Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

Salih, Haron; Gong, Wenfang; He, Shoupu; Sun, Gaofei; Sun, Junling; Du, Xinying

doi:10.1186/s12863-016-0436-8

Cited by 111 publications

(88 citation statements)

References 57 publications

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“…MYB plays crucial roles in different processes, including primary and secondary metabolisms, such as the regulation of various phytochemical biosynthesis pathways, regulation of several developmental processes, such as cell fate determination in root hairs, secondary cell wall biosynthesis, establishment of the axillary branch patterning, leaf proximodistal axis and anther development, and responses to environmental stimuli [92, 93]. For instance, in upland cotton, GhMYB s may be involved in regulating specialized outgrowths of epidermal cells, including cotton fiber development during different developmental stages [93], and several MYB genes in cotton were differentially expressed under salt and drought stress treatments [92]. Additionally, many MYB genes in other plant species were involved in regulating responses to biotic and abiotic stresses, and enhanced the tolerance to stresses in transgenic plants [94, 95].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

et al. 2017

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BackgroundSuperoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton.ResultsIn the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified and phylogenetically classified into five subgroups which corroborated their classifications based on gene-structure patterns and subcellular localizations. The GhSOD sequences were distributed at different densities across 12 of the 26 chromosomes. The conserved domains, gene family evolution cis-acting elements of promoter regions and miRNA-mediated posttranscriptional regulation were predicted and analyzed. In addition, the expression pattern of 18 GhSOD genes were tested in different tissues/organs and developmental stages, and different abiotic stresses and abscisic acid, which indicated that the SOD gene family possessed temporal and spatial specificity expression specificity and may play important roles in reactive oxygen species scavenging caused by various stresses in upland cotton.ConclusionsThis study describes the first genome-wide analysis of the upland cotton SOD gene family, and the results will help establish a foundation for the further cloning and functional verification of the GhSOD gene family during stress responses, leading to crop improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3768-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

et al. 2017

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“…Transcription factors also regulate fiber strength (Salih et al 2016). We identified common DEGs associated with these processes ( e.g.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton (Gossypium barbadense) Increase Fiber Strength in Upland Cotton (Gossypium hirsutum)

Lú

Shí

Xiao

et al. 2017

G3 Genes|Genomes|Genetics

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As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high-strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality. We then selected two CSSLs with significantly higher fiber strength than CCRI45 (MBI7747 and MBI7561), and one CSSL with lower fiber strength than CCRI45 (MBI7285), for further analysis. We sequenced all four transcriptomes at four different time points postanthesis, and clustered the 44,678 identified genes by function. We identified 2200 common differentially-expressed genes (DEGs): those that were found in both high quality CSSLs (MBI7747 and MBI7561), but not in the low quality CSSL (MBI7285). Many of these genes were associated with various metabolic pathways that affect fiber strength. Upregulated DEGs were associated with polysaccharide metabolic regulation, single-organism localization, cell wall organization, and biogenesis, while the downregulated DEGs were associated with microtubule regulation, the cellular response to stress, and the cell cycle. Further analyses indicated that three genes, XLOC_036333 [mannosyl-oligosaccharide-α-mannosidase (MNS1)], XLOC_029945 (FLA8), and XLOC_075372 (snakin-1), were potentially important for the regulation of cotton fiber strength. Our results suggest that these genes may be good candidates for future investigation of the molecular mechanisms of fiber strength formation and for the improvement of cotton fiber quality through molecular breeding.

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“…Myeloblastosis genes comprise a large family of transcription factors in plants and are involved in a variety of biological functions (Allan et al, 2008). There are at least 524 nonredundant MYB genes in cotton (Salih et al, 2016a). GL1 is a well-characterized MYB gene that plays an essential role in Arabidopsis leaf trichome initiation (Larkin et al, 1994).…”

Section: Myb Genes and Their Roles In Fiber Initiationmentioning

confidence: 99%

Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era

2018

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Cotton (Gossypium spp.) fibers are unicellular trichomes that differentiate from ovule epidermal cells. Cotton fiber development is divided into four distinct yet overlapping stages: initiation, elongation, secondary cell wall (SCW) biosynthesis, and maturation. There are numerous naturally occurring and man‐made fiber mutants that display aberrant phenotypes ranging from fiberless to extremely short fiber, and to immature fiber. These mutants have provided cotton researchers an excellent model system to study fiber growth and development. During the past two decades, much advancement in the understanding of fiber development has been achieved through comparative analyses of fiber mutants and wild‐type cotton lines using a variety of technologies such as transcriptomic analysis and genetic mapping. The causative genes of five mutations related to fiber initiation, elongation, or SCW assembly have been identified. Lint and fuzz fiber initiations are regulated by MYBMIXTA‐like transcription factors along with many other genes. Cytoskeleton actins play a critical role in fiber elongation. Genes that are involved in biological processes such as transporting osmoticum or loosening cell walls are highly expressed during the elongation stage. Production of large amounts of cellulose at the SCW stage requires a sustainable supply of energy and carbohydrate precursors. Plant hormones affect fiber development. In this paper, we review progress in the elucidation of fiber development mechanisms based on analyzing fiber mutants and summarize genes and mechanisms that are critical to fiber development. We identify research gaps that should be future research priorities and provide a future perspective.

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Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

Cited by 111 publications

References 57 publications

Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton (Gossypium barbadense) Increase Fiber Strength in Upland Cotton (Gossypium hirsutum)

Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era

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