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Sun P, Nishiyama S, Li H, Mai Y, Han W, Suo Y, Liang C, Du H, Diao S, Wang Y, Yuan J, Zhang Y, Tao R, Li F, Fu J. Genetic insights into the dissolution of dioecy in diploid persimmon Diospyros oleifera Cheng. BMC PLANT BIOLOGY 2023; 23:606. [PMID: 38030968 PMCID: PMC10688080 DOI: 10.1186/s12870-023-04610-3] [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: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Dioecy, a sexual system of single-sexual (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sexual individuals. RESULTS In this study, co-sexual expression (monoecy and hermaphroditic development), previously thought to be polyploid-specific in Diospyros species, was identified in the diploid D. oleifeara historically. We characterized potential genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. We found all co-sexual plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying the presence of genetic factors controlling gynoecia development in genetically male D. oleifera. Importantly, discrepancies in the OGI/MeGI module were found in diploid monoecious D. oleifera compared with polyploid monoecious D. kaki, including no Kali insertion on the promoter of OGI, no different abundance of smRNAs targeting MeGI (a counterpart of OGI), and no different expression of MeGI between female and male floral buds. On the contrary, in both single- and co-sexual plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype and several regions that may contribute to andromonoecy. CONCLUSIONS Collectively, our findings demonstrate stable breakdown of the dioecious system in D. oleifera, presumably also a result of genomic features of the Y-linked region.
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Affiliation(s)
- Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
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Bienias A, Góralska M, Masojć P, Milczarski P, Myśków B. The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity. BMC Genomics 2020; 21:578. [PMID: 32831010 PMCID: PMC7444254 DOI: 10.1186/s12864-020-06991-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/13/2020] [Indexed: 11/15/2022] Open
Abstract
Background Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for development and germination of cereal grain and involved in anther formation. It activates many genes including high-molecular-weight glutenin and α-amylase gene families. This study presents the first attempt to characterize the rye gene encoding GAMYB in relation to its sequence, polymorphisms, and phenotypic effects. Results ScGAMYB was mapped on rye chromosome 3R using high-density Diversity Arrays Technology (DArT)/DArTseq-based maps developed in three mapping populations. The ScGAMYB sequences were identified in RNA-seq libraries of four rye inbred lines. The transcriptome used for the search contained almost 151,000 transcripts with a median contig length of 500 nt. The average amount of total base raw data was approximately 9 GB. Comparative analysis of the ScGAMYB sequence revealed its high level of homology to wheat and barley orthologues. Single nucleotide polymorphisms (SNPs) detected among rye inbred lines allowed the development of allele specific-PCR (AS-PCR) markers for ScGAMYB that might be used to detect this gene in wide genetic stocks of rye and triticale. Segregation of the ScGAMYB alleles showed significant relationship with α-amylase activity (AMY). Conclusions The research showed the strong similarity of rye GAMYB sequence to its orthologues in other Graminae and confirmed the position in the genome consistent with the collinearity rule of cereal genomes. Concurrently, the ScGAMYB coding sequence (cds) showed stronger variability (24 SNPs) compared to the analogous region of wheat (5 SNPs) and barley (7 SNPs). The moderate regulatory effect of ScGAMYB on AMY was confirmed, therefore, ScGAMYB was identified as a candidate gene for partial control of α-amylase production in rye grain. The predicted structural protein change in the aa region 362–372, caused by a single SNP (C/G) at the 1100 position in ScGAMYB cds and single aa sequence change (S/C) at the 367 position, is the likely cause of the differences in the effectiveness of ScGAMYB regulatory function associated with AMY. The development of sequence-based, allele-specific (AS) PCR markers could be useful in research and application.
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Affiliation(s)
- Anna Bienias
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin; ul, Słowackiego 17, 71-434, Szczecin, Poland
| | - Magdalena Góralska
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin; ul, Słowackiego 17, 71-434, Szczecin, Poland
| | - Piotr Masojć
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin; ul, Słowackiego 17, 71-434, Szczecin, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin; ul, Słowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Szczecin; ul, Słowackiego 17, 71-434, Szczecin, Poland.
