Characterization, Evolution, Expression and Functional Divergence of the Gene Family in Plants.

The (DOMAIN OF UNKNOWN FUNCTION 679 membrane protein) domain, containing a family of membrane proteins specific to green plants, is involved in numerous biological functions including physiological processes, reproductive development and senescence in , but their evolutionary relationship and biological function in most crops remains unknown. In this study, we scrutinized phylogenetic relationships, gene structure, conserved domains and motifs, promoter regions, gene loss/duplication events and expression patterns. Overall, 240 s were identified and analyzed in 24 plant species selected from lower plants to angiosperms.

GhSBI1, a CUP-SHAPED COTYLEDON 2 homologue, modulates branch internode elongation in cotton.

Branch length is an important plant architecture trait in cotton (Gossypium) breeding. Development of cultivars with short branch has been proposed as a main object to enhance cotton yield potential, because they are suitable for high planting density. Here, we report the molecular cloning and characterization of a semi-dominant quantitative trait locus, Short Branch Internode 1(GhSBI1), which encodes a NAC transcription factor homologous to CUP-SHAPED COTYLEDON 2 (CUC2) and is regulated by microRNA ghr-miR164.

Comprehensive identification and systematical characterization of BRX gene family and the functional of GhBRXL5A in response to salt stress.

Background: BRVIS RADIX (BRX) family is a small gene family with the highly conserved plant-specific BRX domains, which plays important roles in plant development and response to abiotic stress. Although BRX protein has been studied in other plants, the biological function of cotton BRX-like (BRXL) gene family is still elusive.

Result: In this study, a total of 36 BRXL genes were identified in four cotton species.

Genome-Wide Identification of Calmodulin-Binding Protein 60 Gene Family and the Function of in Cotton Growth and Development and Abiotic Stress Response.

The calmodulin-binding protein 60 () family is a gene family unique to plants, and its members play a crucial role in plant defense responses to pathogens and growth and development. Considering that cotton is the primary source of natural cotton textile fiber, the functional study of its gene family members is critical. In this research, we successfully identified 162 members from the genomes of 21 species.

A Genome-Wide Analysis of the CEP Gene Family in Cotton and a Functional Study of in Plant Development.

() are a class of peptide hormones that have been shown in previous studies to play an important role in regulating the development and response to abiotic stress in model plants. However, their role in cotton is not well understood. In this study, we identified 54, 59, 34, and 35 CEP genes from (2n = 4x = 52, AD1), (AD2), (2n = 2X = 26, A2), and (2n = 2X = 26, D5), respectively.

Comprehensive identification and functional characterization of GhpPLA gene family in reproductive organ development.

Background: Phospholipases As (PLAs) are acyl hydrolases that catalyze the release of free fatty acids in phospholipids and play multiple functions in plant growth and development. The three families of PLAs are: PLA1, PLA2 (sPLA), and patatin-related PLA (pPLA). The diverse functions that pPLAs play in the growth and development of a broad range of plants have been demonstrated by prior studies.

Characteristic of GEX1 genes reveals the essential roles for reproduction in cotton.

GEX1 (gamete expressed 1) proteins are critical membrane proteins conserved among flowering plants that are involved in the nuclear fusion and embryonic development. Herein, we identified the 32 GEX1 proteins from representative land plants. In cotton, GEX1 genes expressed in various tissues across all stages of the life cycle, especially in pollen.

GhCKX14 responding to drought stress by modulating antioxi-dative enzyme activity in Gossypium hirsutum compared to CKX family genes.

Background: Cytokinin oxidase/dehydrogenase (CKX) plays a vital role in response to abiotic stress through modulating the antioxidant enzyme activities. Nevertheless, the biological function of the CKX gene family has yet to be reported in cotton.

Result: In this study, a total of 27 GhCKXs were identified by the genome-wide investigation and distributed across 18 chromosomes.

Evolutionary Relationships and Divergence of Gene Family Involved in Development and Stress in Cotton ( L.).

Filamin protein is characterized by an N-terminal actin-binding domain that is followed by 24 Ig (immunoglobulin)-like repeats, which act as hubs for interactions with a variety of proteins. In humans, this family has been found to be involved in cancer cell invasion and metastasis and can be involved in a variety of growth signal transduction processes, but it is less studied in plants. Therefore, in this study, 54 gene family members from 23 plant species were investigated and divided into two subfamilies: FLMN and GEX2.

Identification, Classification and Characterization Analysis of Gene in Cotton.

(), Leucine-rich repeats in F-box proteins, belongs to the Skp1-Cullin1-F-box protein (SCF) E3 ligase family. genes play important roles in plant growth, such as plant hormones, responses to environmental stress, and floral organ development. Here, a total of 518 genes were identified and analyzed in six plant species.

Systematical Characterization of the Cotton Gene Family and the Role of and as Two Negative Regulators in Response to Salt Stress.

Drought-induced 19 (Di19) protein is a Cys2/His2 (C2H2) type zinc-finger protein, which plays a crucial role in plant development and in response to abiotic stress. This study systematically investigated the characteristics of the gene family, including the member number, gene structure, chromosomal distribution, promoter cis-elements, and expression profiles. Transcriptomic analysis indicated that some were up-regulated under heat and salt stress.

