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Li W, Chu C, Li H, Zhang H, Sun H, Wang S, Wang Z, Li Y, Foster TM, López-Girona E, Yu J, Li Y, Ma Y, Zhang K, Han Y, Zhou B, Fan X, Xiong Y, Deng CH, Wang Y, Xu X, Han Z. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet 2024; 56:505-516. [PMID: 38347217 DOI: 10.1038/s41588-024-01657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/08/2024] [Indexed: 03/16/2024]
Abstract
Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.
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Affiliation(s)
- Wei Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Hui Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Haochen Sun
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Shiyao Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zijun Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yuqi Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Toshi M Foster
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Motueka, New Zealand
| | - Elena López-Girona
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Jiaxin Yu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, USA
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yongming Han
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Bowen Zhou
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Xingqiang Fan
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yao Xiong
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Auckland, New Zealand.
| | - Yi Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
| | - Xuefeng Xu
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zhenhai Han
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
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Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E, Podkolodnyy N, Ponomarenko P, Savinkova L, Tverdokhleb N, Khandaev B, Kondratyuk E, Podkolodnaya O, Zemlyanskaya E, Kolchanov NA, Ponomarenko M. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L. Int J Mol Sci 2024; 25:607. [PMID: 38203780 PMCID: PMC10779315 DOI: 10.3390/ijms25010607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/18/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Sergey Filonov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Bato Khandaev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk 630501, Novosibirsk Region, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
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3
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Arpita K, Sharma S, Srivastava H, Kumar K, Mushtaq M, Gupta P, Jain R, Gaikwad K. Genome-wide survey, molecular evolution and expression analysis of Auxin Response Factor (ARF) gene family indicating their key role in seed number per pod in pigeonpea (C. cajan L. Millsp.). Int J Biol Macromol 2023; 253:126833. [PMID: 37709218 DOI: 10.1016/j.ijbiomac.2023.126833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Auxin Response Factors (ARF) are a family of transcription factors that mediate auxin signalling and regulate multiple biological processes. Their crucial role in increasing plant biomass/yield influenced this study, where a systematic analysis of ARF gene family was carried out to identify the key proteins controlling embryo/seed developmental pathways in pigeonpea. A genome-wide scan revealed the presence of 12 ARF genes in pigeonpea, distributed across the chromosomes 1, 3, 4, 8 and 11. Domain analysis of ARF proteins showed the presence of B3 DNA binding, AUX response, and IAA domains. Majority of them are of nuclear origin, and do not exhibit the level of genomic expansion as observed in Glycine max (51 members). The duplication events seem to range from 31.6 to 42.3 million years ago (mya). Promoter analysis revealed the presence of multiple cis-acting elements related to stress responses, hormone signalling and other development processes. The expression atlas data highlighted the expression of CcARF8 in hypocotyl, bud and flower whereas, CcARF7 expression was significantly high in pod. The real-time expression of CcARF2, CcARF3 and CcARF18 was highest in genotypes with high seed number indicating their key role in regulating embryo development and determining seed set in pigeonpea.
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Affiliation(s)
- Kumari Arpita
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
| | - Harsha Srivastava
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India
| | - Muntazir Mushtaq
- Shoolini Univeristy of Biotechnology and Management Sciences, Himachal Pradesh 173229, India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Rishu Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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4
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Rienstra J, Hernández-García J, Weijers D. To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6922-6932. [PMID: 37431145 PMCID: PMC10690724 DOI: 10.1093/jxb/erad259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Most plant growth and development processes are regulated in one way or another by auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through the nuclear auxin pathway (NAP). In this pathway, Auxin Response Factors (ARFs) are the transcription factors that ultimately determine which genes become auxin regulated by binding to specific DNA sequences. ARFs have primarily been studied in Arabidopsis thaliana, but recent studies in other species have revealed family-wide DNA binding specificities for different ARFs and the minimal functional system of the NAP system, consisting of a duo of competing ARFs of the A and B classes. In this review, we provide an overview of key aspects of ARF DNA binding such as auxin response elements (TGTCNN) and tandem repeat motifs, and consider how structural biology and in vitro studies help us understand ARF DNA preferences. We also highlight some recent aspects related to the regulation of ARF levels inside a cell, which may alter the DNA binding profile of ARFs in different tissues. We finally emphasize the need to study minimal NAP systems to understand fundamental aspects of ARF function, the need to characterize algal ARFs to understand how ARFs evolved, how cutting-edge techniques can increase our understanding of ARFs, and which remaining questions can only be answered by structural biology.
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Affiliation(s)
- Juriaan Rienstra
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Jorge Hernández-García
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
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5
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Iohannes SD, Jackson D. Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. THE NEW PHYTOLOGIST 2023; 240:1381-1389. [PMID: 37724752 DOI: 10.1111/nph.19267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed 'a geneticist's nightmare': It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies - the next frontier in plant functional studies.
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Affiliation(s)
- Sessen Daniel Iohannes
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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Ruidong S, Shijin H, Yuwei Q, Yimeng L, Xiaohang Z, Ying L, Xihang L, Mingyang D, Xiangling L, Fenghai L. Identification of QTLs and their candidate genes for the number of maize tassel branches in F 2 from two higher generation sister lines using QTL mapping and RNA-seq analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1202755. [PMID: 37641589 PMCID: PMC10460468 DOI: 10.3389/fpls.2023.1202755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
Tassel branch number is an important agronomic trait that is closely associated with maize kernels and yield. The regulation of genes associated with tassel branch development can provide a theoretical basis for analyzing tassel branch growth and improving maize yield. In this study. we used two high-generation sister maize lines, PCU (unbranched) and PCM (multiple-branched), to construct an F2 population comprising 190 individuals, which were genotyped and mapped using the Maize6H-60K single-nucleotide polymorphism array. Candidate genes associated with tassel development were subsequently identified by analyzing samples collected at three stages of tassel growth via RNA-seq. A total of 13 quantitative trait loci (QTLs) and 22 quantitative trait nucleotides (QTNs) associated with tassel branch number (TBN) were identified, among which, two major QTLs, qTBN6.06-1 and qTBN6.06-2, on chromosome 6 were identified in two progeny populations, accounting for 15.07% to 37.64% of the phenotypic variation. Moreover, we identified 613 genes that were differentially expressed between PCU and PCM, which, according to Kyoto Encyclopedia of Genes and Genomes enrichment analysis, were enriched in amino acid metabolism and plant signal transduction pathways. Additionally, we established that the phytohormone content of Stage I tassels and the levels of indole-3-acetic acid (IAA) and IAA-glucose were higher in PCU than in PCM plants, whereas contrastingly, the levels of 5-deoxymonopolyl alcohol in PCM were higher than those in PCU. On the basis of these findings, we speculate that differences in TBN may be related to hormone content. Collectively, by combining QTL mapping and RNA-seq analysis, we identified five candidate genes associated with TBN. This study provides theoretical insights into the mechanism of tassel branch development in maize.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lv Xiangling
- Special Corn Institute, Shenyang Agricultural University, Shenyang, China
| | - Li Fenghai
- Special Corn Institute, Shenyang Agricultural University, Shenyang, China
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Lim H, Kobayashi MJ, Marsoem SN, Irawati D, Kosugi A, Kondo T, Tani N. Transcriptomic responses of oil palm ( Elaeis guineensis) stem to waterlogging at plantation in relation to precipitation seasonality. FRONTIERS IN PLANT SCIENCE 2023; 14:1213496. [PMID: 37636106 PMCID: PMC10448820 DOI: 10.3389/fpls.2023.1213496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Global warming-induced climate change causes significant agricultural problems by increasing the incidence of drought and flooding events. Waterlogging is an inevitable consequence of these changes but its effects on oil palms have received little attention and are poorly understood. Recent waterlogging studies have focused on oil palm seedlings, with particular emphasis on phenology. However, the transcriptomic waterlogging response of mature oil palms remains elusive in real environments. We therefore investigated transcriptomic changes over time in adult oil palms at plantations over a two-year period with pronounced seasonal variation in precipitation. A significant transcriptional waterlogging response was observed in the oil palm stem core but not in leaf samples when gene expression was correlated with cumulative precipitation over two-day periods. Pathways and processes upregulated or enriched in the stem core response included hypoxia, ethylene signaling, and carbon metabolism. Post-waterlogging recovery in oil palms was found to be associated with responses to heat stress and carotenoid biosynthesis. Nineteen transcription factors (TFs) potentially involved in the waterlogging response of mature oil palms were also identified. These data provide new insights into the transcriptomic responses of planted oil palms to waterlogging and offer valuable guidance on the sensitivity of oil palm plantations to future climate changes.
