Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii)

Global gene expression profile and functional analysis reveal the conservation of reproduction-associated gene networks in Gossypium hirsutum

KEY MESSAGE

Lastly, the bZIP gene family encompasses genes that have been reported to play a role in flower development, such as bZIP14 (FD). Notably, bZIP14 is essential for Flowering Locus T (FT) initiation of floral development in Arabidopsis (Abe et al. 2005). Cotton (Gossypium hirsutum L.) is the world's most extensively cultivated fiber crop. However, its reproductive development is poorly characterized at the molecular level. Thus, this study presents a detailed transcriptomic analysis of G. hirsutum at three different reproductive stages. We provide evidence that more than 64,000 genes are active in G. hirsutum during flower development, among which 94.33% have been assigned to functional terms and specific pathways. Gene set enrichment analysis (GSEA) revealed that the biological process categories of floral organ development, pollen exine formation, and stamen development were enriched among the genes expressed during the floral development of G. hirsutum. Furthermore, we identified putative Arabidopsis homologs involved in the G. hirsutum gene regulatory network (GRN) of pollen and flower development, including transcription factors such as WUSCHEL (WUS), INNER NO OUTER (INO), AGAMOUS-LIKE 66 (AGL66), SPOROCYTELESS/NOZZLE (SPL/NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), ABORTED MICROSPORES (AMS), and ASH1-RELATED 3 (ASHR3), which are known crucial genes for plant reproductive success. The cotton MADS-box protein-protein interaction pattern resembles the previously described patterns for AGAMOUS (AG), SEEDSTICK (STK), SHATTERPROOF (SHP), and SEPALLATA3 (SEP3) homolog proteins from Arabidopsis. In addition to serving as a resource for comparative flower development studies, this work highlights the changes in gene expression profiles and molecular networks underlying stages that are valuable for cotton breeding improvement.

GhAGL16 (AGAMOUS-LIKE16) Negatively Regulates Tolerance to Water Deficit in Transgenic Arabidopsis and Cotton

Cotton is one of the most economically important crops in the world, and drought is a key abiotic factor that can significantly reduce cotton yield. MADS-box transcription factors play essential roles in various aspects of plant growth and development as well as responses to biotic and abiotic stress. However, the use of MADS-box transcription factors to regulate water stress responses has not been fully explored in cotton. Here, we showed that GhAGL16 acts as a negative regulator of water deficit in cotton, at least in part by regulating ABA signaling. GhAGL16-overexpressing (GhAGL16-OE) transgenic Arabidopsis had lower survival rates and relative water contents (RWCs) under water stress. Isolated leaves of GhAGL16-OE Arabidopsis had increased water loss rates, likely attributable to their increased stomatal density. GhAGL16-OE Arabidopsis also showed reduced primary root lengths in response to mannitol treatment and decreased sensitivity of seed germination to ABA treatment. By contrast, silencing GhAGL16 in cotton enhanced tolerance to water deficit by increasing proline (Pro) content, increasing superoxide dismutase (SOD) and peroxidase (POD) activities, and reducing malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents under water stress. Subcellular localization and transcriptional activation assays confirmed that GhAGL16 is a nuclear protein that lacks transcriptional self-activation activity. The expression of ABA biosynthesis-related genes (GhNCED3/7/14), a catabolism-related gene (GhCYP707A), and a gene related to the ABA signaling pathway (GhABF4) was altered in GhAGL16-silenced plants. Taken together, our data demonstrate that GhAGL16 plays an important role in cotton resistance to water stress.