Expression Patterns Divergence of Reciprocal F Hybrids Between and Reveals Overdominance Mediating Interspecific Biomass Heterosis.

Hybrid breeding has provided an impetus to the process and achievement of a higher yield and quality of crops. Interspecific hybridization is critical for resolving parental genetic diversity bottleneck problems. The reciprocal interspecific hybrids and their parents ( and ) have been applied in this study to elucidate the transcription regulatory mechanism of early biomass heterosis.

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton.

The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 genes () were identified by genome-wide analysis in upland cotton (), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between and .

The Evolution and Expression Profiles of Gene Family during Development in Cotton.

Fertilization is essential to sexual reproduction of flowering plants. EC1 (EGG CELL 1) proteins have a conserved cysteine spacer characteristic and play a crucial role in double fertilization process in many plant species. However, to date, the role of gene family in cotton is fully unknown.

Cotton DMP gene family: characterization, evolution, and expression profiles during development and stress.

Members of DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (DMP) gene family, a type of plant-specific membrane proteins, have been proposed to function in various physiological processes such as reproductive development and senescence in plants. Here, a total of 174 DMP genes were identified and analyzed in 16 plant species (including 58 DMPs in four cotton species). Phylogenetic analysis showed that these DMPs could be clustered into five subfamilies (I-V).

Evolution and Functional Divergence of Genes in Plants.

SUN-domain containing proteins are crucial nuclear membrane proteins involved in a plethora of biological functions, including meiosis, nuclear morphology, and embryonic development, but their evolutionary history and functional divergence are obscure. In all, 216 SUN proteins from protists, fungi, and plants were divided into two monophyletic clades (Cter-SUN and Mid-SUN). We performed comprehensive evolutionary analyses, investigating the characteristics of different subfamilies in plants.

A Retrotransposon Insertion in Is Likely Responsible for the Lintless Locus of Tetraploid Cotton.

Cotton () seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 ().

Characterization and transcriptome analysis of a dominant genic male sterile cotton mutant.

Background: Male sterility is an efficient trait for hybrid seed production and germplasm innovation. Until now, most studies on male sterility were on cytoplasmic and recessive genic sterility, with few on dominant genic male sterility, especially in cotton, due to lack of such mutant.

Results: We discovered a natural male sterile (MS) Sea Island cotton (G.

Open-Bud Duplicate Loci Are Identified as , Orthologs of MIXTA-Like Genes on Homologous Chromosomes of Allotetraploid Cotton.

The open-bud () mutants in cotton display abnormal flower buds with the stigma and upper anthers exposed before blooming. This characteristic is potentially useful for the efficient production of hybrid seeds. The recessive inheritance pattern of the phenotype in allotetraploid cotton is determined by duplicated recessive loci ().

Highly Efficient Targeted Gene Editing in Upland Cotton Using the CRISPR/Cas9 System.

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system has been shown to be able to induce highly efficient mutagenesis in the targeted DNA of many plants, including cotton, and has become an important tool for investigation of gene function and crop improvement. Here, we developed a simple and easy to operate CRISPR/Cas9 system and demonstrated its high editing efficiency in cotton by targeting-ALARP, a gene encoding alanine-rich protein that is preferentially expressed in cotton fibers. Based on sequence analysis of the target site in the 10 transgenic cottons containing CRISPR/Cas9, we found that the mutation frequencies of and target sites were 71.

Identification and Functional Characterization of a Microtubule-Associated Protein, GhCLASP2, From Upland Cotton ( L.).

Cytoplasmic linker-associated proteins (CLASPs) are microtubule-associated proteins (MAPs) involved in regulation of dynamics of microtubules (MTs) that play an important role in plant growth and development. In this study, we identified cotton genes and investigated the function of . was mainly expressed in stem and developing fibers, especially in fibers of the secondary cell wall deposition stage.

Expression and functional analyses of a Kinesin gene GhKIS13A1 from cotton (Gossypium hirsutum) fiber.

Background: Cotton fiber, a natural fiber widely used in the textile industry, is differentiated from single cell of ovule epidermis. A large number of genes are believed to be involved in fiber formation, but so far only a few fiber genes have been isolated and functionally characterized in this developmental process. The Kinesin13 subfamily was found to play key roles during cell division and cell elongation, and was considered to be involved in the regulation of cotton fiber development.

De novo transcriptome analysis reveals insights into dynamic homeostasis regulation of somatic embryogenesis in upland cotton (G. hirsutum L.).

Plant regeneration via somatic embryogenesis (SE) is the key step for genetic improvement of cotton (Gossypium hirsutum L.) through genetic engineering mediated by Agrobacteria, but the molecular mechanisms underlying SE in cotton is still unclear. Here, RNA-Sequencing was used to analyze the genes expressed during SE and their expression dynamics using RNAs isolated from non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryos (SEs).

Overexpression of GhSARP1 encoding a E3 ligase from cotton reduce the tolerance to salt in transgenic Arabidopsis.

Ubiquitination plays a very important role in the response to abiotic stresses of plant. To identify key regulators of salt stress, a gene GhSARP1(Salt-Associated Ring finger Protein)encoding C3H2C3-type E3 ligase, was cloned from cotton. Transcription level of GhSARP1 was high in leaf, flower and fiber of 24,27 and 27DPA (Days Post-Anthesis), but low in root and stem.