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Zhang L, Song Z, Li F, Li X, Ji H, Yang S. The specific MYB binding sites bound by TaMYB in the GAPCp2/3 promoters are involved in the drought stress response in wheat. BMC PLANT BIOLOGY 2019; 19:366. [PMID: 31426752 PMCID: PMC6701022 DOI: 10.1186/s12870-019-1948-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/29/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Drought stress is one of the major abiotic stresses that affects plant growth and productivity. The GAPCp genes play important roles in drought stress tolerance in multiple species. The aim of this experiment was to identify the core cis-regulatory elements that may respond to drought stress in the GAPCp2 and GAPCp3 promoter sequences. RESULTS In this study, the promoters of GAPCp2 and GAPCp3 were cloned. The promoter activities were significantly improved under abiotic stress via regulation of Rluc reporter gene expression, while promoter sequence analysis indicated that these fragments were not almost identical. In transgenic Arabidopsis with the expression of the GUS reporter gene under the control of one of these promoters, the activities of GUS were strong in almost all tissues except the seeds, and the activities were induced after abiotic stress. The yeast one-hybrid system and EMSA demonstrated that TaMYB bound TaGAPCp2P/3P. By analyzing different 5' deletion mutants of these promoters, it was determined that TaGAPCp2P (- 1312~ - 528) and TaGAPCp3P (- 2049~ - 610), including the MYB binding site, contained enhancer elements that increased gene expression levels under drought stress. We used an effector and a reporter to co-transform tobacco and found that TaMYB interacted with the specific MYB binding sites of TaGAPCp2P (- 1197~ - 635) and TaGAPCp3P (- 1456~ - 1144 and - 718~ - 610) in plant cells. Then, the Y1H system and EMSA assay demonstrated that these MYB binding sites in TaGAPCp2P (- 1135 and - 985) and TaGAPCp3P (- 1414 and - 665) were the target cis-elements of TaMYB. The deletion of the specific MYB binding sites in the promoter fragments significantly restrained the drought response, and these results confirmed that these MYB binding sites (AACTAAA/C) play vital roles in improving the transcription levels under drought stress. The results of qRT-PCR in wheat protoplasts transiently overexpressing TaMYB indicated that the expression of TaGAPCp2/3 induced by abiotic stress was upregulated by TaMYB. CONCLUSION The MYB binding sites (AACTAAA/C) in TaGAPCp2P/3P were identified as the key cis-elements for responding to drought stress and were bound by the transcription factor TaMYB.
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Affiliation(s)
- Lin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhiqiang Song
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fangfang Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xixi Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Haikun Ji
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shushen Yang
- College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
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Kawaura K, Miura M, Kamei Y, Ikeda TM, Ogihara Y. Molecular characterization of gliadins of Chinese Spring wheat in relation to celiac disease elicitors. Genes Genet Syst 2018; 93:9-20. [PMID: 29343665 DOI: 10.1266/ggs.17-00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The wheat seed storage proteins gliadin and glutenin are encoded by multigenes. Gliadins are further classified into α-, γ-, δ- and ω-gliadins. Genes encoding α-gliadins belong to a large multigene family, whose members are located on the homoeologous group 6 chromosomes at the Gli-2 loci. Genes encoding other gliadins are located on the homoeologous group 1 chromosomes at the Gli-1 loci. Two-dimensional polyacrylamide gel electrophoresis (2-DE) was used to characterize and profile the gliadins. The gliadins in aneuploid Chinese Spring wheat lines were then compared in this study. Gliadin proteins separated into 70 spots after 2-DE and a total of 10, 10 and 16 spots were encoded on chromosomes 6A, 6B and 6D, respectively, which suggested that they were α-gliadins. Similarly, six, three and seven spots were encoded on chromosomes 1A, 1B and 1D, respectively, which indicated that they were γ-gliadins. Spots that could not be assigned to chromosomes were N-terminally sequenced and were all determined to be α-gliadins or γ-gliadins. The 2-DE profiles showed that specific α-gliadin spots assigned to chromosome 6D were lost in tetrasomic chromosome 2A lines. Furthermore, western blotting against the Glia-α9 peptide, an epitope for celiac disease (CD), suggested that α-gliadins harboring the CD epitope on chromosome 6D were absent in the tetrasomic chromosome 2A lines. Systematic analysis of α-gliadins using 2-DE, quantitative RT-PCR and genomic PCR revealed that tetrasomic 2A lines carry deletion of a chromosome segment at the Gli-D2 locus. This structural alteration at the Gli-D2 locus may provide a genetic resource in breeding programs for the reduction of CD immunotoxicity.