Genome-Wide Analysis of the MADS-Box Gene Family in Hibiscus syriacus and Their Role in Floral Organ Development

Hibiscus syriacus belongs to the Malvaceae family, and is a plant with medicinal, edible, and greening values. MADS-box transcription factor is a large family of regulatory factors involved in a variety of biological processes in plants. Here, we performed a genome-wide characterization of MADS-box proteins in H. syriacus and investigated gene structure, phylogenetics, cis-acting elements, three-dimensional structure, gene expression, and protein interaction to identify candidate MADS-box genes that mediate petal developmental regulation in H. syriacus. A total of 163 candidate MADS-box genes were found and classified into type I (Mα, Mβ, and Mγ) and type II (MIKC and Mδ). Analysis of cis-acting elements in the promoter region showed that most elements were correlated to plant hormones. The analysis of nine HsMADS expressions of two different H. syriacus cultivars showed that they were differentially expressed between two type flowers. The analysis of protein interaction networks also indicated that MADS proteins played a crucial role in floral organ identification, inflorescence and fruit development, and flowering time. This research is the first to analyze the MADS-box family of H. syriacus and provides an important reference for further study of the biological functions of the MADS-box, especially in flower organ development.

Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model

BACKGROUND

Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica.

RESULTS

In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination.

CONCLUSION

This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.

Genome-wide identification of MADS-box gene family in orchardgrass and the positive role of DgMADS114 and DgMADS115 under different abiotic stress

Abiotic stress, a major factor limit growth and productivity of major crops. Orchardgrass is one of the most important cool-season forage grasses in the world, and it is highly tolerant to abiotic stress. The MADS-box transcription factor family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, MADS-box transcription factors in orchardgrass, especially those involved in abiotic stress, have not yet been elucidated. Here, 123 DgMADS-box members were identified in orchardgrass and a detailed overview has been presented. Syntenic analysis indicated that the expansion of the DgMADS-box genes in orchardgrass is mainly dependent on tandem duplication events. Some DgMADS-box genes were induced by multiple abiotic stresses, indicating that these genes may play critical regulatory roles in orchardgrass response to various abiotic stresses. Heterologous expression showed that DgMADS114 and DgMADS115 could enhance stress tolerance of transgenic Arabidopsis, as revealed by longer root length or higher survival rates under PEG, NaCl, ABA, and heat stress. The results of this study provide a scientific basis for clarifying the functional characterization of MADS-box genes in orchardgrass in response to environmental stress can be further used to improve forages and crops via breeding programs.

SEP-like genes of Gossypium hirsutum promote flowering via targeting different loci in a concentration-dependent manner

SEP genes are famous for their function in the morphological novelty of bisexual flowers. Although the diverse functions of SEP genes were reported, only the regulatory mechanisms underlying floral organ development have been addressed. In this study, we identified SEP-like genes in Gossypium and found that SEP3 genes were duplicated in diploid cotton varieties. GhSEP4.1 and GhSEP4.2 were abundantly transcribed in the shoot apical meristem (SAM), but only GhSEP4.2 was expressed in the leaf vasculature. The expression pattern of GhSEPs in floral organs was conserved with that of homologs in Arabidopsis, except for GhSEP2 that was preponderantly expressed in ovules and fibers. The overexpression and silencing of each single GhSEP gene suggested their distinct role in promoting flowering via direct binding to GhAP1 and GhLFY genomic regions. The curly leaf and floral defects in overexpression lines with a higher expression of GhSEP genes revealed the concentration-dependent target gene regulation of GhSEP proteins. Moreover, GhSEP proteins were able to dimerize and interact with flowering time regulators. Together, our results suggest the dominant role of GhSEP4.2 in leaves to promote flowering via GhAP1-A04, and differently accumulated GhSEP proteins in the SAM alternately participate in forming the dynamic tetramer complexes to target at the different loci of GhAP1 and GhLFY to maintain reproductive growth. The regulatory roles of cotton SEP genes reveal their conserved and diversified functions.

