically and Comprehensively Understanding the Regulation of Cotton Fiber Initiation: A Review

Cotton fibers provide an important source of raw materials for the textile industry worldwide. Cotton fiber is a kind of single cell that differentiates from the epidermis of the ovule and provides a perfect research model for the differentiation and elongation of plant cells. Cotton fiber initiation is the first stage throughout the entire developmental process. The number of fiber cell initials on the seed ovule epidermis decides the final fiber yield. Thus, it is of great significance to clarify the mechanism underlying cotton fiber initiation. Fiber cell initiation is controlled by complex and interrelated regulatory networks. Plant phytohormones, transcription factors, sugar signals, small signal molecules, functional genes, non-coding RNAs, and histone modification play important roles during this process. Here, we not only summarize the different kinds of factors involved in fiber cell initiation but also discuss the mechanisms of these factors that act together to regulate cotton fiber initiation. Our aim is to synthesize a systematic and comprehensive review of different factors during fiber initiation that will provide the basics for further illustrating these mechanisms and offer theoretical guidance for improving fiber yield in future molecular breeding work.

QTL Verification and Candidate Gene Screening of Fiber Quality and Lint Percentage in the Secondary Segregating Population of Gossypium hirsutum

Fiber quality traits, especially fiber strength, length, and micronaire (FS, FL, and FM), have been recognized as critical fiber attributes in the textile industry, while the lint percentage (LP) was an important indicator to evaluate the cotton lint yield. So far, the genetic mechanism behind the formation of these traits is still unclear. Quantitative trait loci (QTL) identification and candidate gene validation provide an effective methodology to uncover the genetic and molecular basis of FL, FS, FM, and LP. A previous study identified three important QTL/QTL cluster loci, harboring at least one of the above traits on chromosomes A01, A07, and D12 via a recombinant inbred line (RIL) population derived from a cross of Lumianyan28 (L28) × Xinluzao24 (X24). A secondary segregating population (F2) was developed from a cross between L28 and an RIL, RIL40 (L28 × RIL40). Based on the population, genetic linkage maps of the previous QTL cluster intervals on A01 (6.70-10.15 Mb), A07 (85.48-93.43 Mb), and D12 (0.40-1.43 Mb) were constructed, which span 12.25, 15.90, and 5.56 cM, with 2, 14, and 4 simple sequence repeat (SSR) and insertion/deletion (Indel) markers, respectively. QTLs of FL, FS, FM, and LP on these three intervals were verified by composite interval mapping (CIM) using WinQTL Cartographer 2.5 software via phenotyping of F2 and its derived F2:3 populations. The results validated the previous primary QTL identification of FL, FS, FM, and LP. Analysis of the RNA-seq data of the developing fibers of L28 and RIL40 at 10, 20, and 30 days post anthesis (DPA) identified seven differentially expressed genes (DEGs) as potential candidate genes. qRT-PCR verified that five of them were consistent with the RNA-seq result. These genes may be involved in regulating fiber development, leading to the formation of FL, FS, FM, and LP. This study provides an experimental foundation for further exploration of these functional genes to dissect the genetic mechanism of cotton fiber development.

A Simplified Microscopy Technique to Rapidly Characterize Individual Fiber Traits in Cotton

Recent advances in phenotyping techniques have substantially improved the ability to mitigate type-II errors typically associated with high variance in phenotyping data sets. In particular, the implementation of automated techniques such as the High-Volume Instrument (HVI) and the Advanced Fiber Information System (AFIS) have significantly enhanced the reproducibility and standardization of various fiber quality measurements in cotton. However, micronaire is not a direct measure of either maturity or fineness, lending to limitations. AFIS only provides a calculated form of fiber diameter, not a direct measure, justifying the need for a visual-based reference method. Obtaining direct measurements of individual fibers through cross-sectional analysis and electron microscopy is a widely accepted standard but is time-consuming and requires the use of hazardous chemicals and specialized equipment. In this study, we present a simplified fiber histology and image acquisition technique that is both rapid and reproducible. We also introduce an automated image analysis program that utilizes machine learning to differentiate good fibers from bad and to subsequently collect critical phenotypic measurements. These methods have the potential to improve the efficiency of cotton fiber phenotyping, allowing for greater precision in unravelling the genetic architecture of critical traits such as fiber diameter, shape, areas of the secondary cell wall/lumen, and others, ultimately leading to larger genetic gains in fiber quality and improvements in cotton.

Using association mapping and local interval haplotype association analysis to improve the cotton drought stress response

Drought stress has a serious impact on the growth and development of cotton. To explore the relevant molecular mechanism of the drought stress response in cotton, gene mapping based on the QTL interval mapped by simplified genome BSA-seq of the drought-resistance-related RIL population was performed. A QTL region spanning 2.02 Mb on chromosome D07 was selected, and 201 resource materials were genotyped using 9 KASP markers in the interval. After local interval haplotype association analysis, the overlap of the 110 kb peak region confirmed the reliability of this region, and at the same time, the role of GhGF14-30, the only gene in the overlapping region, was modeled in the response of cotton to drought stress. qRTPCR analysis of the materials and population parents proved that this gene plays a role in the drought stress response in cotton. Virus-induced gene silencing proved the importance of this gene in drought-sensitive materials, and drought-resistance-related marker genes also proved that the GhGF14-30 gene may play an important role in the ABA and SOS signaling pathways. This study provides a basis for mining drought stress response functional genes in cotton and lays the foundation for the molecular mechanism of the GhGF14-30 gene in response to drought stress in cotton.

