Senescence-associated genes (SAGs) are identified in Arabidopsis and other plants according to their function. Herein, we identified 23 SAGs containing the senescence domain (PF06911) across four cotton species: G. arboreum (4 GaSAG), G. raimondii (4 GrSAG), G. hirsutum (8 GhSAG), and G. barbadense (7 GbSAG). They were phylogenetically classified into four clades, each with similar motif composition and gene structure. The gene distribution and phylogenetic analysis showed the gain and loss of genes from chromosomes during evolution. Additionally, the GhSAGs (Gh_D12G034100, Gh_A12G040600) are expressed at high levels in tissue and developmental stages, while showing low expression in abiotic stress conditions such as cold, drought, heat, and salt. Gh_A02G203200 and Gh_D08G268900 show high expression in stress conditions. Two GhSAG, Gh_A06G075500 and Gh_D06G073900 are predicted to be localized in cell membranes and show low expression under abiotic stress conditions, developmental stages, and tissues, and high expression under biotic stress. We have identified 73 cis-regulatory elements out of which 43 cis-regulatory elements in GhSAGs that belong to different functional categories, viz. Growth and conditional responses, biotic and abiotic stresses, hormonal responses, and other regulatory pathways. AlphaFold's 3-D model of the SAG domain shows that one face has a more positive charge and the other has a more negative charge. The functional enrichment and protein-protein interactions of GhSAG genes reveal their roles in protein transport and stress response processes. The qRT-PCR analysis of selected five GhSAG treated with MeJA, SA, NaCl, and PEG for different time intervals shows that GhSAG expression is relatively downregulated, with unique upregulated expression patterns under SA treatments. Overall, it has been suggested that SAG genes might have a crucial role in tissue functioning, development, and plant survival under stressful conditions. This study will lay the groundwork for future investigations into the detailed function of each gene. (c) 2024 SAAB. Published by Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Being a longest unicellular structure, cotton fiber is the most suitable platform for studying cellular differentiation, development, and cell wall biosynthesis in the plant system. A range of transcription factors, hormones, epigenetic factors and H2O2 play essential role in fiber development. Our previous work reported an accumulation of high H2O2 levels on the epidermis of in-vitro cultured ovules treated with the inhibitors of HSP90 and HSP70, which lead to autophagy and ultimately declined fiber initials. In this study, we investigated the susceptibility of cotton fiber development to cellular ROS imbalance due to altered GhHSP90-7 and GhHSP70-8 expression in transgenic cotton lines. The expression analysis reflected the highest expression of GhHSP90-7 and GhHSP70-8 at 0 Days post anthesis (DPA) in comparison to later developmental stages suggesting their importance in fiber initiation. Suppression and over-expression lines of these Heat Shock Proteins (HSPs) showed the decreased fiber growth in initiation and elongation stages. Almost all fiber-related traits got impacted in all HSP transgenic lines. Further, ROS levels were found imbalanced in transgenic ovules due to alteration in HSPs expression, leading to the disruption of cellular homeostasis. High ROS accumulation in suppression lines lead to autophagy in ovule epidermal cells. Low ROS concentrations also affected fiber initiation as ROS molecules act as signaling molecule and so the expression of fiber initiation specific transcription factors found to be declined significantly. These results show the GhHSP90-7 and GhHSP70-8 play important role in cotton fiber development.