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Affiliation(s)
- Hui Lim
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masaki J. Kobayashi
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | | | - Denny Irawati
- Faculty of Forestry, Universitas Gadjah Mada (UGM), Yogyakarta, Indonesia
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Toshiaki Kondo
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Zhao P, Zhang J, Chen S, Zhang Z, Wan G, Mao J, Wang Z, Tan S, Xiang C. ERF1 inhibits lateral root emergence by promoting local auxin accumulation and repressing ARF7 expression. Cell Rep 2023; 42:112565. [PMID: 37224012 DOI: 10.1016/j.celrep.2023.112565] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/28/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Lateral roots (LRs) are crucial for plants to sense environmental signals in addition to water and nutrient absorption. Auxin is key for LR formation, but the underlying mechanisms are not fully understood. Here, we report that Arabidopsis ERF1 inhibits LR emergence by promoting local auxin accumulation with altered distribution and regulating auxin signaling. Loss of ERF1 increases LR density compared with the wild type, whereas ERF1 overexpression causes the opposite phenotype. ERF1 enhances auxin transport by upregulating PIN1 and AUX1, resulting in excessive auxin accumulation in the endodermal, cortical, and epidermal cells surrounding LR primordia. Furthermore, ERF1 represses ARF7 transcription, thereby downregulating the expression of cell-wall remodeling genes that facilitate LR emergence. Together, our study reveals that ERF1 integrates environmental signals to promote local auxin accumulation with altered distribution and repress ARF7, consequently inhibiting LR emergence in adaptation to fluctuating environments.
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Affiliation(s)
- Pingxia Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Jing Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Siyan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zisheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Guangyu Wan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jieli Mao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zhen Wang
- College of Life Sciences, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Shutang Tan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Chengbin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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Li Y, Han S, Qi Y. Advances in structure and function of auxin response factor in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:617-632. [PMID: 36263892 DOI: 10.1111/jipb.13392] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops.
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Affiliation(s)
- Yonghui Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Shaqila Han
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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10
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Yin Y, Xie X, Zhou L, Yin X, Guo S, Zhou X, Li Q, Shi X, Peng C, Gao J. A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:1003835. [PMID: 36226278 PMCID: PMC9549246 DOI: 10.3389/fpls.2022.1003835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/06/2022] [Indexed: 06/01/2023]
Abstract
Curcuma longa, known as the 'golden spice' and 'life spice', is one of the most commonly utilized spices in the world and also has medicinal, cosmetic, dye and flavoring values. Herein, we present the chromosomal-level genome for turmeric to explore the differences between tubers and rhizomes in the regulation of curcumin biosynthesis and the mechanism of tuber formation. We assembled the turmeric genome into 21 pseudochromosomes using Pacbio long reads complemented with Hi-C technologies, which has a total length of 1.11 Gb with scaffold N50 of 50.12 Mb and contains 49,612 protein-coding genes. Genomic evolutionary analysis indicated that turmeric and ginger have shared a recent WGD event. Contraction analysis of gene families showed possible roles for transcription factors, phytohormone signaling, and plant-pathogen interactions associated genes in adaptation to harsh environments. Transcriptomic data from tubers at different developmental stages indicated that candidate genes related to phytohormone signaling and carbohydrate metabolic responses may be associated with the induction of tuber formation. The difference in curcumin content between rhizomes and tubers reflected the remodeling of secondary metabolites under environmental stress, which was associated with plant defense in response to abiotic stresses. Overall, the availability of the C. longa genome provides insight into tuber formation and curcumin biosynthesis in turmeric as well as facilitating the understanding of other Curcuma species.
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Affiliation(s)
- Yanpeng Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaofang Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Luojing Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianmei Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianjian Zhou
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Traditional Chinese Medicine Sciences, Chengdu, China
| | - Qingmiao Li
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Traditional Chinese Medicine Sciences, Chengdu, China
| | - Xiaodong Shi
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jihai Gao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Zhu X, Sun F, Sang M, Ye M, Bo W, Dong A, Wu R. Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica. FRONTIERS IN PLANT SCIENCE 2022; 13:870876. [PMID: 35783952 PMCID: PMC9240601 DOI: 10.3389/fpls.2022.870876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica, which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica. Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.
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Affiliation(s)
- Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Fengshuo Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Wenhao Bo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Liang F, Zhang Y, Wang X, Yang S, Fang T, Zheng S, Zeng L. Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan ( Dimocarpus longan Lour.). FRONTIERS IN PLANT SCIENCE 2022; 13:923183. [PMID: 35774802 PMCID: PMC9237614 DOI: 10.3389/fpls.2022.923183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 05/27/2023]
Abstract
Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.
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Affiliation(s)
- Fan Liang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiyong Zhang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Wang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuo Yang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Fang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoquan Zheng
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzho, China
| | - Lihui Zeng
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Yue X, Su T, Xin X, Li P, Wang W, Yu Y, Zhang D, Zhao X, Wang J, Sun L, Jin G, Yu S, Zhang F. The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 13:918112. [PMID: 35755702 PMCID: PMC9224592 DOI: 10.3389/fpls.2022.918112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.
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Affiliation(s)
- Xiaozhen Yue
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiao Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Liling Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Guihua Jin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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Zhao Y, Wang Y, Zhao X, Yan M, Ren Y, Yuan Z. ARF6s Identification and Function Analysis Provide Insights Into Flower Development of Punica granatum L. FRONTIERS IN PLANT SCIENCE 2022; 13:833747. [PMID: 35321445 PMCID: PMC8937018 DOI: 10.3389/fpls.2022.833747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1-14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1-12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers.