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Affiliation(s)
- Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University
| | - Mayuko Miura
- Kihara Institute for Biological Research, Yokohama City University
| | - Yoko Kamei
- Kihara Institute for Biological Research, Yokohama City University
| | - Tatsuya M Ikeda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University
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Rashid MAR, Zhao Y, Zhang H, Li J, Li Z. Nucleotide diversity, natural variation, and evolution of Flexible culm-1 and Strong culm-2 lodging resistance genes in rice. Genome 2017; 59:473-83. [PMID: 27373308 DOI: 10.1139/gen-2016-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lodging resistance is one of the vital traits in yield improvement and sustainability. Culm wall thickness, diameter, and strength are different traits that can govern the lodging resistance in rice. The genes SCM2 and FC1 have been isolated for culm thickness, strength, and flexibility, but their functional nucleotide variations were still unknown. We used a 13× deep sequence of 795 diverse genotypes to present the functional variation and SNP diversity in SCM2 and FC1. The major functional variant for the SCM2 gene was at position 27480181 and for the FC1 gene at position 31072992. Haplotype analysis of both genes provided their various allelic differences among haplotypes. SCM2 alleles further presented the evolution of Oryza sativa L. subsp. indica and subsp. japonica genomes from common parent in different geographical zones, while the haplotypes of FC1 suggested their evolution from different strains of the common parent Oryza rufipogon. SCM2 showed purifying selection and functional associations with rare alleles, while FC1 displayed balanced selection favored by multiple heterozygous alleles. Genotypes with an allelic combination of SCM2-3 and FC1-2 in japonica background exhibited striking resistance against lodging, which can be used in further breeding programs.
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Affiliation(s)
- Muhammad Abdul Rehman Rashid
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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Djemal R, Khoudi H. Isolation and molecular characterization of a novel WIN1/SHN1 ethylene-responsive transcription factor TdSHN1 from durum wheat (Triticum turgidum. L. subsp. durum). PROTOPLASMA 2015; 252:1461-73. [PMID: 25687296 DOI: 10.1007/s00709-015-0775-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/29/2015] [Indexed: 05/27/2023]
Abstract
Over the last decade, APETALA2/Ethylene Responsive Factor (AP2/ERF) proteins have become the subject of intensive research activity due to their involvement in a variety of biological processes. This research led to the identification of AP2/ERF genes in many species; however, little is known about these genes in durum wheat, one of the most important cereal crops in the world. In this study, a new member of the AP2/ERF transcription factor family, designated TdSHN1, was isolated from durum wheat using thermal asymetric interlaced PCR (TAIL-PCR) method. Protein sequence analysis showed that TdSHN1 contained an AP2/ERF domain of 63 amino acids and a putative nuclear localization signal (NLS). Phylogenetic analysis showed that TdSHN1 belongs to a group Va protein in the ERF subfamily which contains the Arabidopsis ERF proteins (SHN1, SHN2, and SHN3). Expression of TdSHN1 was strongly induced by salt, drought, abscisic acid (ABA), and cold. In planta, TdSHN1 protein was able to activate the transcription of GUS reporter gene driven by the GCC box and DRE element sequences. In addition, TdSHN1 was targeted to the nucleus when transiently expressed in tobacco epidermal cells. In transgenic yeast, overexpression of TdSHN1 increased tolerance to multiple abiotic stresses. Taken together, the results showed that TdSHN1 encodes an abiotic stress-inducible, transcription factor which confers abiotic stress tolerance in yeast. TdSHN1 is therefore a promising candidate for improvement of biotic and abiotic stress tolerance in wheat as well as other crops.