Linseed (Linum usitatissimum L.), a member of the Linaceae family, is a versatile crop valued for its oil, fibre, nutritional and medicinal applications. Recognized as a superfood, linseed is rich in omega-3 fatty acid (~55%), lignans, high-quality proteins, dietary fibre and bioactive secondary metabolites. Previously published genome assemblies of linseed are quite fragmented and non-contiguous. In this study, we present a telomere-to-telomere (T2T) chromosome-scale genome assembly of the Indian linseed variety T397 using advanced sequencing approaches. The assembly comprises ~595 Mb of genomic sequences, with a scaffold N50 of 32.86 Mb, spanning 15 chromosomes, including 29 telomeres and 15 centromeres. A total of 34 572 protein-encoding genes were predicted with an average length of 2980.7 bp and an average of 5.0 exons per gene. Gene family analysis determines a considerable number of unique genes in linseed and its close relationship with Manihot esculenta and Ricinus communis. The higher expression of oleosin and FAD3 genes in linseed highlights their roles in oil accumulation and enrichment for omega-3 fatty acid. The metabolites found in the seeds were enriched for the biosynthesis of unsaturated fatty acids. Various potential key structural genes and transcription factors that regulate oil metabolism especially unsaturated fatty acids biosynthesis has been identified. Overall, the present study provides the potential genomic resources for accelerated genetic studies and improvement of linseed.

This study investigates the response of ethyl methanesulfonate-derived twenty mutant lines of Gossypium herbaceum, along with the parent type Wagad cultivar, to drought stress. Physiological parameters, such as relative water content (RWC), net photosynthesis (A), stomatal conductance (gs), transpiration rate (E), and water use efficiency (WUE), were examined. The mutant line mut_3219 exhibited superior drought tolerance, maintaining high RWC and water retention capacity, with minimal reductions in A, gs, and E, leading to higher WUE than parent type and other mutant lines. Chlorophyll pigments declined in all the mutants under drought. However, mut_3219 retained higher levels than mut_4785. Anthocyanin accumulation indicated a protective response. Chlorophyll fluorescence showed mut_3219 is less sensitive to drought-induced PSII damage than mut_4785, with better membrane stability and higher proline accumulation, among all other mutant lines and parent type. The morphological parameters were less affected in mut_3219 compared to mut_4785 and parent type. Molecular analyses under control and drought conditions revealed significant variations in the expression of seven drought-related genes (GhbHLH, GhMYB5, GhWRKY33, GhRAF4, GhRAF19, GhNAC2, and GhCAMTA). The relative expression of GhbHLH, GhNAC2, GhRAF4, GhRAF19, and GhCAMTA increased under drought conditions, with notable changes in mut_3219 compared to parent type and all other mutant lines, indicating its enhanced drought tolerance. These findings provide valuable insights into the molecular and physiological mechanisms underlying drought tolerance in cotton.

Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. In particular, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-sequencing was performed in two foxtail millet cultivars with contrasting dehydration tolerances (IC403579, cv. IC4-tolerant, and IC480117, cv. IC41-sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4, and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.

In flowering plants, the tapetum degeneration in post-meiotic anther occurs through developmental programmed cell death (dPCD), which is one of the most critical and sensitive steps for the proper development of male gametophytes and fertility. Yet the pathways of dPCD, its regulation, and its interaction with autophagy remain elusive. Here, we report that high-level expression of Arabidopsis autophagy-related gene BECLIN1 (BECN1 or AtATG6) in the tobacco tapetum prior to their dPCD resulted in developmental defects. BECN1 induces severe autophagy and multiple cytoplasm-to-vacuole pathways, which alters tapetal cell reactive oxygen species (ROS)-homeostasis that represses the tapetal dPCD. The transcriptome analysis reveals that BECN1- expression caused major changes in the pathway, resulting in altered cellular homeostasis in the tapetal cell. Moreover, BECN1-mediated autophagy reprograms the execution of tapetal PCD by altering the expression of the key developmental PCD marker genes: SCPL48, CEP1, DMP4, BFN1, MC9, EXI1, and Bcl-2 member BAG5, and BAG6. This study demonstrates that BECN1-mediated autophagy is inhibitory to the dPCD of the tapetum, but the severity of autophagy leads to autophagic death in the later stages. The delayed and altered mode of tapetal degeneration resulted in male sterility.

