A Transcriptome Profile for Developing Seed of Polyploid Cotton

Hovav, Ran; Faigenboim-Doron, Adi; Kadmon, Noa; Hu, Guanjing; Zhang, Xia; Gallagher, Joseph P.; Wendel, Jonathan F.

doi:10.3835/plantgenome2014.08.0041

Cited by 32 publications

(45 citation statements)

References 66 publications

(72 reference statements)

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“…The results from RNA-seq analysis also show that while both homeologs of the GoPGF (synonym CGF3) gene are expressed in the developing embryos of glanded cotton, the A subgenome homeolog is more active, thus providing confirmation for the earlier contention that Gl 2 is expressed at higher level compared to Gl 3 gene in glanded cotton (Lee, 1965). Hovav et al (2015) conducted global transcriptome analysis on developing seeds of G. hirsutum (TM1) at 10, 20, 30 and 40 dpa and found that about 20% of the genes showed homeolog expression bias. This group also observed that the ACGF3 homeolog in TM1 had higher level of expression than DCGF3 in the seeds at 30-and 40-dpa.…”

Section: -3supporting

confidence: 58%

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Genes regulating gland development in the cotton plant

Janga

Pandeya

Campbell

et al. 2018

Plant Biotechnology Journal

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Summary In seeds and other parts of cultivated, tetraploid cotton ( Gossypium hirsutum L.), multicellular groups of cells lysigenously form dark glands containing toxic terpenoids such as gossypol that defend the plant against pests and pathogens. Using RNA ‐seq analysis of embryos from near‐isogenic glanded ( Gl 2 Gl 2 Gl 3 Gl 3 ) versus glandless ( gl 2 gl 2 gl 3 gl 3 ) plants, we identified 33 genes that expressed exclusively or at higher levels in embryos just prior to gland formation in glanded plants. Virus‐induced gene silencing against three gene pairs led to significant reductions in the number of glands in the leaves, and significantly lower levels of gossypol and related terpenoids. These genes encode transcription factors and have been designated the ‘Cotton Gland Formation’ ( CGF ) genes. No sequence differences were found between glanded and glandless cotton for CGF 1 and CGF 2 gene pairs. The glandless cotton has a transposon insertion within the coding sequence of the Go PGF (synonym CGF 3 ) gene of the A subgenome and extensive mutations in the promoter of D subgenome homeolog. Overexpression of Go PGF (synonym CGF 3 ) led to a dramatic increase in gossypol and related terpenoids in cultured cells, whereas CRISPR /Cas9 knockout of Go PGF (synonym CGF 3 ) genes resulted in glandless phenotype. Taken collectively, the results show that the Go PGF (synonym CGF 3 ) gene plays a critical role in the formation of glands in the cotton plant. Seed‐specific silencing of CGF genes, either individually or in combination, could eliminate glands, thus gossypol, from the cottonseed to render it safe as food or feed for monogastrics.

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Section: -3supporting

confidence: 58%

“…Hovav et al . () conducted global transcriptome analysis on developing seeds of G. hirsutum (TM1) at 10, 20, 30 and 40 dpa and found that about 20% of the genes showed homeolog expression bias. This group also observed that the ACGF3 homeolog in TM1 had higher level of expression than DCGF3 in the seeds at 30‐ and 40‐dpa.…”

Section: Discussionmentioning

confidence: 99%

Genes regulating gland development in the cotton plant

Janga

Pandeya

Campbell

et al. 2018

Plant Biotechnology Journal

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“…Among them, acetyl-CoA carboxylase (ACCase) (E.C. 6.4.1.2) is an important enzyme, which catalyze acetyl-CoA to produce malonyl-CoA, and can be served as a committed step for de novo fatty acid biosynthesis in plastid (Sasaki and Nagano, 2004; Fukuda et al, 2013; Ran et al, 2015; Sood and Chauhan, 2015). In dicotyledon and non-graminaceous monocotyledon plants, plastidial ACCase is a multi-subunit complex comprised of four different polypeptides (biotin carboxyl carrier protein, BCCP; biotin carboxylase, BC; α- and β-carboxyltransferase subunits, α-CT and β-CT) with the exception of rapeseed plastid, which contains multifunctional ACCase comprised of a large multifunctional polypeptide (Elborough et al, 1996; Schulte et al, 1997; Sasaki and Nagano, 2004; Cui et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Biotin Carboxyl Carrier Subunits of Heteromeric Acetyl-CoA Carboxylase in Gossypium