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Affiliation(s)
- Rania Djemal
- Laboratory of Plant Protection and Improvement, Center of Biotechnology of Sfax, University of Sfax, B.P' 1177, Route Sidi Mansour Km 6, 3018, Sfax, Tunisia
| | - Habib Khoudi
- Laboratory of Plant Protection and Improvement, Center of Biotechnology of Sfax, University of Sfax, B.P' 1177, Route Sidi Mansour Km 6, 3018, Sfax, Tunisia.
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Guo W, Yang H, Liu Y, Gao Y, Ni Z, Peng H, Xin M, Hu Z, Sun Q, Yao Y. The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:347-59. [PMID: 26332346 DOI: 10.1111/tpj.13003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 05/23/2023]
Abstract
Glutenin proteins in wheat (Triticum aestivum L.) flour confer unique viscoelastic properties to dough products and, therefore, the concentration and composition of the glutenin proteins determine its end-use value. However, the mechanisms governing the glutenin gene expression remain elusive. In this study, we report that wheat TaGAMyb activates the high-molecular-weight glutenin subunit genes (TaGLU) through recruiting the histone acetyltransferase GCN5. By sequencing the promoters of TaGLU-1 genes from 40 modern wheat cultivars, we identified eight types of TaGAMyb binding motifs and verified these by electrophoretic mobility shift assays. The number of TaGAMyb binding motifs in TaGLU-1 genes is correlated with the abundance of glutenin in different cultivars. Chromatin immunoprecipitation plus polymerase chain reaction (ChIP-PCR) analysis reveals that TaGCN5 directly targets the promoters of TaGLU-1 genes in wheat endosperm. We find that TaGAMyb physically interacts with the wheat histone acetyltransferase TaGCN5 and also interacts with Arabidopsis thaliana AtGCN5. TaGAMyb ectopically expressed in Arabidopsis binds to the TaGLU-1Dy promoter on a TaGLU-1Dy transgene and activates its expression. AtGCN5 also targets the TaGLU-1Dy transgene and is involved in the establishment of acetylation at H3K9 and H3K14. These results demonstrate that TaGAMyb plays a dual role in activating expression of glutenin gene by directly binding to the TaGLU promoter and by recruiting GCN5 to modulate histone acetylation during wheat endosperm development.
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Affiliation(s)
- Weiwei Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongqiang Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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8
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Bimolata W, Kumar A, M SKR, Sundaram RM, Laha GS, Qureshi IA, Ghazi IA. Nucleotide diversity analysis of three major bacterial blight resistance genes in rice. PLoS One 2015; 10:e0120186. [PMID: 25807168 PMCID: PMC4373814 DOI: 10.1371/journal.pone.0120186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/23/2015] [Indexed: 11/25/2022] Open
Abstract
Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR. The greatest nucleotide diversity and singleton variable sites (SVS) were present in Xa26 (π = 0.01958; SVS = 182) followed by xa5 and Xa21 alleles. The highest frequency of single nucleotide polymorphisms were observed in Xa21 alleles and least in xa5. Transition bias was observed in all the genes and ‘G’ to ‘A’ transitions were more favored than other form of transitions. Neutrality tests failed to show the presence of selection at these loci, though negative Tajima’s D values indicate the presence of a rare form of polymorphisms. At the interspecies level, O. nivara exhibited more diversity than O. sativa. We have also identified two nearly identical resistant alleles of xa5 and two sequentially identical alleles of Xa21. The alleles of xa5 showed basal levels of expression while Xa21 alleles were functionally not expressed.
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Affiliation(s)
- Waikhom Bimolata
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Anirudh Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Sai Kiran Reddy M
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | | | - Gouri Sankar Laha
- Crop Protection Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
- * E-mail:
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Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R, Martre P. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. FRONTIERS IN PLANT SCIENCE 2014; 5:621. [PMID: 25429295 PMCID: PMC4228979 DOI: 10.3389/fpls.2014.00621] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.