Male sterility is an important agronomical trait in self-pollinating plants for producing cost-effective F1 hybrids to harness the heterosis. Still, large-scale development and maintenance of male sterile lines and restoring fertility in F1 hybrids pose significant challenges in plant hybrid breeding. Cotton is a self-pollinating crop and exhibits strong hybrid vigor. However, there are currently few breeding methods to achieve cost-effective production of F1 hybrid cotton. Here, we utilized novel functions of the Arabidopsis autophagy-related BECLIN1/ATG6 and a mutant of E3 ubiquitin ligase COP1 (COP1L105A) genes in developing rescuable male sterility in cotton. We have generated multiple male-sterile (MS) and restorer (RS) cotton lines expressing BECLIN1 and COP1L105A, respectively. Cytological observation showed that post-meiotic tapetal expression of BECLIN1 delays tapetum developmental programmed cell death (dPCD) by affecting reactive oxygen species (ROS) balance-this delay in dPCD results in early microspore defects and later small-sized flowers with indehiscent anthers. Furthermore, the evaluation of F1 hybrids developed by crossing MS and RS lines showed that early tapetal COP1L105A expression abolishes expression of BECLIN1 resulting in normal tapetum degeneration, pollen development, and fertility. In addition, the F1 hybrid developed with MS and RS cotton lines in transgenic glass-house and net-house conditions showed the rescued fertility comparable with control plants (WT). In terms of cotton fiber productivity, the COP1L105A-expressing transgenic cotton lines outperformed the WT. The current work effectively demonstrates the wider applicability of the new F1 cotton production system.

Ferric Reductase Oxidase (FRO) genes are pivotal in iron uptake and homeostasis in plants, yet they are not studied in cotton. Here, we identify and analyze 65 FRO homologs (21 GhFRO, 21 GbFRO, 11 GaFRO, 12 GrFRO) across four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, G. raimondii). FRO exhibit conserved ferric reductase activity and conserved domain structures; Ferric_reduct (PF01794), FAD_binding_8 (PF08022), and NAD_binding_6 (PF08030) across species. Physicochemical properties and subcellular localization analysis provided insights into FRO proteins' functional characteristics, mainly localized to the plasma membrane. Phylogenetic analysis delineates 11 groups, indicating both conserved and divergent evolutionary patterns. Gene structure analysis unveils varying exon-intron compositions. Chromosomal localization shows distribution across A and D genomes, suggesting evolutionary dynamics. Synteny analysis reveals paralogous and orthologous gene pairs subjected to purifying selection. The cis-regulatory elements analysis implicates diverse regulatory mechanisms. Expression profiling highlights dynamic regulation across developmental stages, abiotic and biotic stress conditions. GhFRO interacts with Ca++-dependent protein kinases-10/28-like (CDPKs10/28-like) and metal transporter Natural resistance-associated macrophage protein 6 (Nramp6) to regulate metal ion transport and iron homeostasis. The three-dimensional protein structure prediction suggests potential ligand-binding sites in FRO proteins. Moreover, qRT-PCR analysis of selected eight GhFROs in leaves treated with stress elicitors, MeJA, SA, NaCl, and PEG for 1h, 2h, 4h, and 6h revealed significant downregulation. Overall, this comprehensive study provides insights into FRO gene diversity, evolution, structure, regulation, and function in cotton, with implications for understanding plant iron homeostasis and stress responses.

Autophagy is an evolutionarily conserved process mediated by AuTophaGy (ATG) genes, in which cellular components are degraded and recycled within vacuoles or lysosome. Yeast ATG was extensively studied; their homologs are reported in plants including Arabidopsis. However, they have not been reported in cotton. In the present study, the ATG cascade genes were studied in four Gossypium species, namely G. hirsutum, G. arboreum, G. herbaceum, and G. raimondii. A total of 40 GhirATG, 33 GaATG, 34 GherbATG, and 25 GrATG genes were identified in these species. These ATG sequences exhibited conserved ATG domains and other overlapping domains, including Ras, Pkinase, Snf7, WD40, Glyco_hydro_17, and bZIP_1, and were named based on their phylogenetic relationships with Arabidopsis ATGs. A phylogenetic analysis revealed evolutionary relationships among ATG genes among these species, as well as significant sub-clades indicating patterns of gene retention. Based on synonymous and non-synonymous substitutions, cotton groups diverged at different times from Arabidopsis. Gene structure analysis and chromosome localization showed exon-intron patterns and locations. Expression analysis of ATGs in different tissues during development and under stress conditions indicated their functional specificity. The ATG8 subclass genes were significantly expressed under abiotic stress conditions, indicating their role in stress response. In addition, qRT-PCR analysis of selected 12 GhirATGs in leaves treated with stress elicitors, MeJA, SA, NaCl, and PEG for varying time intervals showed a pattern of their significant upregulation. The findings contribute to our understanding of autophagy-related processes in cotton, including their potential role in stress response and development.