et al. 2017

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Acetyl-CoA carboxylase is an important enzyme, which catalyzes acetyl-CoA’s carboxylation to produce malonyl-CoA and to serve as a committed step for de novo fatty acid biosynthesis in plastids. In this study, 24 putative cotton BCCP genes were identified based on the lately published genome data in Gossypium . Among them, 4, 4, 8, and 8 BCCP homologs were identified in Gossypium raimondii, G. arboreum, G. hirsutum , and G. barbadense , respectively. These genes were divided into two classes based on a phylogenetic analysis. In each class, these homologs were relatively conserved in gene structure and motifs. The chromosomal distribution pattern revealed that all the BCCP genes were distributed equally on corresponding chromosomes or scaffold in the four cotton species. Segmental duplication was a predominant duplication event in both of G. hirsutum and G. barbadense. The analysis of the expression profile showed that 8 GhBCCP genes expressed in all the tested tissues with changed expression levels, and GhBCCP genes belonging to class II were predominantly expressed in developing ovules. Meanwhile, the expression analysis for the 16 cotton BCCP genes from G. raimondii, G. arboreum and G. hirsutum showed that they were induced or suppressed by cold or salt stress, and their expression patterns varied among different tissues. These findings will help to determine the functional and evolutionary characteristics of the BCCP genes in Gossypium species.

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“…Compared with these methods, high-throughput RNA sequencing (RNA-seq) can provide information on whole-genome gene expression with low background signals, more accurate quantification, a large dynamic range in expression levels and high levels of reproducibility [ 21 ]. In recent years, RNA-seq has been frequently used to investigate the transcriptomes of plant seeds, such as cotton [ 22 ], wheat [ 23 ], Brassica napus [ 24 ] and chrysanthemum [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

Liu

Wang

2020

Plants

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Polyploidization is a universal phenomenon in plants and plays a crucial role in evolution. In this study, the transcriptomes of developing seeds of a synthetic Brassica hexaploid and its parents (B. rapa and B. carinata) were analyzed to find the gene expression changes in hexaploid seeds. There were 3166 and 3893 DEGs between the Brassica hexaploid and its parents at the full-size stage and mature stage, respectively, most of which were upregulated in hexaploid seeds compared to its parents. At the mature stage, the hexaploid seeds showed a greater difference from its parents. These DEGs had a wide range of functions, which may account for the physiological and morphological differences between the Brassica hexaploid and its parents. The KEGG pathway analysis revealed that hexaploid seeds had higher levels of expression of genes involved in metabolic pathways, RNA transport and biosynthesis of secondary metabolites, and the expression levels in the photosynthesis-related pathways were significantly higher than those in B. rapa. Transgressive expression was the main non-additive expression pattern of the Brassica hexaploid. The gene expression difference between the Brassica hexaploid and its paternal parent was more significant than that with its maternal parent, which may be due in part to the cytoplasmic and maternal effects. Moreover, transcription factor genes, such as G2-like, MYB and mTERF, were highly expressed in hexaploid seeds, possibly promoting their resistance to stress. Our results may provide valuable insights into the adaptation mechanisms of polyploid plants.

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A Transcriptome Profile for Developing Seed of Polyploid Cotton

Cited by 32 publications

References 66 publications

Genes regulating gland development in the cotton plant

Genes regulating gland development in the cotton plant

Genome-Wide Identification and Expression Analysis of the Biotin Carboxyl Carrier Subunits of Heteromeric Acetyl-CoA Carboxylase in Gossypium

Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

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