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Affiliation(s)
- Catherine Ravel
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Samuel Fiquet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Julie Boudet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Mireille Dardevet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Jonathan Vincent
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Marielle Merlino
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Robin Michard
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Pierre Martre
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
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Jääskeläinen M, Chang W, Moisy C, Schulman AH. Retrotransposon BARE displays strong tissue-specific differences in expression. THE NEW PHYTOLOGIST 2013; 200:1000-8. [PMID: 24033286 DOI: 10.1111/nph.12470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/30/2013] [Indexed: 05/25/2023]
Abstract
The BARE retrotransposon comprises c. 10% of the barley (Hordeum vulgare) genome. It is actively transcribed, translated and forms virus-like particles (VLPs). For retrotransposons, the inheritance of new copies depends critically on where in the plant replication occurs. In order to shed light on the replication strategy of BARE in the plant, we have used immunolocalization and in situ hybridization to examine expression of the BARE capsid protein, Gag, at a tissue-specific level. Gag is expressed in provascular tissues and highly localized in companion cells surrounding the phloem sieve tubes in mature vascular tissues. BARE Gag and RNA was not seen in the shoot apical meristem of young seedlings, but appeared, following transition to flowering, in the developing floral spike. Moreover, Gag has a highly specific localization in pre-fertilization ovaries. The strong presence of Gag in the floral meristems suggests that newly replicated copies there will be passed to the next generation. BARE expression patterns are consistent with transcriptional regulation by predicted response elements in the BARE promoter, and in the ovary with release from epigenetic transcriptional silencing. To our knowledge, this is the first analysis of the expression of native retrotransposon proteins within a plant to be reported.
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Affiliation(s)
- Marko Jääskeläinen
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, Viikinkaari 1, FIN-00014, Helsinki, Finland
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11
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Peukert M, Weise S, Röder MS, Matthies IE. Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley. BMC Genet 2013; 14:97. [PMID: 24088365 PMCID: PMC3852699 DOI: 10.1186/1471-2156-14-97] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 09/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flavonoids are an important class of secondary compounds in angiosperms. Next to certain biological functions in plants, they play a role in the brewing process and have an effect on taste, color and aroma of beer. The aim of this study was to reveal the haplotype diversity of candidate genes involved in the phenylpropanoid biosynthesis pathway in cultivated barley varieties (Hordeum vulgare L.) and to determine associations to kernel and malting quality parameters. RESULTS Five genes encoding phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS), flavanone 3-hydroxylase (F3H) and dihydroflavonol reductase (DFR) of the phenylpropanoid biosynthesis pathway were partially resequenced in 16 diverse barley reference genotypes. Their localization in the barley genome, their genetic structure, and their genetic variation e.g. single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel) patterns were revealed. In total, 130 SNPs and seven InDels were detected. Of these, 21 polymorphisms were converted into high-throughput pyrosequencing markers. The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters. CONCLUSIONS SNP patterns were found to be highly variable for the investigated genes. The developed high-throughput markers are applicable for assessing the genetic variability and for the determination of haplotype patterns in a set of barley accessions. The candidate genes PAL, C4H and F3H were shown to be associated to several malting properties like glassiness (PAL), viscosity (C4H) or to final attenuation (F3H).
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Affiliation(s)
- Manuela Peukert
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Stephan Weise
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Marion S Röder
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Inge E Matthies
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
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Plessis A, Ravel C, Bordes J, Balfourier F, Martre P. Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3627-44. [PMID: 23881399 PMCID: PMC3745720 DOI: 10.1093/jxb/ert188] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat grain storage protein (GSP) content and composition are the main determinants of the end-use value of bread wheat (Triticum aestivum L.) grain. The accumulation of glutenins and gliadins, the two main classes of GSP in wheat, is believed to be mainly controlled at the transcriptional level through a network of transcription factors. This regulation network could lead to stable cross-environment allometric scaling relationships between the quantity of GSP classes/subunits and the total quantity of nitrogen per grain. This work conducted a genetic mapping study of GSP content and composition and allometric scaling parameters of grain N allocation using a bread wheat worldwide core collection grown in three environments. The core collection was genotyped with 873 markers for genome-wide association and 167 single nucleotide polymorphism markers in 51 candidate genes for candidate association. The candidate genes included 35 transcription factors (TFs) expressed in grain. This work identified 74 loci associated with 38 variables, of which 19 were candidate genes or were tightly linked with candidate genes. Besides structural GSP genes, several loci putatively trans-regulating GSP accumulation were identified. Seven candidate TFs, including four wheat orthologues of barley TFs that control hordein gene expression, were associated or in strong linkage disequilibrium with markers associated with the composition or quantity of glutenin or gliadin, or allometric grain N allocation parameters, confirming the importance of the transcriptional control of GSP accumulation. Genome-wide association results suggest that the genes regulating glutenin and gliadin compositions are mostly distinct from each other and operate differently.