Vascular wilt disease incited by Fusarium oxysporum f. sp. carthami (Foc) in Safflower poses a significant threat to its production in India. A comprehensive understanding of the molecular underpinning of compatible and incompatible interaction is of extreme economic importance. In the present study, the genome of a virulent (IARI-5175) and a avirulent (F-00845) Foc strain were sequenced and assembled using data generated from Illumina in combination with Nanopore technologies and HiC. Foc genomes were assembled into 88 and 23 scaffolds with an estimated total size of 46 Mb and 42 Mb respectively for IARI-5175 and F-00845 strains. Reference based mapping of Foc genome with F. oxysporum f. sp. lycopersici (Fol) resulted in chromosomal level ordering of genome and simultaneous identification of accessory genome. Additionally, two lineage specific chromosomes were also identified for virulent Foc strain IARI-5175. Genomic comparisons were made on the basis of effectors, CAZymes, secondary metabolites and mycotoxins to understand the global view pathogenicity in Foc. Moreover, the transcriptome of Foc during compatible and incompatible interaction was sequenced and analyzed leading to the identification of differentially regulated genes. Taken together our study laid a solid foundation to explore novel effector genes that play a crucial role in the establishment of disease and can further be used as targets to devise new strategies to curb wilt disease in safflower.### Competing Interest StatementThe authors have declared no competing interest.

Transcript isoform dynamics, spatiotemporal expression, and mutational analysis uncover that Arabidopsis RabC1 GTPase is required for root length, flowering time, seed size, and seed mucilage. Rab GTPases are crucial regulators for moving different molecules to their specific compartments according to the needs of the cell. In this work, we illustrate the role of RabC1 GTPase in Arabidopsis growth and seed development. We identify and analyze the expression pattern of three transcript isoforms of RabC1 in different development stages, along with their tissue-specific transcript abundance. The promoter activity of RabC1 using promoter-GUS fusion shows that it is widely expressed during the growth of Arabidopsis, particularly in seed tissues such as chalazal seed coat and chalazal endosperm. Lack of RabC1 function led to shorter roots, lesser biomass, delayed flowering, and sluggish plant development. The mutants had smaller seeds than the wildtype, less seed mass, and lower seed coat permeability. Developing seeds also revealed a smaller endosperm cavity and shorter integument cells. Additionally, we found that the knock-out mutant had downregulated expression of genes implicated in the transit of sugars and amino acids from maternal tissue to developing seed. The seeds of the loss-of-function mutant had reduced seed mucilage. All the observed mutant phenotypes were restored in the complemented lines confirming the function of RabC1 in seed development and plant growth.