Carpel-specific down-regulation of GhCKXs in cotton significantly enhances seed and fiber yield

Cytokinin is considered to be an important driver of seed yield. To increase the yield of cotton while avoiding the negative consequences caused by constitutive overproduction of cytokinin, we down-regulated specifically the carpel genes for cytokinin oxidase/dehydrogenase (CKX), a key negative regulator of cytokinin levels, in transgenic cotton. The carpel-specific down-regulation of CKXs significantly enhanced cytokinin levels in the carpels. The elevated cytokinin promoted the expression of carpel- and ovule-development-associated genes, GhSTK2, GhAG1, and GhSHP, boosting ovule formation and thus producing more seeds in the ovary. Field experiments showed that the carpel-specific increase of cytokinin significantly increased both seed yield and fiber yield of cotton, without resulting in detrimental phenotypes. Our study details the regulatory mechanism of cytokinin signaling for seed development, and provides an effective and feasible strategy for yield improvement of seed crops.

MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress

Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.

Functional divergence of GhAP1.1 and GhFUL2 associated with flowering regulation in upland cotton (Gossypium hirsutum L.)

The AP1/FUL transcription factors are important for floral development, but the underlying molecular mechanisms remain unclear. In this study, we cloned and identified two AP1/FUL-like genes, GhAP1.1 and GhFUL2, in upland cotton, which is a commonly cultivated economically valuable crop. Sequence alignment and phylogenetic analysis indicated that GhAP1.1 and GhFUL2, which are encoded by genes in the AP1/FUL clade, have conserved N-terminal regions but diverse C-terminal domains. Quantitative real-time PCR analysis revealed that GhAP1.1 and GhFUL2 were expressed in the flower and root, and showed opposite expression patterns during shoot apical meristem development. The upregulated expression of GhAP1.1 in Arabidopsis did not result in significant changes to the flowering time or floral organ development, and the transcript levels of the florigen FT increased and those of LFY decreased. Overexpression of GhFUL2 in Arabidopsis delayed flowering and promoted bolting by decreasing FT and LFY transcript levels. Silencing GhFUL2 in cotton dramatically increased the expression of GhFT and GhAP1.3 and promoted flowering. Yeast two-hybrid and bimolecular fluorescence complementation assays indicated that GhAP1.1 could interact with the SVP homolog GhSVP2.2, whereas GhFUL2 formed heterodimers with GhSEP3/GhSEP4 homologs and GhSVP2.2. The present results demonstrated that the functional divergence of GhAP1.1 and GhFUL2, which involved changes in sequences and expression patterns, influenced the regulation of cotton flower development.

Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense

Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.

GhSOC1s Evolve to Respond Differently to the Environmental Cues and Promote Flowering in Partially Independent Ways

Gossypium hirsutum is most broadly cultivated in the world due to its broader adaptation to the environment and successful breeding of early maturity varieties. However, how cotton responds to environmental cues to adjust flowering time to achieve reproductive success is largely unknown. SOC1 functions as an essential integrator for the endogenous and exogenous signals to maximize reproduction. Thus we identified six SOC1-like genes in Gossypium that clustered into two groups. GhSOC1-1 contained a large intron and clustered with monocot SOC1s, while GhSOC1-2/3 were close to dicot SOC1s. GhSOC1s expression gradually increased during seedling development suggesting their conserved function in promoting flowering, which was supported by the early flowering phenotype of 35S:GhSOC1-1 Arabidopsis lines and the delayed flowering of cotton silencing lines. Furthermore, GhSOC1-1 responded to short-day and high temperature conditions, while GhSOC1-2 responded to long-day conditions. GhSOC1-3 might function to promote flowering in response to low temperature and cold. Taken together, our results demonstrate that GhSOC1s respond differently to light and temperature and act cooperatively to activate GhLFY expression to promote floral transition and enlighten us in cotton adaptation to environment that is helpful in improvement of cotton maturity.

Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

Background

Alfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa.

Results

In the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mβ, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses.

Conclusions

In this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding.

Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07911-9.

Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response

MADS-box transcription factors play vital roles in multiple biological processes in plants. At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.) has not been reported. In this study, we identified 72 MADS-box genes in the foxtail millet genome and give an overview of the phylogeny, chromosomal location, gene structures, and potential functions of the proteins encoded by these genes. We also found that the expression of 10 MIKC-type MADS-box genes was induced by abiotic stresses (PEG-6000 and NaCl) and exogenous hormones (ABA and GA), which suggests that these genes may play important regulatory roles in response to different stresses. Further studies showed that transgenic Arabidopsis and rice (Oryza sativa L.) plants overexpressing SiMADS51 had reduced drought stress tolerance as revealed by lower survival rates and poorer growth performance under drought stress conditions, which demonstrated that SiMADS51 is a negative regulator of drought stress tolerance in plants. Moreover, expression of some stress-related genes were down-regulated in the SiMADS51-overexpressing plants. The results of our study provide an overall picture of the MADS-box gene family in foxtail millet and establish a foundation for further research on the mechanisms of action of MADS-box proteins with respect to abiotic stresses.

Functional Characterization of the EMBRYONIC FLOWER 2 Gene Involved in Flowering in Ginkgo biloba

Ginkgo biloba has edible, medicinal, and ornamental value. However, the long juvenile phase prevents the development of the G. biloba industry, and there are few reports on the identification and functional analysis of genes regulating the flowering time of G. biloba. EMBRYONIC FLOWER 2 (EMF), an important protein in flower development, functions to promote vegetative growth and repress flowering. In this study, a novel EMF gene (GbEMF2) was cloned and characterized from G. biloba. GbEMF2 contains a 2,193 bp open reading frame (ORF) encoding 730 amino acids. GbEMF2 harbors conserved VEFS-Box domain by the plant EMF protein. The phylogenic analysis showed that GbEMF2 originated from a polycomb-group (Pc-G) protein ancestor and was a member of the EMF2 protein. The quantitative real-time PCR (qRT-PCR) analysis revealed that GbEMF2 was expressed in all detected organs, and it showed a significantly higher level in ovulating strobilus and microstrobilus than in other organs. Compared with emf2 mutant plants, overexpression of GbEMF2 driven by the CaMV 35S promoter in emf2 mutant Arabidopsis plants delayed flowering but earlier than wild-type (WT) plants. This result indicated that GbEMF2 repressed flowering in G. biloba. Moreover, the RNA-seq analysis of GbEMF2 transgenic Arabidopsis plants (GbEMF2-OE/emf2), WT plants, and emf2 mutants screened out 227 differentially expressed genes (DEGs). Among these DEGs, FLC, MAF5, and MAF5-1 genes were related to flower organ development and regulated by GbEMF2. In addition, some genes participating in sugar metabolism, such as Alpha-amylase 1 (AMY1), BAM1, and Sucrose synthase 3 (SUS3) genes, were also controlled by GbEMF2. Overall, our results suggested that GbEMF2 negatively regulates flowering development in G. biloba. This finding provided a foundation and target gene for shortening the Ginkgo juvenile period by genetic engineering technology.

Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development

BACKGROUND

Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus.

RESULTS

To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis.

CONCLUSION

These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.

The MADS transcription factor GhAP1.7 coordinates the flowering regulatory pathway in upland cotton (Gossypium hirsutum L.)

MADS-box gene family plays an important role in the molecular regulatory network of flower development. APETALA1 (AP1), a MADS-box gene, plays an important role in the development of flower organs. Although many studies about MADS-box family genes have been reported, the function of AP1 is still not clear in cotton. In this study, GhAP1.7 (Gh_D03G0922), a candidate gene for cotton flower time and plant height obtained from our previous studies, was cloned from CCRI50 cotton variety and functionally characterized. Subcellular localization demonstrated that GhAP1.7 was located in nucleus. Infection test of Arabidopsis revealed that GhAP1.7 could cause precocious flowering and virus-induced gene silence (VIGS) assay demonstrated that GhAP1.7 could lead to delayed flowering of cotton plants. Yeast one-hybrid assays and transient dual-luciferase assays suggested that floral meristem identity control gene LEAFY (LFY) can bind the promoter of GhAP1.7 and negatively regulate it. Our research indicated that GhAP1.7 might work as a positive regulator in plant flowering. Moreover, GhAP1.7 may negatively regulated by GhLFY in the regulatory pathways. This work laid the foundation for subsequent functional studies of GhAP1.7.