2-NBDG Uptake in Gossypium hirsutum in vitro ovules: exploring tissue-specific accumulation and its impact on hexokinase-mediated glycolysis regulation

Fluorescent glucose derivatives are valuable tools as glucose analogs in plant research to explore metabolic pathways, study enzyme activity, and investigate cellular processes related to glucose metabolism and sugar transport. They allow visualization and tracking of glucose uptake, its utilization, and distribution within plant cells and tissues. This study investigates the phenotypic and metabolic impact of the exogenously fed glucose derivative, 2-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-2-deoxyglucose) (2-NBDG) on the fibers of Gossypium hirsutum (Upland cotton) ovule in vitro cultures. The presence of 2-NBDG in the culture medium did not lead to macroscopic morphological alterations in ovule and fiber development or to the acquisition of fluorescence or yellow coloration. Confocal laser scanning microscope imaging and chromatographic analysis of cotton ovules' outer rim cross-sections showed that the 2-NBDG is transported from the extracellular space and accumulated inside some outer integument cells, epidermal cells, and fertilized epidermal cells (fibers), but is not incorporated into the cell walls. Untargeted metabolic profiling of the fibers revealed significant changes in the relative levels of metabolites involved in glycolysis and upregulation of alternative energy-related pathways. To provide biochemical and structural evidence for the observed downregulation of glycolysis pathways in the fibers containing 2-NBDG, kinetics analysis and docking simulations were performed on hexokinase from G. hirsutum (GhHxk). Notably, the catalytic activity of heterologously expressed recombinant active GhHxk exhibited a five-fold decrease in reaction rates compared to D-glucose. Furthermore, GhHxk exhibited a linear kinetic behavior in the presence of 2-NBDG instead of the Michaelis-Menten kinetics found for D-glucose. Docking simulations suggested that 2-NBDG interacts with a distinct binding site of GhHxk9, possibly inducing a conformational change. These results highlight the importance of considering fluorescent glucose derivatives as ready-to-use analogs for tracking glucose-related biological processes. However, a direct comparison between their mode of action and its extrapolation into biochemical considerations should go beyond microscopic inspection and include complementary analytical techniques.

Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population

Textiles made from cotton fibers are flammable and thus often include flame retardant additives for consumer safety. Transgressive segregation in multi-parent populations facilitates new combinations of alleles of genes and can result in traits that are superior to those of any of the parents. A screen of 257 recombinant inbred lines from a multi-parent advanced generation intercross (MAGIC) population for naturally enhance flame retardance (FR) was conducted. All eleven parents, like all conventional white fiber cotton cultivars produce flammable fabric. MAGIC recombinant inbred lines (RILs) that produced fibers with significantly lower heat release capacities (HRC) as measured by microscale combustion calorimetry (MCC) were identified and the stability of the phenotypes of the outliers were confirmed when the RILs were grown at an additional location. Of the textiles fabricated from the five superior RILs, four exhibited the novel characteristic of inherent flame resistance. When exposed to open flame by standard 45° incline flammability testing, these four fabrics self-extinguished. To determine the genetic architecture of this novel trait, linkage, epistatic and multi-locus genome wide association studies (GWAS) were conducted with 473k SNPs identified by whole genome sequencing (WGS). Transcriptomes of developing fiber cells from select RILs were sequenced (RNAseq). Together, these data provide insight into the genetic mechanism of the unexpected emergence of flame-resistant cotton by transgressive segregation in a breeding program. The incorporation of this trait into global cotton germplasm by breeding has the potential to greatly reduce the costs and impacts of flame-retardant chemicals.

Fine-mapping and candidate gene analysis of qFL-c10-1 controlling fiber length in upland cotton (Gossypium hirsutum L.)

A fiber length QTL, qFL-c10-1, was fine-mapped to a 96.5-kb region containing one gene that has not been characterized in plants. Fiber length is an important component of cotton fiber quality, which is associated with other quality properties such as fiber strength, fiber maturity, and fineness. In our previous studies, a stable QTL qFL-c10-1 controlling fiber length had been identified on chromosome A10 in an upland cotton recombinant inbred line (RIL) population from a cross between Jimian5 and DH962. To fine-map qFL-c10-1, an F₂ population with 1081 individual plants from a cross between a recombinant line DJ61 and Jimian5 was established. Using linkage analysis and progeny recombination experiment, qFL-c10-1 was mapped into a 96.5-kb genomic region that just contained one proper transcript Ghir_A10G022020 (described as GhFL10), an undescribed gene in plants. One 214-bp deletion was identified in the promoter region of DJ61 compared with Jimian5. Quantitative real-time PCR (qRT-PCR) and comparative analysis of parental sequences suggested that GhFL10 was the most promising candidate gene for qFL-c10-1. According to RNA-seq, yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC), we speculate that GhFL10 interacts with NF-YA transcription factors to negatively regulate fiber elongation.