Stomata play a principal role in adjusting carbon dioxide (CO2) intake and water use for plant adaptation and tolerance to water-restricted conditions. In the present study, impact of water stress-mediated stomatal development in drought-tolerant LRA-5166 and sensitive NBRI-67 cotton varieties was elucidated through transcript level of stomatal genes, leaf gas exchange, stomatal traits, and growth parameters under water stress conditions. Our findings showed that the tolerance of LRA-5166 was associated with higher stomatal density, stomatal index and smaller guard cells as compared to the sensitive NBRI-67. These developmental changes in stomata result in comparatively better stomatal regulation in LRA-5166 than NBRI-67 to transpiration and stomatal conductance. The expression analysis of stomatal genes showed transcript levels of EPIDERMAL PATTERNING FACTOR 2 (EPF2), STOMATAL DENSITY AND DISTRIBUTION 1 (SDD1), and TOO MANY MOUTH (TMM) were distinctly enhanced in both LRA-5166 and NBRI-67 under the water stress, while the transcript level of STOMAGEN (STG) was reduced in both the varieties. The up-regulation of EPF2, SDD1, and TMM genes in sensitive variety reduced the stomatal density and index more than the tolerant variety. Our studies reveal that regulated increase of EPF2, SDD1 and TMM to drought could be involved in plasticity of stomatal numbers and guard cell length and, therefore, more efficiently regulates instantaneous water use efficiency (WUEinst) and plant’s ability to combat drought.

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

Solanum is one of the largest genera of the family Solanaceae that contains about 1500 species mainly dispersed around the tropical and subtropical regions of the globe. A great number of economically important plant species used for food, ornamental, and medicinal purposes belong to Solanum. Fruits of S. viarum are known as rich sources of steroidal alkaloids and glycoalkaloids, which exhibit a variety of biological activities such as anti-inflammatory, anticancerous, antifungal, antimicrobial, antiviral, insecticidal, etc. Various reports also show the presence of significant amounts of other important phytochemicals such as phenolics, flavonoids, saponins, and terpenoids. These plants provide the raw material for the commercial production of several pharmaceutically important steroidal drugs, which are used for the treatment of several chronic diseases. Due to the paramount medicinal properties of these plants, considerable effort has been made to unravel the phytoconstituents for in vitro establishment and for the enrichment of essential bioactive compounds. This chapter provides detailed information about phytochemistry and pharmaceutical uses, in vitro mechanisms for large-scale micropropagation and enrichment of vital phytochemicals, and conservation approaches for these natural resources.

Tobacco’s PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, the epigenetic modifications of the inducible promoter of the PR-1a gene are not fully understood yet. Southern approach was used to scan the promoter of PR-1a to identify presence of nucleosomes, ChIP assays were performed using anti-histones antibodies of repressive chromatin by di- methylated at H3K9 and H4K20 or active chromatin by acetylated H3K9/14 and H4K16 to find epigenetic malleability of nucleosome over core promoter in uninduced or induced state post SA treatment. Class I and II mammalian histone deacetylase (HDAC) inhibitor TSA treatment was used to enhance the expression of PR-1a by facilitating the histone acetylation post SA treatment. Here, we report correlated consequences of the epigenetic modifications correspond to disassembly of the nucleosome (spans from − 102 to + 55 bp, masks TATA and transcription initiation) and repressor complex from core promoter, eventually initiates the transcription of PR-1a gene post SA treatment. While active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased which are associated to the transcription initiation of PR-1a following SA treatment. However, in uninduced state constitutive expression of a negative regulator (SNI1) of AtPR1, suppresses AtPR1 expression by six-fold in Arabidopsis thaliana. Further, we report 50-to-1000-fold increased expression of AtPR1 in uninduced lsd1 mutant plants, up to threefold increased expression of AtPR1 in uninduced histone acetyl transferases (HATs) mutant plants, SNI1 dependent negative regulation of AtPR1, all together our results suggest that inactive state of PR-1a is indeed maintained by a repressive complex. The study aimed to reveal the mechanism of transcription initiation of tobacco PR-1a gene in presence or absence of SA. This is the first study that reports nucleosome and repressor complex over core promoter region maintains the inactivation of gene in uninduced state, and upon induction disassembling of both initiates the downstream gene activation process.