Characterization of floral morphoanatomy and identification of marker genes preferentially expressed during specific stages of cotton flower development

Characterization of anther and ovule developmental programs and expression analyses of stage-specific floral marker genes in Gossypium hirsutum allowed to build a comprehensive portrait of cotton flower development before fiber initiation. Gossypium hirsutum is the most important cotton species that is cultivated worldwide. Although cotton reproductive development is important for fiber production, since fiber is formed on the epidermis of mature ovules, cotton floral development remains poorly understood. Therefore, this work aims to characterize the cotton floral morphoanatomy by performing a detailed description of anther and ovule developmental programs and identifying stage-specific floral marker genes in G. hirsutum. Using light microscopy and scanning electron microscopy, we analyzed anther and ovule development during 11 stages of flower development. To better characterize the ovule development in cotton, we performed histochemical analyses to evaluate the accumulation of phenolic compounds, pectin, and sugar in ovule tissues. After identification of major hallmarks of floral development, three key stages were established in G. hirsutum floral development: in stage 1 (early-EF), sepal, petal, and stamen primordia were observed; in stage 2 (intermediate-IF), primordial ovules and anthers are present, and the differentiating archesporial cells were observed, marking the beginning of microsporogenesis; and in stage 6 (late-LF), flower buds presented initial anther tapetum degeneration and microspore were released from the tetrad, and nucellus and both inner and outer integuments are developing. We used transcriptome data of cotton EF, IF and LF stages to identify floral marker genes and evaluated their expression by real-time quantitative PCR (qPCR). Twelve marker genes were preferentially expressed in a stage-specific manner, including the putative homologs for AtLEAFY, AtAPETALA 3, AtAGAMOUS-LIKE 19 and AtMALE STERILITY 1, which are crucial for several aspects of reproductive development, such as flower organogenesis and anther and petal development. We also evaluated the expression profile of B-class MADS-box genes in G. hirsutum floral transcriptome (EF, IF, and LF). In addition, we performed a comparative analysis of developmental programs between Arabidopsis thaliana and G. hirsutum that considered major morphoanatomical and molecular processes of flower, anther, and ovule development. Our findings provide the first detailed analysis of cotton flower development.

Genome-wide identification and evolution of Dof transcription factor family in cultivated and ancestral cotton species

The DNA-binding with one finger (Dof) proteins are transcription factors involved in many biological processes in plants. To predict the evolutionary pattern, a genome-wide in-silico analysis of Dof TFs family in diploid (Gossypium arboreum and Gossypium raimondii) and allotetraploid (Gossypium hirsutum and Gossypium barbadense) cotton species were carried out. In G. arboreum, we have identified 58 non-redundant genes encoding Dof proteins renamed as GaDof (G. arboreum Dof), 55 Dof genes were identified in G. raimondii (GrDof), 89 were predicted ffrom G. hirsutum (GhDof) and the highest, 110 Dof genes were identified in G. barbadense (GbDof). The phylogenetic analysis, physical location, gene structure, conserved domain analyses were also investigated for G. arboreum, G. raimondii, and G. hirsutum. The gene expression pattern in G. hirsutum, at different growth stages, revealing the probable involvement of some GhDof genes in growth and development. These genes may improve seed germination and growth in cotton.

Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.