Analysis of the MIR396 gene family and the role of MIR396b in regulating fiber length in cotton

Cotton fiber is one of the most important natural raw materials in the world textile industry. Improving fiber yield and quality has always been the main goal. MicroRNAs, as typical small noncoding RNAs, could affect fiber length during different stages of fiber development. Based on differentially expressed microRNA in the two interspecific backcross inbred lines (BILs) with a significant difference in fiber length, we identified the miR396 gene family in the two tetraploid cotton genomes and found MIR396b_D13 as the functional precursor to produce mature miR396 during the fiber elongation stage. Among 46 target genes regulated by miR396b, the GROWTH-REGULATING FACTOR 5 gene (GRF5, Gh_A10G0492) had a differential expression level in the two BILs during fiber elongation stage. The expression patterns indicated that the miR396b-GRF5 regulatory module has a critical role in fiber development. Furthermore, virus-induced gene silencing (VIGS) of miR396b significantly produced longer fiber than the wild type, and the expression level of GRF5 showed the reverse trends of the miR396b expression level. The analysis of co-expression network for the GRF5 gene suggested that a cytochrome P450 gene functions as an allene oxide synthase (Gh_D06G0089, AOS), which plays a critical role in jasmonate biosynthetic pathway. In conclusion, our results revealed that the miR396b-GRF5 module has a critical role in fiber development. These findings provide a molecular foundation for fiber quality improvement in the future.

Development of Superior Fibre Quality Upland Cotton Cultivar Series 'Ravnaq' Using Marker-Assisted Selection

Marker-assisted selection (MAS) helps to shorten breeding time as well as reduce breeding resources and efforts. In our MAS program, we have targeted one of previously reported LD-blocks with its simple sequence repeat (SSR) marker(s), putatively associated with, at least, four different fibre quality QTLs such as fibre length, strength, micronaire and uniformity. In order to transfer targeted QTLs from a donor genotype to a cultivar of choice, we selected G. hirsutum donor genotypes L-141 and LN-1, possessing a fibre quality trait-associated LD-block from the chromosome 7/16. We crossed the donor lines with local elite G. hirsutum cultivars 'Andijan-35' and 'Mekhnat' as recipients. As a result, two segregating populations on LD-block of interest containing fibre QTLs were developed through backcrossing (BC) of F₁ hybrids with their relative recipients (used as recurrent parents) up to five generations. In each BC and segregating BC₁-₅F₁ populations, a transfer of targeted LD-block/QTLs was monitored using a highly polymorphic SSR marker, BNL1604 genotype. The homozygous cultivar genotypes with superior fibre quality and agronomic traits, bearing a targeted LD-block of interest, were individually selected from self-pollinated BC₅F₁ (BC₅F_2-5) population plants using the early-season PCR screening analysis of BNL1604 marker locus and the end-of-season fibre quality parameters. Only improved hybrids with superior fibre quality compared to original recipient parent were used for the next cycle of breeding. We successfully developed two novel MAS-derived cotton cultivars (named as 'Ravnaq-1' and 'Ravnaq-2') of BC₅F₅ generations. Both novel MAS cultivars possessed stronger and longer fibre as well as improved fibre uniformity and micronaire compared to the original recurrent parents, 'Andijan-35' and 'Mekhnat'. Our efforts demonstrated a precise transfer of the same LD-block with, at least, four superior fibre QTLs in the two independent MAS breeding experiments exploiting different parental genotypes. Results exemplify the feasibility of MAS in cotton breeding.

The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton

Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.

QTL controlling fiber quality traits under salt stress in upland cotton (Gossypium hirsutum L.)

QTL for fiber quality traits under salt stress discerned candidate genes controlling fatty acid metabolism. Salinity stress seriously affects plant growth and limits agricultural productivity of crop plants. To dissect the genetic basis of response to salinity stress, a recombinant inbred line population was developed to compare fiber quality in upland cotton (Gossypium hirsutum L.) under salt stress and normal conditions. Based on three datasets of (1) salt stress, (2) normal growth, and (3) the difference value between salt stress and normal conditions, 51, 70, and 53 QTL were mapped, respectively. Three QTL for fiber length (FL) (qFL-Chr1-1, qFL-Chr5-5, and qFL-Chr24-4) were detected under both salt and normal conditions and explained 4.26%, 9.38%, and 3.87% of average phenotypic variation, respectively. Seven genes within intervals of two stable QTL (qFL-Chr1-1 and qFL-Chr5-5) were highly expressed in lines with extreme long fiber. A total of 35 QTL clusters comprised of 107 QTL were located on 18 chromosomes and exhibited pleiotropic effects. Thereinto, two clusters were responsible for improving five fiber quality traits, and 6 influenced FL and fiber strength (FS). The QTL with positive effect for fiber length exhibited active effects on fatty acid synthesis and elongation, but the ones with negative effect played passive roles on fatty acid degradation under salt stress.