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Affiliation(s)
- Yujie Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuying Wang
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xueqing Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ming Yan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuan Ren
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaohe Yuan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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15
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Mobile Messenger RNAs in Grafts of Salix matsudana Are Associated with Plant Rooting. FORESTS 2022. [DOI: 10.3390/f13020354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Messenger RNAs exchanged between scions and rootstocks of grafted plants seriously affect their traits performance. The study goals were to identify the long-distance mRNA transmission events in grafted willows using a transcriptome analysis and to reveal the possible effects on rooting traits. The results showed that the Salix matsudana variety 9901 has better rooting ability than YJ, which reasonably improved the rooting performance of the heterologous grafts 9901 (scion)/YJ (rootstock). A transcriptome analysis showed that 2948 differentially expressed genes (DEGs) were present in the rootstock of 9901/YJ grafted plants in comparison with YJ/YJ. Among them, 692 were identified as mRNAs moved from 9901 scion based on SNP analysis of two parents. They were mostly 1001–1500 bp, had 40–45% GC contents, or had expression abundance values less than 10. However, mRNAs over 4001 bp, having 50–55% GC contents, or having expression abundance values of 10–20 were preferentially transferred. Eight mRNAs subjected to long-distance trafficking were involved in the plant hormone pathways and may significantly promote the root growth of grafted plants. In summary, heterologous grafts of Salix matsudana could efficiently influence plant rooting of the mRNAs transport from scion to rootstock.
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Auxin Response Factors Are Ubiquitous in Plant Growth and Development, and Involved in Crosstalk between Plant Hormones: A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031360] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Auxin response factors (ARFs) are an important family of transcription factors involved in the exertion of auxin in plants and play a key role in regulating the growth and development of plant nutritional and reproductive organs such as roots, stems, leaves, flowers, fruits, and seeds. Foods of plant origin occupy an important place in the nutritional structure of the human diet, and the main edible parts of different plants vary. In this paper, we review recent research reports on ARFs and summarize its role in the regulation of leaf, flower, root, and fruit growth, as well as other important life activities. We also present the challenges and opportunities that ARFs will present in the future. It will be important to deepen our understanding of the mechanisms by which ARFs interact with other proteins or genes. In addition, it is worth considering that more technical tools should be put into the study of ARFs and that the research should be oriented towards solving practical problems. In the future, it is expected that the nutrition and function of plant-derived foods can be improved through gene editing and other means.
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17
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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18
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Li S, Chen K, Grierson D. Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening. Cells 2021; 10:1136. [PMID: 34066675 PMCID: PMC8151651 DOI: 10.3390/cells10051136] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.
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Affiliation(s)
- Shan Li
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
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19
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Medina-Puche L, Martínez-Rivas FJ, Molina-Hidalgo FJ, García-Gago JA, Mercado JA, Caballero JL, Muñoz-Blanco J, Blanco-Portales R. Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110830. [PMID: 33691964 DOI: 10.1016/j.plantsci.2021.110830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 05/22/2023]
Abstract
PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.
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Affiliation(s)
- L Medina-Puche
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - F J Martínez-Rivas
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - F J Molina-Hidalgo
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - J A García-Gago
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Biología Vegetal, Universidad de Málaga, Málaga, Spain.
| | - J A Mercado
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Biología Vegetal, Universidad de Málaga, Málaga, Spain.
| | - J L Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - J Muñoz-Blanco
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - R Blanco-Portales
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
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20
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Li SW. Molecular Bases for the Regulation of Adventitious Root Generation in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:614072. [PMID: 33584771 PMCID: PMC7876083 DOI: 10.3389/fpls.2021.614072] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 05/08/2023]
Abstract
The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.
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21
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Li K, Wang S, Wu H, Wang H. Protein Levels of Several Arabidopsis Auxin Response Factors Are Regulated by Multiple Factors and ABA Promotes ARF6 Protein Ubiquitination. Int J Mol Sci 2020; 21:ijms21249437. [PMID: 33322385 PMCID: PMC7763875 DOI: 10.3390/ijms21249437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 11/21/2022] Open
Abstract
The auxin response factor (ARF) transcription factors are a key component in auxin signaling and play diverse functions in plant growth, development, and stress response. ARFs are regulated at the transcript level and posttranslationally by protein modifications. However, relatively little is known regarding the control of ARF protein levels. We expressed five different ARFs with an HA (hemagglutinin) tag and observed that their protein levels under the same promoter varied considerably. Interestingly, their protein levels were affected by several hormonal and environmental conditions, but not by the auxin treatment. ABA (abscisic acid) as well as 4 °C and salt treatments decreased the levels of HA-ARF5, HA-ARF6, and HA-ARF10, but not that of HA-ARF19, while 37 °C treatment increased the levels of the four HA-ARFs, suggesting that the ARF protein levels are regulated by multiple factors. Furthermore, MG132 inhibited the reduction of HA-ARF6 level by ABA and 4 °C treatments, suggesting that these treatments decrease HA-ARF6 level through 26S proteasome-mediated protein degradation. It was also found that ABA treatment drastically increased HA-ARF6 ubiquitination, without strongly affecting the ubiquitination profile of the total proteins. Together, these results reveal another layer of control on ARFs, which could serve to integrate multiple hormonal and environmental signals into the ARF-regulated gene expression.
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Affiliation(s)
- Keke Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresouces, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresouces, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
- Correspondence: (H.W.); (H.W.)
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
- Correspondence: (H.W.); (H.W.)
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Waziri A, Singh DK, Sharma T, Chatterjee S, Purty RS. Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica. Noncoding RNA Res 2020; 5:191-200. [PMID: 33163736 PMCID: PMC7610035 DOI: 10.1016/j.ncrna.2020.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/24/2020] [Accepted: 10/24/2020] [Indexed: 11/24/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857–3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance. Total of 44 Plant homeo-domain (PHD) finger proteins were identified & classified into 10 groups in Oryza sativa Indica. This is the first report showing 5 newly identified putative miRNAs targeting three OsPHD genes i.e., OsPHD2, 11 and 35. Expression analysis of PHD finger genes showed up-regulation of the 2 genes OsPHD 6 & 12 under salinity stress treatment. Protein-protein network of OsPHDs showed protein partners that are involved in plant growth and abiotic stress tolerance.
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Affiliation(s)
- Aafrin Waziri
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Deepak Kumar Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Tarun Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Sayan Chatterjee
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Ram Singh Purty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
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23
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Zhang T, Li W, Xie R, Xu L, Zhou Y, Li H, Yuan C, Zheng X, Xiao L, Liu K. CpARF2 and CpEIL1 interact to mediate auxin-ethylene interaction and regulate fruit ripening in papaya. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1318-1337. [PMID: 32391615 DOI: 10.1111/tpj.14803] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Papaya (Carica papaya L.) is a commercially important fruit crop. Various phytohormones, particularly ethylene and auxin, control papaya fruit ripening. However, little is known about the interaction between auxin and ethylene signaling during the fruit ripening process. In the present study, we determined that the interaction between the CpARF2 and CpEIL1 mediates the interaction between auxin and ethylene signaling to regulate fruit ripening in papaya. We identified the ethylene-induced auxin response factor CpARF2 and demonstrated that it is essential for fruit ripening in papaya. CpARF2 interacts with an important ethylene signal transcription factor CpEIL1, thus increasing the CpEIL1-mediated transcription of the fruit ripening-associated genes CpACS1, CpACO1, CpXTH12 and CpPE51. Moreover, CpEIL1 is ubiquitinated by CpEBF1 and is degraded through the 26S proteasome pathway. However, CpARF2 weakens the CpEBF1-CpEIL1 interaction and interferes with CpEBF1-mediated degradation of CpEIL1, promoting fruit ripening. Therefore, CpARF2 functions as an integrator in the auxin-ethylene interaction and regulates fruit ripening by stabilizing CpEIL1 protein and promoting the transcriptional activity of CpEIL1. To our knowledge, we have revealed a novel module of CpARF2/CpEIL1/CpEBF1 that fine-tune fruit ripening in papaya. Manipulating this mechanism could help growers tightly control papaya fruit ripening and prolong shelf life.