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Affiliation(s)
- Anne Plessis
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Catherine Ravel
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Jacques Bordes
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - François Balfourier
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - Pierre Martre
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- To whom correspondence should be addressed. E-mail:
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Wilhelm EP, Mackay IJ, Saville RJ, Korolev AV, Balfourier F, Greenland AJ, Boulton MI, Powell W. Haplotype dictionary for the Rht-1 loci in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1733-47. [PMID: 23553443 DOI: 10.1007/s00122-013-2088-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/19/2013] [Indexed: 05/25/2023]
Abstract
The introduction of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties was a key component of the 'green revolution' and today these alleles are the primary sources of semi-dwarfism in wheat. The Rht-1 loci encode DELLA proteins, which are transcription factors that affect plant growth and stress tolerance. In bread wheat, Rht-D1b and Rht-B1b influence resistance to the disease Fusarium Head Blight. To identify Rht-1 variants, locus specific primers were developed and used to sequence the entire open reading frame (ORF) and 1.7 kb of the 5' and 0.5 kb of the 3' flanking regions of Rht-A1 (Rht-A1+f), Rht-B1 (Rht-B1+f), and Rht-D1 (Rht-D1+f) in bread wheat (36 sequences from each genome) and tetraploid and diploid wheat (TDW) (one to three sequences from each genome). Among the bread wheat accessions, the Rht-A1+f and Rht-D1+f sequences contained relatively low genetic diversity and few haplotypes relative to the Rht-B1+f sequences. The TDW accessions were relatively rich in genetic diversity and contained the majority of the polymorphic sites. Novel polymorphisms, relative to 'Chinese Spring', discovered among the accessions include 160 and 197 bp insertions 5' of Rht-B1 and a frameshift in the Rht-B1 ORF. Quantitative real-time PCR using shoot and leaf tissue from 5-day-old seedlings of genotypes lacking or containing the 5' insertions revealed no major effect on Rht-B1 transcript accumulation. This research provides insights into the genetic diversity present at the Rht-1 loci in modern bread wheat and in relation to ancestral wheat accessions.
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Affiliation(s)
- Edward P Wilhelm
- National Institute of Agricultural Botany, Huntingdon Rd, Cambridge, CB3 0LE, UK.
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Wang Y, Sun F, Cao H, Peng H, Ni Z, Sun Q, Yao Y. TamiR159 directed wheat TaGAMYB cleavage and its involvement in anther development and heat response. PLoS One 2012; 7:e48445. [PMID: 23133634 PMCID: PMC3486836 DOI: 10.1371/journal.pone.0048445] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/26/2012] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis and rice, miR159-regulated GAMYB-like family transcription factors function in flower development and gibberellin (GA) signaling in cereal aleurone cells. In this study, the involvement of miR159 in the regulation of its putative target TaGAMYB and its relationship to wheat development were investigated. First, we demonstrated that cleavage of TaGAMYB1 and TaGAMYB2 was directed by miR159 using 5′-RACE and a transient expression system. Second, we overexpressed TamiR159, TaGAMYB1 and mTaGAMYB1 (impaired in the miR159 binding site) in transgenic rice, revealing that the accumulation in rice of mature miR159 derived from the precursor of wheat resulted in delayed heading time and male sterility. In addition, the number of tillers and primary branches in rice overexpressing mTaGAMYB1 increased relative to the wild type. Our previous study reported that TamiR159 was downregulated after two hours of heat stress treatment in wheat (Triticum aestivum L.). Most notably, the TamiR159 overexpression rice lines were more sensitive to heat stress relative to the wild type, indicating that the downregulation of TamiR159 in wheat after heat stress might participate in a heat stress-related signaling pathway, in turn contributing to heat stress tolerance.
