scholarly journals Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat (Triticum aestivum L.) and Possible Roles in Anther Development

2020 ◽  
Vol 21 (2) ◽  
pp. 608 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Gan Hu ◽  
Qi Liu ◽  
Wei Li ◽  
...  
Keyword(s):  
Heat Shock ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Heat Shock Protein 90 ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Anther Development ◽  
Male Sterile ◽  
Specific Expression ◽  
Genome Wide

Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Recently, HSFs have been shown to play roles in anther development. Thus, investigating the HSF family members and identifying their protective roles in anthers are essential for the further development of male sterile wheat breeding. In the present study, 61 wheat HSF genes (TaHsfs) were identified in the whole wheat genome and they are unequally distributed on 21 chromosomes. According to gene structure and phylogenetic analyses, the 61 TaHsfs were classified into three categories and 12 subclasses. Genome-wide duplication was identified as the main source of the expansion of the wheat HSF gene family based on 14 pairs of homeologous triplets, whereas only a very small number of TaHsfs were derived by segmental duplication and tandem duplication. Heat shock protein 90 (HSP90), HSP70, and another class of chaperone protein called htpG were identified as proteins that interact with wheat HSFs. RNA-seq analysis indicated that TaHsfs have obvious period- and tissue-specific expression patterns, and the TaHsfs in classes A and B respond to heat shock, whereas the C class TaHsfs are involved in drought regulation. qRT-PCR identified three TaHsfA2bs with differential expression in sterile and fertile anthers, and they may be candidate genes involved in anther development. This comprehensive analysis provides novel insights into TaHsfs, and it will be useful for understanding the mechanism of plant fertility conversion.

scholarly journals Genome-wide investigation of heat shock transcription factor family in wheat (Triticum aestivum L.)

2019 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Sha Li ◽  
Wei Li ◽  
Qi Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Reference Genome ◽  
Phylogenetic Analyses ◽  
Triticum Aestivum L ◽  
Growth Stages ◽  
Rna Seq ◽  
Male Sterile ◽  
Heat Shock Transcription Factors ◽  
Genome Wide ◽  
Resistance To Heat

Abstract Background: Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Investigating the HSF family is essential for understanding the fertility conversion mechanism in thermo-sensitive male sterile wheat. Previous studies have investigated the HSF family in wheat but it is necessary to conduct more in-depth and systematic analyses based on the newly published reference genome. Results: In the present study, 61 wheat Hsf (TaHsf) genes were identified using two main strategies and renamed based on their physical locations on chromosomes. According to the gene structure and phylogenetic analyses, the 61 TaHsf genes were classified into three categories and eleven subclasses. The genes were unequally distributed on 21 chromosomes, including two pairs of tandem duplication genes and 52 TaHsf segmental duplication genes. According to the cis-elements identified, most of the TaHsfs can be activated by Ca++ and MYB, and they respond to drought, light, copper, and other stresses as well as heat shock. RNA-seq analysis indicated that the A2 class TaHsf genes exhibited persistently upregulated expression levels in the leaves/shoots, roots (except in the vegetative growth and reproductive growth stages), spikes, and grains in wheat under normal conditions. The A and B class TaHsf genes were positively regulated during the resistance to heat, whereas the C class genes were involved in drought regulation in wheat. Only the A and B class TaHsf genes were upregulated under fertile conditions in thermo-sensitive male sterile wheat. Conclusion: In this study, 61 wheat Hsf genes were identified based on the complete wheat reference genome. This comprehensive analysis provides novel insights into the TaHsf genes, including their diverse functions and involvement in metabolic pathways.

scholarly journals Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiseong Jeong ◽  
Sunhee Park ◽  
Jeong Hui Im ◽  
Hankuil Yi
Keyword(s):  
Promoter Region ◽  
Expression Patterns ◽  
Leaf Primordia ◽  
Start Codon ◽  
Male Sterile ◽  
Base Pairs ◽  
Specific Expression ◽  
Group Iii ◽  
Genome Wide ◽  
Floral Abscission

Abstract Background The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results As a first step to understand regulation and molecular functions of Group III subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13–1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13–1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions Sixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) in BoGH3.13–1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.

scholarly journals Genome-Wide Identification of GH3 Genes in Brassica Oleracea and Identification of a Promoter Region for Anther-Specific Expression of a GH3 Gene

2020 ◽  
Author(s):  
Hankuil Yi ◽  
Jiseong Jeong ◽  
Sunhee Park ◽  
Jeong Hui Im
Keyword(s):  
Brassica Oleracea ◽  
Promoter Region ◽  
Expression Patterns ◽  
Leaf Primordia ◽  
Start Codon ◽  
Male Sterile ◽  
Specific Expression ◽  
Genome Wide ◽  
Tapetal Cells ◽  
Floral Abscission