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Affiliation(s)
- Tao Zhang
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Weijin Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Ruxiu Xie
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Ling Xu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Yan Zhou
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Haili Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Changchun Yuan
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Xiaolin Zheng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Langtao Xiao
- College of Bioscience and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
- College of Bioscience and Technology, Hunan Agricultural University, Changsha, 410128, China
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24
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Wang H, Xie Y, Liu W, Tao G, Sun C, Sun X, Zhang S. Transcription factor LkWOX4 is involved in adventitious root development in Larix kaempferi. Gene 2020; 758:144942. [PMID: 32640309 DOI: 10.1016/j.gene.2020.144942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
WUSCHEL-related homeobox4 (WOX4) plays important roles in vascular formation and adventitious root (AR) development. Here, we cloned the WOX4 from the AR of Larix kaempferi, whose cDNA is 1452 bp in length and encodes 483 amino acids. LkWOX4 is mainly expressed in the layer formation area of the stem at 10 days after cutting and its expression levels in the middles and ends of the ARs were higher than that in the AR tips. The fused protein LkWOX4-GFP localized in the nucleus. The heterologous overexpression of LkWOX4 in 84 K poplar significantly increased AR numbers and decreased AR lengths. In LkWOX4 plants, the endogenous jasmonic acid and abscisic acid contents significantly decreased in stems, while the auxin, jasmonic acid and abscisic acid contents significantly increased in ARs. RNA-Seq of those LkWOX4 overexpression poplar plants showed that the expression of plant hormone signaling genes (ARF2, ARF3, ARF7 and ARF18), rooting-related transcription factors (WOX5, LBD29 and SCR) and root development-related genes (CYCD3, GRF1 and TAA1) were affected. Moreover, we found that LkWOX4 interacts with LkPAT18, LkACBP6, and LkCIP7 using yeast two hybrid screening. Thus, we found LkWOX4 involves in the AR initiation and development, which might be regulated through the IAA, JA and ABA signaling pathways.
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Affiliation(s)
- Hongming Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu 741000, China
| | - Yunhui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh 27695, USA
| | - Guiyun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaomei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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Cui J, Li X, Li J, Wang C, Cheng D, Dai C. Genome-wide sequence identification and expression analysis of ARF family in sugar beet ( Beta vulgaris L.) under salinity stresses. PeerJ 2020; 8:e9131. [PMID: 32547857 PMCID: PMC7276148 DOI: 10.7717/peerj.9131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 04/14/2020] [Indexed: 02/05/2023] Open
Abstract
Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet's growth, development and responses to salinity stress.
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Affiliation(s)
- Jie Cui
- Harbin Institute of Technology, Harbin, China
| | - Xinyan Li
- Harbin Institute of Technology, Harbin, China
| | - Junliang Li
- Harbin Institute of Technology, Harbin, China
| | - Congyu Wang
- Harbin Institute of Technology, Harbin, China
| | - Dayou Cheng
- Harbin Institute of Technology, Harbin, China
| | - Cuihong Dai
- Harbin Institute of Technology, Harbin, China
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26
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Wu B, Wang L, Pan G, Li T, Li X, Hao J. Genome-wide characterization and expression analysis of the auxin response factor (ARF) gene family during melon (Cucumis melo L.) fruit development. PROTOPLASMA 2020; 257:979-992. [PMID: 32043172 PMCID: PMC7203594 DOI: 10.1007/s00709-020-01484-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
ARFs in plants mediate auxin signaling transduction and regulate growth process. To determine genome-wide characterization of ARFs family in melon (Cucumis melo L.), ARFs were identified via analysis of information within the melon genomic database, and bioinformatic analyses were performed using various types of software. Based on different treatment methods involving dipping with the growth regulator Fengchanji No. 2 and artificial pollination, Jingmi No. 11 melon was used as the test material, and melon plants with unpollinated ovaries served as controls. The expression of ARFs during the early development of melon was analyzed via qRT-PCR. Seventeen genes that encode ARF proteins were identified in the melon genome for the first time. The expression of these ARFs differed in different tissues. The expression levels of CmARF2, CmARF16-like, CmARF18-like2, and CmARF19-like were especially high in melon fruits. The expression of ARFs during the early development of melon fruits differed in response to the different treatments, which suggested that CmARF9, CmARF16-like, CmARF19-like, CmARF19, CmARF1, CmARF2, CmARF3, and CmARF5 may be associated with melon fruit growth during early development. Interestingly, the increase in the transverse diameter of fruits treated with growth regulators was significantly greater than that of fruits resulting from artificial pollination, while the increase in the longitudinal diameter of the fruits resulting from artificial pollination was significantly greater.
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Affiliation(s)
- Bei Wu
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Lu Wang
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Gaoyang Pan
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Ting Li
- Beijing Agricultural Technology Extension Station, Beijing, 100029, China
| | - Xin Li
- Agricultural and Rural Bureau of Jing County of Hebei Province, Hebei, 053500, China
| | - Jinghong Hao
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
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27
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Xue L, Sun M, Wu Z, Yu L, Yu Q, Tang Y, Jiang F. LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network. BMC PLANT BIOLOGY 2020; 20:162. [PMID: 32293294 PMCID: PMC7161180 DOI: 10.1186/s12870-020-02373-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/31/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. RESULTS Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, 'LA1698' (cracking-resistant, CR) and 'LA2683' (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the 'hormone metabolic process', 'cell wall organization', 'oxidoreductase activity' and 'catalytic activity' categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 (Peroxide, POD), Solyc01g008710.3 (Mannan endo-1,4-beta-mannosidase, MAN), Solyc08g077910.3 (Expanded, EXP), Solyc09g075330.3 (Pectinesterase, PE), Solyc07g055990.3 (Xyloglucan endotransglucosylase-hydrolase 7, XTH7), Solyc12g011030.2 (Xyloglucan endotransglucosylase-hydrolase 9, XTH9), Solyc10g080210.2 (Polygalacturonase-2, PG2), Solyc08g081010.2 (Gamma-glutamylcysteine synthetase, gamma-GCS), Solyc09g008720.2 (Ethylene receptor, ER), Solyc11g042560.2 (Ethylene-responsive transcription factor 4, ERF4) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. CONCLUSIONS This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H2O2) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs (XLOC_16662 and XLOC_033910, etc.).
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Affiliation(s)
- Lingzi Xue
- College of Horticulture, Nanjing Agricultural University, Weigang NO 1, Nanjing, 210095 Xuanwu District China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 China
| | - Mintao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun South St, Beijing, 10081 Haidian District China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Weigang NO 1, Nanjing, 210095 Xuanwu District China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 China
| | - Lu Yu
- College of Horticulture, Nanjing Agricultural University, Weigang NO 1, Nanjing, 210095 Xuanwu District China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 China
| | - Qinghui Yu
- Institute of Vegetables, Xinjiang Academy of Agricultural Sciences, Nanchang Road 403, Urumchi, 830091 Shayibake District China
| | - Yaping Tang
- Institute of Vegetables, Xinjiang Academy of Agricultural Sciences, Nanchang Road 403, Urumchi, 830091 Shayibake District China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Weigang NO 1, Nanjing, 210095 Xuanwu District China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 China
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Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans. FORESTS 2020. [DOI: 10.3390/f11020245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Auxins have long been implicated in many aspects of plant growth and development. Auxin response factors (ARFs) are important proteins in auxin-mediated pathways and they play key roles in plant physiological and biochemical processes, including flower development. Endogenous indoleacetic acid (IAA) levels were measured and ARFs were studied in the flowers during the developmental stages in order to further elucidate the role of auxin in flower development of Osmanthus fragrans. A systematic analysis of OfARFs was conducted by carrying out a genome-wide search of ARFs. A total of 50 ARF genes (OfARFs) were detected and validated from the Osmanthus fragrans genome. Furthermore, a comprehensive overview of the OfARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, motifs, promoters, chromosome locations, gene duplications, and subcellular locations of the gene product. Finally, expression profiling, while using transcriptome sequencing from a previous study and quantitative real-time PCR (qRT-PCR), revealed that many OfARF genes have different expression levels in various tissues and flower developmental stages. By comparing the expression profiles among the flower developmental stages, and the relationship between ARFs and endogenous IAA levels, it can be supposed that OfARFs function in flower development of O. fragrans in an auxin-mediated pathway.