Cytochrome P450 (CYPs) is a functionally diversified third-largest gene family that exploded in the plant kingdom. Their role in different organ development has been illustrated by the intervention of phytohormone. Cotton is a model organism for cell differentiation and cell elongation. To decipher the participation of CYPs in different cotton fiber developmental stages, we identified and characterized 2460 CYPs in three diploids and two allotetraploid cottons. Furthermore, In-silico expression and cluster analysis of cotton CYPs was conducted to distinguish the fiber stage-specific clusters that have the determining role in different stages of fiber development. The subgenome expression of two conserved Gossypium hirsutum CYPs, namely, GhCYP78A197 and GhCYP78A198 contributed to fiber initiation at an early stage of fiber development, governed by the co-occurrence of TATA and MYB TFs binding sites. Coexpression network partners of these two GhCYP78A annotated as auxin, kinases, chromatin remodeler, epigenetic regulator and cyclin-related genes that possibly induce the endoreduplication and cell proliferation for fiber cell initiation to define the high yield and biomass.

The circadian clock is regulated by signaling networks that enhance a plant's ability to coordinate internal events with the external environment. In this study, we examine the rhythmic expression of long non-coding RNAs (lncRNAs) using multiple transcriptomes of Arabidopsis thaliana in the diel light cycle and integrated this information to have a better understanding of the functions of lncRNAs in regulating the circadian clock. We identified 968, 1050, and 998 lncRNAs at 8 h light, 16 h light and 8 h dark conditions, respectively. Among these, 423, 486, and 417 lncRNAs were uniquely present at 8 h light, 16 h light, and 8 h dark, respectively, whereas 334 lncRNAs were common under the three conditions. The specificity of identified lncRNAs under different light conditions was verified using qRT-PCR. The identified lncRNAs were less GC-rich and expressed at a significantly lower level than the mRNAs of protein-coding genes. In addition, we identified enriched motifs in lncRNA transcribing regions that were associated with light-responsive genes (SORLREP and SORLIP), flower development (AGAMOUS), and circadian clock (CCA1) under all three light conditions. We identified 10 and 12 different lncRNAs targeting different miRNAs with perfect and interrupted complementarity (endogenous target mimic). These predicted lncRNA-interacting miRNAs govern the function of a set of genes involved in the developmental process, reproductive structure development, gene silencing and transcription regulation. We demonstrated that the lncRNA transcribing regions were enriched for epigenetic marks such as H3.3, H3K4me2, H3K4me3, H4K16ac, H3K36ac, H3K56ac and depleted for heterochromatic (H3K9me2 and H3K27me1) and repressive (H3K27me3) histone modifications. Further, we found that hypermethylated genomic regions negatively correlated with lncRNA transcribing regions. Overall, our study showed that lncRNAs expressed corresponding to the diel light cycle are implicated in regulating the circadian rhythm and governing the developmental stage-specific growth.

Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the "CottonExpress-omics" database.

The recombinant inbred lines of inter-specific cross, Gossypium hirsutum cv. DS-28 × G. barbadense cv. SBYF-425 was evaluated in three consecutive rainy seasons of 2017–18 (F13), 2018–19 (F14) and 2019–20 (F15) in an augmented design. The preponderance of huge continuous variability for both productivity and fiber quality traits was recorded. The principal component analysis revealed that the mapping population was well suited for mapping of productivity and fiber quality traits. On the basis the Z-scores for skewness and kurtosis, 178 RILs with normal distribution were selected for genetic linkage mapping. A high-density saturated linkage map was constructed using SNP arrays of CottonSNP63K, an Illumina’s infinium array and CottonSNP50K, CSIR-National Botanical Research Institute’s Axiom array with a total spanned length of 2402.65 cM, an average marker density of 1.54 and with map coverage of 96.99% of the reference genome. The developed genetic map of inter specific cross of Indian cotton varieties is a highly saturated in terms of coverage and highly comparable to the published maps. In QTL analysis, altogether 99 QTLs were identified for productivity and fiber quality traits. Among those, eight were stable and 38 were major QTLs. Cluster 1, 4 and 6 respectively on chromosome AD_chr.03, AD_chr.14 and AD_chr.18 were the biggest QTL clusters each with four QTLs and cluster 4 and 6 were QTL hotspots for fiber quality traits.