Genome-wide identification and expression profile of the MADS-box gene family in Erigeron breviscapus

The MADS-box gene family encodes transcription factors with many biological functions that extensively regulate plant growth, development and reproduction. Erigeron breviscapus is a medicinal herb used widely in traditional Chinese medicine, and is believed to improve blood circulation and ameliorate platelet coagulation. In order to gain a detailed understanding of how transcription factor expression may regulate the growth of this potentially important medicinal plant, a genome-wide analysis of the MADS-box gene family of E. breviscapus is needed. In the present study, 44 MADS-box genes were identified in E. breviscapus and categorized into five subgroups (MIKC, Mα, Mβ, Mγ and Mδ) according to their phylogenetic relationships with the Arabidopsis MADS-box genes. Additionally, the functional domain, subcellular location and motif compositions of the E. breviscapus MADS-box gene products were characterized. The expression levels for each of the E. breviscapus MADS-box (EbMADS) genes were analyzed in flower, leaf, stem and root organs, and showed that the majority of EbMADS genes were expressed in flowers. Meanwhile, some MADS genes were found to express high levels in leaf, stem and root, indicating that the MADS-box genes are involved in various aspects of the physiological and developmental processes of the E. breviscapus. The results from gene expression analysis under different pollination treatments revealed that the MADS-box genes were highly expressed after non-pollinated treatment. To the best of our knowledge, this study describes the first genome-wide analysis of the E. breviscapus MADS-box gene family, and the results provide valuable information for understanding of the classification, cloning and putative functions of the MADS-box family.

Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.)

MADS-box genes play a pivotal role in various processes, including floral and seed development, controlling flowering time, regulation of fruits ripening, and respond to abiotic and biotic stressors in planta. Tobacco (Nicotiana tabacum) has been widely used as a model plant for analyzing the gene function, however, there has been less information on the regulation of flowering, and the associated genes. In the present study, a total of 168 NtMADS-box genes were identified from tobacco, and their phylogenetic relationship, chromosome locations, and gene structures were further analyzed. NtMADS-box genes can be clustered into four sub-families of Mα, Mγ, MIKC*, and MIKCC. A total of 111 NtMADS-box genes were distributed on 20 chromosomes, and 57 NtMADS-box genes were located on the unanchored scaffolds due to the complex and incomplete assembly of the tobacco genome. Expression profiles of NtMADS-box genes by microarray from 23 different tissues indicated that members in different NtMADS-box gene subfamilies might play specific roles in the growth and flower development, and the transcript levels of 24 NtMADS-box genes were confirmed by quantitative real-time PCR. Importantly, overexpressed NtSOC1/NtMADS133 could promote early flowering and dwarfism in transgenic tobacco plants. Therefore, our findings provide insights on the characterization of NtMADS-box genes to further study their functions in plant development.

Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum)

Genome-wide identification, expression analysis and potential functional characterization of previously uncharacterized MADS family of tartary buckwheat, emphasized the importance of this gene family in plant growth and development. The MADS transcription factor is a key regulatory factor in the development of most plants. The MADS gene in plants controls all aspects of tissue and organ growth and reproduction and can be used to regulate plant seed cracking. However, there has been little research on the MADS genes of tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allows us to study the tissue and expression profiles of the MADS gene in tartary buckwheat at a genome-wide level. In this study, 65 MADS genes of tartary buckwheat were identified and renamed according to the chromosomal distribution of the FtMADS genes. Here, we provide a complete overview of the gene structure, gene expression, genomic mapping, protein motif organization, and phylogenetic relationships of each member of the gene family. According to the phylogenetic relationship of MADS genes, the transcription factor family was divided into two subfamilies, the M subfamily (28 genes) and the MIKC subfamily (37 genes). The results showed that the FtMADS genes belonged to related sister pairs and the chromosomal map showed that the replication of FtMADSs was related to the replication of chromosome blocks. In different tissues and at different fruit development stages, the FtMADS genes obtained by real-time quantitative PCR (RT-qPCR) showed obvious expression patterns. A comprehensive analysis of the MADS genes in tartary buckwheat was conducted. Through systematic analysis, the potential genes that may regulate the growth and development of tartary buckwheat and the genes that may regulate the easy dehulling of tartary buckwheat fruit were screened, which laid a solid foundation for improving the quality of tartary buckwheat.