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Zhang Y, Wang Y, Ye D, Xing J, Duan L, Li Z, Zhang M. Ethephon-regulated maize internode elongation associated with modulating auxin and gibberellin signal to alter cell wall biosynthesis and modification. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110196. [PMID: 31779899 DOI: 10.1016/j.plantsci.2019.110196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 05/12/2023]
Abstract
Ethephon efficiently regulates plant growth to modulate the maize (Zea mays L.) stalk strength and yield potential, yet there is little information on how ethylene governs a specific cellular response for altering internode elongation. Here, the internode elongation kinetics, cell morphological and physiological properties and transcript expression patterns were investigated in the ethephon-treated elongating internode. Ethephon decreased the internode elongation rate, shortened the effective elongation duration, and advanced the growth process. Ethephon regulated the expression patterns of expansin and secondary cell wall-associated cellulose synthase genes to alter cell size. Moreover, ethephon increased the activities and transcripts level of phenylalanine ammonia-lyase and peroxidase, which contributed to lignin accumulation. Otherwise, ethephon-boosted ethylene evolution activated ethylene signal and increased ZmGA2ox3 and ZmGA2ox10 transcript levels while down-regulating ZmPIN1a, ZmPIN4 and ZmGA3ox1 transcript levels, which led to lower accumulation of gibberellins and auxin. In addition, transcriptome profiles confirmed previous results and identified several transcription factors that are involved in the ethephon-modulated transcriptional regulation of cell wall biosynthesis and modification and responses to ethylene, gibberellins and auxin. These results indicated that ethylene-modulated auxin and gibberellins signaling mediated the transcriptional operation of cell wall modification to regulate cell elongation in the ethephon-treated maize internode.
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Affiliation(s)
- Yushi Zhang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yubin Wang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Delian Ye
- College of Crop Science, Fujian Agriculture and Forestry University, Fujian, 350002, China
| | - Jiapeng Xing
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Liusheng Duan
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaohu Li
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingcai Zhang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Perotti MF, Ribone PA, Cabello JV, Ariel FD, Chan RL. AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1224-1236. [PMID: 31444832 DOI: 10.1111/tpj.14511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.
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Affiliation(s)
- María F Perotti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Pamela A Ribone
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Julieta V Cabello
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
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Wang J, Wang R, Mao X, Li L, Chang X, Zhang X, Jing R. TaARF4 genes are linked to root growth and plant height in wheat. ANNALS OF BOTANY 2019; 124:903-915. [PMID: 30590478 PMCID: PMC6881231 DOI: 10.1093/aob/mcy218] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 12/08/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Auxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated. METHODS Tissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits. KEY RESULTS TaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes. CONCLUSIONS Ectopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- For correspondence. E-mail
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Wang Y, Guo H. On hormonal regulation of the dynamic apical hook development. THE NEW PHYTOLOGIST 2019; 222:1230-1234. [PMID: 30537131 DOI: 10.1111/nph.15626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/18/2018] [Indexed: 05/21/2023]
Abstract
Contents Summary 1230 I. Introduction 1230 II. Apical hook development is a spatio-temporally dynamic process orchestrated by a complex signaling network 1231 III. Central players of apical hook development: auxin and HOOKLESS1 1232 IV. Towards a cellular-based understanding of hormonal regulation of apical hook development with cutting-edge toolboxes 1232 V. Conclusions 1233 Acknowledgements 1233 References 1233 SUMMARY: To deal with the ever-changing environment, sessile plants adapt diverse and plastic organ structures during postembryonic development. Among these, the apical hook forms shortly after seed germination of most dicots, and protects the delicate shoot meristem from mechanical damage during soil emergence. For decades, this structure has been taken as an excellent model for the investigation of the mechanisms underlying the differential growth of plant tissues. Here, we summarize recent advances in the investigation of the hormonal regulation of apical hook development, focusing on the convergence to auxin and a central regulator HOOKLESS1 (HLS1). We propose the revisitation of hook curvature kinematics at suborgan and single-cell resolution, and further pursuance of the mechanistics of apical hook development through combinatorial approaches of automated imaging and multidimensional modeling.
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Affiliation(s)
- Yichuan Wang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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The auxin response factor gene family in allopolyploid Brassica napus. PLoS One 2019; 14:e0214885. [PMID: 30958842 PMCID: PMC6453480 DOI: 10.1371/journal.pone.0214885] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/21/2019] [Indexed: 12/20/2022] Open
Abstract
Auxin response factor (ARF) is a member of the plant-specific B3 DNA binding superfamily. Here, we report the results of a comprehensive analysis of ARF genes in allotetraploid Brassica napus (2n = 38, AACC). Sixty-seven ARF genes were identified in B. napus (BnARFs) and divided into four subfamilies (I–IV). Sixty-one BnARFs were distributed on all chromosomes except C02; the remaining were on Ann and Cnn. The full length of the BnARF proteins was highly conserved especially within each subfamily with all members sharing the N-terminal DNA binding domain (DBD) and the middle region (MR), and most contained the C-terminal dimerization domain (PBI). Twenty-one members had a glutamine-rich MR that may be an activator and the remaining were repressors. Accordingly, the intron patterns are highly conserved in each subfamily or clade, especially in DBD and PBI domains. Several members in subfamily III are potential targets for miR167. Many putative cis-elements involved in phytohormones, light signaling responses, and biotic and abiotic stress were identified in BnARF promoters, implying their possible roles. Most ARF proteins are likely to interact with auxin/indole-3-acetic acid (Aux/IAA) -related proteins, and members from different subfamilies generally shared many common interaction proteins. Whole genome-wide duplication (WGD) by hybridization between Brassica rapa and Brassica oleracea and segmental duplication led to gene expansion. Gene loss following WGD is biased with the An-subgenome retaining more ancestral genes than the Cn-subgenome. BnARFs have wide expression profiles across vegetative and reproductive organs during different developmental stages. No obvious expression bias was observed between An- and Cn-subgenomes. Most synteny-pair genes had similar expression patterns, indicating their functional redundancy. BnARFs were sensitive to exogenous IAA and 6-BA treatments especially subfamily III. The present study provides insights into the distribution, phylogeny, and evolution of ARF gene family.
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Xia F, Sun T, Yang S, Wang X, Chao J, Li X, Hu J, Cui M, Liu G, Wang D, Sun Y. Insight into the B3Transcription Factor Superfamily and Expression Profiling of B3 Genes in Axillary Buds after Topping in Tobacco( Nicotiana tabacum L.). Genes (Basel) 2019; 10:E164. [PMID: 30791672 PMCID: PMC6409620 DOI: 10.3390/genes10020164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.