Abstract Background:The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group Ⅲ subgroup 6 GH3 genes, and their expression patterns in economically important kale-type Brassica oleracea have not been systematically identified. Results:As a first step to understand regulation and molecular functions of Group Ⅲ subgroup 6 GH3 genes, thirty-four GH3 genes including four subgroup 6 genes were identified In B. oleracea var. oleracea, using TO1000. Synteny found around subgroup 6 GH3 genes in TO1000 and Arabidopsis indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in TO1000 is not induced by auxin, gibberellic acid, and jasmonic acid, the genes show different organ-dependent expression patterns. Only one TO1000 subgroup 6 GH3 gene, Bo2g011210, is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic Arabidopsis subgroup 6 GH3 genes. Detailed analyses of promoter activities of Bo2g011210 further showed that Bo2g011210 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions:Sixty-two base pair (bp) region (-340 ~ -279 bp upstream from start codon) and about 450 bp region (-1489 to -1017 bp) in Bo2g011210 promoter were found to be important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region will be useful to develop male sterile transgenic Brassica plants.

scholarly journals Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene

2020 ◽  
Author(s):  
Jiseong Jeong ◽  
Sunhee Park ◽  
Jeong Hui Im ◽  
Hankuil Yi
Keyword(s):  
Promoter Region ◽  
Expression Patterns ◽  
Leaf Primordia ◽  
Start Codon ◽  
Male Sterile ◽  
Base Pairs ◽  
Specific Expression ◽  
Genome Wide ◽  
Tapetal Cells ◽  
Floral Abscission

Abstract Background: The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group Ⅲ subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results: As a first step to understand regulation and molecular functions of Group Ⅲ subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13-1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13-1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions: Sixty-two base pairs (bp) region (-340 ~ -279 bp upstream from start codon) and about 450 bp region (-1489 to -1017 bp) in BoGH3.13-1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.

scholarly journals Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene

2020 ◽  
Author(s):  
Jiseong Jeong ◽  
Sunhee Park ◽  
Jeong Hui Im ◽  
Hankuil Yi
Keyword(s):  
Promoter Region ◽  
Expression Patterns ◽  
Leaf Primordia ◽  
Start Codon ◽  
Male Sterile ◽  
Base Pairs ◽  
Specific Expression ◽  
Genome Wide ◽  
Tapetal Cells ◽  
Floral Abscission

Abstract Background: The Gretchen Hagen 3 ( GH3 ) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group Ⅲ subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results: As a first step to understand regulation and molecular functions of Group Ⅲ subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea . Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea , only BoGH3.13-1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13-1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions: Sixty-two base pairs (bp) region (-340 ~ -279 bp upstream from start codon) and about 450 bp region (-1489 to -1017 bp) in BoGH3.13-1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.

scholarly journals A comprehensive analysis of the polygalacturonase family of wheat (Triticum aestivum L.) shed light on important genes affecting pollen development and anther dehiscence

2019 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Wei Li ◽  
Qi Liu ◽  
Fuqiang Niu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Pollen Development ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Male Sterile ◽  
Specific Expression ◽  
Meristematic Tissue ◽  
Hormonal Stimulation ◽  
Wide Range

Abstract Background: Polygalacturonase (PG) belongs to a large family of hydrolases that undertake many important functions in cell separation during plant growth and development by degrading pectin. The specific expression of PG genes in pollen may have great significance for plant male sterile research and hybrid wheat breeding. However, it has not been reported in wheat ( Triticum aestivum L.). Results: Therefore, we systematically studied the PG gene family using the latest published wheat reference genomic information. A total of 113 PGs were identified and renamed as TaPG01 - 113 based on their position on the chromosome. They were unequally distributed on 21 chromosomes and were classified into six categories of A-F. Analysis of gene structures and conserved motifs revealed that the TaPGs of Class C and D had relatively short gene sequences and a small number of introns, and Class E TaPGs were the least conserved and all members did not have III conserved domain. Segmental duplication has been shown to be one of the major drivers of the expansion of the wheat PG gene family. The cis-element predictions indicate that wheat PGs had a wide range of functions, including response to light, hypothermia, anaerobic and hormonal stimulation, and also involved in meristematic tissue expression. In addition, twelve spike-specific expressions of TaPGs were screened using RNA-seq data, and finally three important genes were identified by expression analysis in the sterile and fertile anthers of thermo-sensitive male sterile wheat. TaPG93 was involved in the pollen development and elongation of pollen tubes, and TaPG87 and TaPG95 played important roles in the separation of pollen grains and the cracking of anthers dehiscence. Conclusions: This study, we performed a thorough analysis of the wheat PG gene family and finally obtained three TaPGs that affect wheat fertility. This will lay a solid foundation for the function exploration of wheat PG gene family and provide new enlightenment for the fertility conversion mechanism of male sterile wheat.

scholarly journals Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Dezhou Wang ◽  
Zhichen Cao ◽  
Weiwei Wang ◽  
Wengen Zhu ◽  
Xiaocong Hao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Drought Tolerance ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
Genetically Engineer

OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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