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Affiliation(s)
- Yu Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Fenglong Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Hua Cao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis, Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, People’s Republic of China
- * E-mail:
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Zhang H, Mao X, Zhang J, Chang X, Wang C, Jing R. Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat. Genetica 2011; 139:743-53. [PMID: 21637995 DOI: 10.1007/s10709-011-9579-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
Abstract
Sucrose non-fermenting1-related protein kinase 2 (SnRK2) plays a key role in plant stress signaling transduction pathways. In this study, one copy of TaSnRK2.7, a SnRK2 member of common wheat, was isolated and characterized for nucleotide diversity among 45 wheat accessions with different stress-response features. Most of the accessions were elite wheat cultivars, which had been subject to population bottlenecks and intensive selection during breeding. Nucleotide and haplotype diversity across the entire TaSnRK2.7-A region was 0.00076 and 0.590, respectively, and diversity in non-coding regions was higher than that in coding regions. Sliding-window analysis showed variable levels of nucleotide variation along the entire TaSnRK2.7-A region; the sixth intron and ninth exon represented variation-enriched regions. As predicted, neutrality tests revealed that population bottlenecks or purifying selection had acted on the TaSnRK2.7-A gene, a relatively conserved gene. Furthermore, strong linkage disequilibrium between SNP loci extends across the entire TaSnRK2.7-A region. These findings demonstrate that the TaSnRK2.7-A genomic region has evolved under extensive selection pressure during crop breeding.
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Affiliation(s)
- Hongying Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Giordani T, Buti M, Natali L, Pugliesi C, Cattonaro F, Morgante M, Cavallini A. An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1039-1049. [PMID: 21184050 DOI: 10.1007/s00122-010-1509-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/29/2010] [Indexed: 05/30/2023]
Abstract
With the aim to study variability in genes involved in ecological adaptations, we have analysed sequence polymorphisms of eight unique genes putatively involved in drought response by isolation and analysis of allelic sequences in eight inbred lines of sunflower of different origin and phenotypic characters and showing different drought response in terms of leaf relative water content (RWC). First, gene sequences were amplified by PCR on genomic DNA from a highly inbred line and their products were directly sequenced. In the absence of single nucleotide polymorphisms, the gene was considered as unique. Then, the same PCR reaction was performed on genomic DNAs of eight inbred lines to isolate allelic variants to be compared. The eight selected genes encode a dehydrin, a heat shock protein, a non-specific lipid transfer protein, a z-carotene desaturase, a drought-responsive-element-binding protein, a NAC-domain transcription regulator, an auxin-binding protein, and an ABA responsive-C5 protein. Nucleotide diversity per synonymous and non-synonymous sites was calculated for each gene sequence. The π (a)/π (s) ratio range was usually very low, indicating strong purifying selection, though with locus-to-locus differences. As far as non-coding regions, the intron showed a larger variability than the other regions only in the case of the dehydrin gene. In the other genes tested, in which one or more introns occur, variability in the introns was similar or even lower than in the other regions. On the contrary, 3'-UTRs were usually more variable than the coding regions. Linkage disequilibrium in the selected genes decayed on average within 1,000 bp, with large variation among genes. A pairwise comparison between genetic distances calculated on the eight genes and the difference in RWC showed a significant correlation in the first phases of drought stress. The results are discussed in relation to the function of analysed genes, i.e. involved in gene regulation and signal transduction, or encoding enzymes and defence proteins.