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Affiliation(s)
- Fei Xia
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Tingting Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Xiao Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Xiaoxu Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Junhua Hu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Mengmeng Cui
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Dawei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Yuhe Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
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Genome-wide Identification, Expression Profiling and Evolutionary Analysis of Auxin Response Factor Gene Family in Potato (Solanum tuberosum Group Phureja). Sci Rep 2019; 9:1755. [PMID: 30742001 PMCID: PMC6370904 DOI: 10.1038/s41598-018-37923-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/13/2018] [Indexed: 01/02/2023] Open
Abstract
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.
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Zeng W, Dai X, Sun J, Hou Y, Ma X, Cao X, Zhao Y, Cheng Y. Modulation of Auxin Signaling and Development by Polyadenylation Machinery. PLANT PHYSIOLOGY 2019; 179:686-699. [PMID: 30487141 PMCID: PMC6426405 DOI: 10.1104/pp.18.00782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/18/2018] [Indexed: 05/25/2023]
Abstract
Polyadenylation influences gene expression by affecting mRNA stability, transport, and translatability. Here, we report that Cleavage stimulation Factor 77 (AtCstF77), a component of the pre-mRNA 3'-end polyadenylation machinery, affects polyadenylation site (PAS) selection in transcripts of some auxin signaling genes in Arabidopsis (Arabidopsis thaliana). Disruption of AtCstF77 reduced auxin sensitivity and decreased the expression of the auxin reporter DR5-GFP Null mutations of cstf77 caused severe developmental defects, but were not lethal as previously reported. cstf77-2 genetically interacted with transport inhibitor response 1 auxin signaling f-box 2 auxin receptor double mutants, further supporting that polyadenylation affects auxin signaling. AtCstF77 was ubiquitously expressed in embryos, seedlings, and adult plants. The AtCstF77 protein was localized in the nucleus, which is consistent with its function in pre-mRNA processing. We observed that PASs in transcripts from approximately 2,400 genes were shifted in the cstf77-2 mutant. Moreover, most of the PAS shifts were from proximal to distal sites. Auxin treatment also caused PAS shifts in transcripts from a small number of genes. Several auxin signaling or homeostasis genes had different PASs in their transcripts in the cstf77-2 mutant. The expression levels of AUXIN RESISTANT 2/INDOLE-3-ACETIC ACID 7 were significantly increased in the cstf77-2 mutant, which can partially account for the auxin resistance phenotype of this mutant. Our results demonstrate that AtCstF77 plays pleiotropic and critical roles in Arabidopsis development. Moreover, disruption of AtCstF64, another component of the polyadenylation machinery, led to developmental defects and reduced auxin response, similar to those of the cstf77-2 mutant. We conclude that AtCstF77 affects auxin responses, likely by controlling PAS selection of transcripts of some auxin signaling components.
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Affiliation(s)
- Wei Zeng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California, San Diego, California 92093-0116
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuan Ma
- College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Xiaofeng Cao
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, California 92093-0116
| | - Youfa Cheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Nziengui H, Lasok H, Kochersperger P, Ruperti B, Rébeillé F, Palme K, Ditengou FA. Root Gravitropism Is Regulated by a Crosstalk between para-Aminobenzoic Acid, Ethylene, and Auxin. PLANT PHYSIOLOGY 2018; 178:1370-1389. [PMID: 30275058 PMCID: PMC6236604 DOI: 10.1104/pp.18.00126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/13/2018] [Indexed: 05/04/2023]
Abstract
Plants respond to gravitational force through directional growth along the gravity vector. Although auxin is the central component of the root graviresponse, it works in concert with other plant hormones. Here, we show that the folate precursor para-aminobenzoic acid (PABA) is a key modulator of the auxin-ethylene interplay during root gravitropism in Arabidopsis (Arabidopsis thaliana). In gravistimulated roots, PABA promotes an asymmetric auxin response, which causes the asymmetric growth responsible for root curvature. This activity requires the auxin response transcription factors AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 as well as ethylene biosynthesis and signaling, indicating that PABA activity requires both auxin and ethylene pathways. Similar to ethylene, exogenous PABA reverses the agravitropic root growth of the auxin transport mutant pin-formed2 (pin2) and the auxin biosynthetic double mutant with loss of function of weak ethylene insensitive (wei) genes, wei8wei2, but not the pin2wei8wei2 triple mutant. This finding suggests that PABA regulates the ethylene-dependent reciprocal compensation between auxin transport and biosynthesis. Furthermore, manipulation of endogenous free PABA levels by modulating the expression of the gene encoding its glucosylation enzyme, UDP-GLYCOSYL TRANSFERASE75B1, impacts the root graviresponse, suggesting that endogenous free PABA levels may play a crucial role in modulating the auxin-ethylene cross talk necessary for root gravitropism.
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Affiliation(s)
- Hugues Nziengui
- Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Hanna Lasok
- Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Philip Kochersperger
- Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro (Padova), Italy
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Universite Grenoble Alpes, Bioscience and Biotechnologies Institute of Grenoble, Commissariat à l'Energie Atomique-Grenoble, F-38054 Grenoble cedex 9, France
| | - Klaus Palme
- Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
- Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Franck Anicet Ditengou
- Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
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Hu Z, Wang R, Zheng M, Liu X, Meng F, Wu H, Yao Y, Xin M, Peng H, Ni Z, Sun Q. TaWRKY51 promotes lateral root formation through negative regulation of ethylene biosynthesis in wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:372-388. [PMID: 30044519 DOI: 10.1111/tpj.14038] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 05/27/2023]
Abstract
Common wheat (Triticum aestivum L.) is an important staple food crop worldwide. Lateral roots (LRs), as the major component of root architecture, affect water and nutrient uptake in wheat. The phytohormone ethylene is known to affect LR formation; however, the factor(s) modulating ethylene during this process have not yet been elucidated in wheat. Here we identified wheat TaWRKY51 as a key factor that functions in LR formation by modulating ethylene biosynthesis. Wheat TaWRKY51RNA interference lines (TaWRKY51-RNAi) and the homozygous mutants tawrky51-2a and tawrky51-2b all produced fewer LRs than the wild type and negative transgenic plants, whereas the TaWRKY51 overexpression lines (TaWRKY51-OE) had the opposite phenotype. Transcription analysis revealed that 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes (TaACS2, TaACS7 and TaACS8) involved in ethylene biosynthesis were downregulated in TaWRKY51-OE lines but upregulated in TaWRKY51-RNAi lines. The rate of ethylene production also decreased in TaWRKY51-OE lines but increased in TaWRKY51-RNAi lines compared with their respective negative transgenic controls. Electrophoretic mobility shift and transient expression assays revealed that TaWRKY51 inhibits the expression of ACS genes by binding to the W-box cis-element present in their promoter region. Moreover, overexpression of ACS2 or exogenous application of 1-aminocyclopropane-1-carboxylic acid reversed the phenotype of enhanced LR number in TaWRKY51-OE Arabidopsis lines, and overexpression of TaWRKY51 in the ethylene-overproducing mutant eto1-1 rescued its LR defect phenotype. In addition, genetic evidence demonstrates that TaWRKY51-regulated LR formation is also dependent on ethylene and auxin signaling pathways. Our findings reveal a molecular genetic mechanism by which a WRKY gene coordinates ethylene production and LR formation in wheat.
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Affiliation(s)
- Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rui Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mei Zheng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xingbei Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Fei Meng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hualing Wu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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Kang C, He S, Zhai H, Li R, Zhao N, Liu Q. A Sweetpotato Auxin Response Factor Gene ( IbARF5) Is Involved in Carotenoid Biosynthesis and Salt and Drought Tolerance in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1307. [PMID: 30254657 PMCID: PMC6141746 DOI: 10.3389/fpls.2018.01307] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/17/2018] [Indexed: 05/23/2023]
Abstract
Auxin response factors (ARFs) compose a family of transcription factors and have been found to play major roles in the process of plant growth and development. However, their roles in plant carotenoid biosynthesis and responses to abiotic stresses are rarely known to date. In the present study, we found that the IbARF5 gene from sweetpotato (Ipomoea batatas (L.) Lam.) line HVB-3 increased the contents of carotenoids and enhanced the tolerance to salt and drought in transgenic Arabidopsis. The transgenic Arabidopsis plants exhibited the increased abscisic acid (ABA) and proline contents and superoxide dismutase (SOD) activity and the decreased H2O2 content. Furthermore, it was found that IbARF5 positively regulated the genes associated with carotenoid and ABA biosynthesis and abiotic stress responses. These results suggest that IbARF5 is involved in carotenoid biosynthesis and salt and drought tolerance in transgenic Arabidopsis. This study provides a novel ARF gene for improving carotenoid contents and salt and drought tolerance of sweetpotato and other plants.
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Affiliation(s)
- Chen Kang
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Ruijie Li
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Ning Zhao
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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40
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Wang Y, Ji Y, Fu Y, Guo H. Ethylene-induced microtubule reorientation is essential for fast inhibition of root elongation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:864-877. [PMID: 29752856 DOI: 10.1111/jipb.12666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/09/2018] [Indexed: 05/22/2023]
Abstract
Microtubule reorientation is a long-standing observation that has been implicated in regulating the inhibitory effect of ethylene on axial elongation of plant cells. However, the signaling mechanism underlying ethylene-induced microtubule reorientation has remained elusive. Here, we reveal, by live confocal imaging and kinetic root elongation assays, that the time courses of ethylene-induced microtubule reorientation and root elongation inhibition are highly correlated, and that microtubule reorientation is required for the full responsiveness of root elongation to ethylene treatment. Our genetic analysis demonstrated that the effect of ethylene on microtubule orientation and root elongation is mainly transduced through the canonical linear ethylene signaling pathway. By using pharmacological and genetic analyses, we demonstrate further that the TIR1/AFBs-Aux/IAAs-ARFs auxin signaling pathway, but not the ABP1-ROP6-RIC1 auxin signaling branch, is essential for ethylene-induced microtubule reorientation and root elongation inhibition. Together, these findings offer evidence for the functional significance and elucidate the signaling mechanism for ethylene-induced microtubule reorientation in fast root elongation inhibition in Arabidopsis.
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Affiliation(s)
- Yichuan Wang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yusi Ji
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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41
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Tang Y, Bao X, Liu K, Wang J, Zhang J, Feng Y, Wang Y, Lin L, Feng J, Li C. Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut. PLoS One 2018; 13:e0201024. [PMID: 30067784 PMCID: PMC6070241 DOI: 10.1371/journal.pone.0201024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress.
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Affiliation(s)
- Yuehui Tang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
| | - Xinxin Bao
- School of Journalism and Communication, Zhoukou Normal University, Henan, Zhoukou, China
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
| | - Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
| | - Youwei Feng
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Yangyang Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Luoxiao Lin
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Jingcheng Feng
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Chengwei Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
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42
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Zhou X, Wu X, Li T, Jia M, Liu X, Zou Y, Liu Z, Wen F. Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon. Funct Integr Genomics 2018; 18:709-724. [PMID: 29926224 DOI: 10.1007/s10142-018-0622-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 11/30/2022]
Abstract
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B. distachyon was performed. A comprehensive overview of the characterization of the BdARFs was obtained by multiple bioinformatics analyses, including the gene and protein structure, chromosome locations, conserved motifs of proteins, phylogenetic analysis, and cis-elements in promoters of BdARF. Results showed that all BdARFs contained conserved DBD, MR, and CTD could be divided into four classes, Ia, IIa, IIb, and III. Expression profiles of BdARF genes indicated that they were expressed across various tissues and organs, which could be clustered into three main expression groups, and most of BdARF genes were involved in phytohormone signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. And predicted regulatory network between B. distachyon ARFs and IAAs was also discussed. Our genomics analysis of BdARFs could yield new insights into the complexity of the control of BdARF genes and lead to potential applications in the investigation of the accurate regulatory mechanisms of ARFs in herbaceous plants.
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Affiliation(s)
- Xiaojian Zhou
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinshen Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yulan Zou
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zixia Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass. Int J Genomics 2018; 2018:7658910. [PMID: 29854720 PMCID: PMC5949158 DOI: 10.1155/2018/7658910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/11/2018] [Indexed: 11/18/2022] Open
Abstract
Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L.), a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs) were identified in the switchgrass genome (2n = 4x = 36), 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167). Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves), which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA) treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.
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Liu Y, Xu C, Tang X, Pei S, Jin D, Guo M, Yang M, Zhang Y. Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis. Gene 2018; 665:119-126. [PMID: 29705127 DOI: 10.1016/j.gene.2018.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage.
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Affiliation(s)
- Yan Liu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Cui Xu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Xuebing Tang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, PR China
| | - Di Jin
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Minghao Guo
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng Yang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Yaowei Zhang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, PR China.
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45
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Liu S, Zhang Y, Feng Q, Qin L, Pan C, Lamin-Samu AT, Lu G. Tomato AUXIN RESPONSE FACTOR 5 regulates fruit set and development via the mediation of auxin and gibberellin signaling. Sci Rep 2018; 8:2971. [PMID: 29445121 PMCID: PMC5813154 DOI: 10.1038/s41598-018-21315-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 02/02/2018] [Indexed: 12/21/2022] Open
Abstract
Auxin response factors (ARFs) encode transcriptional factors that function in the regulation of plant development processes. A tomato ARF gene, SlARF5, was observed to be expressed at high levels in emasculated ovaries but maintained low expression levels in pollinated ovaries. The amiRNA SlARF5 lines exhibited ovary growth and formed seedless fruits following emasculation. These parthenocarpic fruits developed fewer locular tissues, and the fruit size and weight were decreased in transgenic lines compared to those of wild-type fruits. Gene expression analysis demonstrated that several genes involved in the auxin-signaling pathway were downregulated, whereas some genes involved in the gibberellin-signaling pathway were enhanced by the decreased SlARF5 mRNA levels in transgenic plants, indicating that SlARF5 may play an important role in regulating both the auxin- and gibberellin-signaling pathways during fruit set and development.
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Affiliation(s)
- Songyu Liu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Youwei Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Qiushuo Feng
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Li Qin
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Changtian Pan
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Anthony Tumbeh Lamin-Samu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Gang Lu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China.
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46
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Han S, Hwang I. Integration of multiple signaling pathways shapes the auxin response. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:189-200. [PMID: 28992118 DOI: 10.1093/jxb/erx232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phytohormone auxin is a pivotal signaling molecule that functions throughout the plant lifecycle. Proper regulation of the auxin response is critical for optimizing plant growth under ever-changing environmental conditions. Recent studies have demonstrated that the signaling components that modulate auxin sensitivity and responses are functionally and mechanically diverse. In addition to auxin itself, various environmental and hormonal signals are integrated to modulate the auxin response through directly controlling auxin signaling components. This review explores the non-canonical mechanisms that modulate auxin signaling components, including transcriptional, translational, and post-translational regulation. All of these contribute to the wide range in sensitivity and complexity in auxin responses to various signaling cues.
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Affiliation(s)
- Soeun Han
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Republic of Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Republic of Korea
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47
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Chennareddy S, Cicak T, Clark L, Russell S, Skokut M, Beringer J, Yang X, Jia Y, Gupta M. Expression of a novel bi-directional Brassica napus promoter in soybean. Transgenic Res 2017; 26:727-738. [PMID: 28916981 DOI: 10.1007/s11248-017-0042-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The expression profile of a natural bi-directional promoter, derived from the Brassica napus EPSPS-A gene, was studied in transgenic soybean (Glycine max C.V. Maverick) lines. Two constructs, pDAB100331 and pDAB100333, were assembled to test the bi-directionality of the promoter. Two reporter genes, gfp and gusA, were employed and they were interchangeably placed in both constructs, one on each end of the promoter such that both proteins expressed divergently in each construct. In the T0 generation, GUS expression was more uniform throughout the leaf of pDAB100333 transgenic plants, where the gusA gene was expressed from the downstream or EPSPS-A end of the bi-directional promoter. Comparatively, GUS expression was more localized in the midrib and veins of the leaf of pDAB100331 transgenic plants, where the gusA gene was expressed from the upstream end of the bi-directional promoter. These observations indicated a unique expression pattern from each end of the promoter and consistently higher expression in genes expressed from the downstream end (e.g., EPSPS-A end) of the promoter in the tissues examined. The GFP expression pattern followed that of GUS when placed in the same position relative to the promoter. In the T1 generation, transcript analysis also showed higher expression of both gusA and gfp when those genes were located at the downstream end of the promoter. Accordingly, the pDAB100331 events exhibited a higher gfp/gusA transcript ratio, while pDAB100333 events produced a higher gusA/gfp transcript ratio consistent with the observations in T0 plants. These results demonstrated that the EPSPS-A gene bidirectional promoter can be effectively utilized to drive expression of two transgenes for the desired traits.
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Affiliation(s)
| | - Toby Cicak
- Dow AgroSciences, West Lafayette, IN, 47906, USA
| | | | | | | | | | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yi Jia
- Dow AgroSciences, Indianapolis, IN, 46268, USA
| | - Manju Gupta
- Dow AgroSciences, Indianapolis, IN, 46268, USA
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Owji H, Hajiebrahimi A, Seradj H, Hemmati S. Identification and functional prediction of stress responsive AP2/ERF transcription factors in Brassica napus by genome-wide analysis. Comput Biol Chem 2017; 71:32-56. [PMID: 28961511 DOI: 10.1016/j.compbiolchem.2017.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
Abstract
Using homology and domain authentication, 321 putative AP2/ERF transcription factors were identified in Brassica napus, called BnAP2/ERF TFs. BnAP2/ERF TFs were classified into five major subfamilies, including DREB, ERF, AP2, RAV, and BnSoloist. This classification is based on phylogenetic analysis, motif identification, gene structure analysis, and physiochemical characterization. These TFs were annotated based on phylogenetic relationship with Brassica rapa. BnAP2/ERF TFs were located on 19 chromosomes of B. napus. Orthologs and paralogs were identified using synteny-based methods Ks calculation within B. napus genome and between B. napus with other species such as B. rapa, Brassica oleracea, and Arabidopsis thaliana indicated that BnAP2/ERF TFs were formed through duplication events occurred before B. napus formation. Kn/Ks values were between 0 and 1, suggesting the purifying selection among BnAP2/ERF TFs. Gene ontology annotation, cis-regulatory elements and functional interaction networks suggested that BnAP2/ERF TFs participate in response to stressors, including drought, high salinity, heat and cold as well as developmental processes particularly organ specification and embryogenesis. The identified cis-regulatory elements in the upstream of BnAP2/ERF TFs were responsive to abscisic acid. Analysis of the expression data derived from Illumina Hiseq 2000 RNA sequencing revealed that BnAP2/ERF genes were highly expressed in the roots comparing to flower buds, leaves, and stems. Also, the ERF subfamily was over-expressed under salt and fungal treatments. BnERF039 and BnERF245 are candidates for salt-tolerant B. napus. BnERF253-256 and BnERF260-277 are potential cytokinin response factors. BnERF227, BnERF228, BnERF234, BnERF134, BnERF132, BnERF176, and BnERF235 were suggested for resistance against Leptosphaeria maculan and Leptosphaeria biglobosa.
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Affiliation(s)
- Hajar Owji
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Seradj
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Baranwal VK, Negi N, Khurana P. Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses. Genes (Basel) 2017; 8:genes8090202. [PMID: 28841197 PMCID: PMC5615343 DOI: 10.3390/genes8090202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 12/31/2022] Open
Abstract
Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wild mulberry species genome has been sequenced and offers an opportunity to investigate this important gene family. A total of 17 ARFs have been identified from mulberry (Morus notabilis) which show a wide range of expression patterns. Of these 17 ARFs, 15 have strong acidic isoelectric point (pI) values and a molecular mass ranging from 52 kDa to 101 kDa. The putative promoters of these ARFs harbour cis motifs related to light-dependent responses, various stress responses and hormone regulations suggestive of their multifactorial regulation. The gene ontology terms for ARFs indicate their role in flower development, stress, root morphology and other such development and stress mitigation related activities. Conserved motif analysis showed the presence of all typical domains in all but four members that lack the PB1 domain and thus represent truncated ARFs. Expression analysis of these ARFs suggests their preferential expression in tissues ranging from leaf, root, winter bud, bark and male flowers. These ARFs showed differential expression in the leaf tissue of M. notabilis, Morus laevigata and Morus serrata. Insights gained from this analysis have implications in mulberry improvement programs.
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Affiliation(s)
- Vinay Kumar Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - Nisha Negi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Liang WW, Huang JH, Li CP, Yang LT, Ye X, Lin D, Chen LS. MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing. BMC Genomics 2017; 18:657. [PMID: 28836935 PMCID: PMC5571589 DOI: 10.1186/s12864-017-3999-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/01/2017] [Indexed: 01/17/2023] Open
Abstract
Background Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Citrus orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ (Citrus sinensis) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for Citrus Mg-deficiency tolerance. Results We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of Citrus roots to Mg-deficiency was related to the several aspects: (a) inhibiting root respiration and related gene expression via inducing miR158 and miR2919; (b) enhancing antioxidant system by down-regulating related miRNAs (miR780, miR6190, miR1044, miR5261 and miR1151) and the adaptation to low-phosphorus (miR6190); (c) activating transport-related genes by altering the expression of miR6190, miR6485, miR1044, miR5029 and miR3437; (d) elevating protein ubiquitination due to decreased expression levels of miR1044, miR5261, miR1151 and miR5029; (e) maintaining root growth by regulating miR5261, miR6485 and miR158 expression; and (f) triggering DNA repair (transcription regulation) by regulating miR5176 and miR6485 (miR6028, miR6190, miR6485, miR5621, miR160 and miR7708) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in Citrus Mg-deficiency tolerance. Conclusions We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3999-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei-Wei Liang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing-Hao Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Pomological Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China
| | - Chun-Ping Li
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Lin
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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