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Affiliation(s)
- T Giordani
- Department of Crop Plant Biology, University of Pisa, Pisa, Italy
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17
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Saintenac C, Faure S, Remay A, Choulet F, Ravel C, Paux E, Balfourier F, Feuillet C, Sourdille P. Variation in crossover rates across a 3-Mb contig of bread wheat (Triticum aestivum) reveals the presence of a meiotic recombination hotspot. Chromosoma 2010; 120:185-98. [PMID: 21161258 DOI: 10.1007/s00412-010-0302-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/27/2010] [Accepted: 11/20/2010] [Indexed: 10/18/2022]
Abstract
In bread wheat (Triticum aestivum L.), initial studies using deletion lines indicated that crossover (CO) events occur mainly in the telomeric regions of the chromosomes with a possible correlation with the presence of genes. However, little is known about the distribution of COs at the sequence level. To investigate this, we studied in detail the pattern of COs along a contig of 3.110 Mb using two F2 segregating populations (Chinese Spring × Renan (F2-CsRe) and Chinese Spring × Courtot (F2-CsCt)) each containing ~2,000 individuals. The availability of the sequence of the contig from Cs enabled the development of 318 markers among which 23 co-dominant polymorphic markers (11 SSRs and 12 SNPs) were selected for CO distribution analyses. The distribution of CO events was not homogeneous throughout the contig, ranging from 0.05 to 2.77 cM/Mb, but was conserved between the two populations despite very different contig recombination rate averages (0.82 cM/Mb in F2-CsRe vs 0.35 cM/Mb in F2-CsCt). The CO frequency was correlated with the percentage of coding sequence in Cs and with the polymorphism rate between Cs and Re or Ct in both populations, indicating an impact of these two factors on CO distribution. At a finer scale, COs were found in a region covering 2.38 kb, spanning a gene coding for a glycosyl transferase (Hga3), suggesting the presence of a CO hotspot. A non-crossover event covering at least 453 bp was also identified in the same interval. From these results, we can conclude that gene content could be one of the factors driving recombination in bread wheat.
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Affiliation(s)
- Cyrille Saintenac
- UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, INRA-UBP, Domaine de Crouël, 234 Avenue du Brézet, Clermont-Ferrand, 63100, France
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Kumar GR, Sakthivel K, Sundaram R, Neeraja C, Balachandran S, Rani NS, Viraktamath B, Madhav M. Allele mining in crops: Prospects and potentials. Biotechnol Adv 2010; 28:451-61. [DOI: 10.1016/j.biotechadv.2010.02.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 09/21/2009] [Accepted: 09/25/2009] [Indexed: 12/26/2022]
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Haseneyer G, Stracke S, Piepho HP, Sauer S, Geiger HH, Graner A. DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits. BMC PLANT BIOLOGY 2010; 10:5. [PMID: 20064201 PMCID: PMC2822787 DOI: 10.1186/1471-2229-10-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 01/08/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach. RESULTS Within the sequenced fragments of four candidate genes we observed different levels of nucleotide diversity. The effect of selection on the candidate genes was tested by Tajima's D which revealed significant values for BLZ1, BLZ2, and BPBF in the subset of two-rowed barleys. Pair-wise LD estimates between the detected SNPs within each candidate gene revealed different intra-genic linkage patterns. On the basis of a more extensive examination of genomic regions surrounding the four candidate genes we found a sharp decrease of LD (r2<0.2 within 1 cM) in all but one flanking regions.Significant marker-trait associations between SNP sites within BLZ1 and flowering time, BPBF and crude protein content and BPBF and starch content were detected. Most haplotypes occurred at frequencies <0.05 and therefore were rejected from the association analysis. Based on haplotype information, BPBF was associated to crude protein content and starch content, BLZ2 showed association to thousand-grain weight and BLZ1 was found to be associated with flowering time and plant height. CONCLUSIONS Differences in nucleotide diversity and LD pattern within the candidate genes BLZ1, BLZ2, BPBF, and HvGAMYB reflect the impact of selection on the nucleotide sequence of the four candidate loci.Despite significant associations, the analysed candidate genes only explained a minor part of the total genetic variation although they are known to be important factors influencing the expression of seed quality traits. Therefore, we assume that grain quality as well as plant height and flowering time are influenced by many factors each contributing a small part to the expression of the phenotype. A genome-wide association analysis could provide a more comprehensive picture of loci involved in the regulation of grain quality, thousand grain weight and the other agronomic traits that were analyzed in this study. However, despite available high-throughput genotyping arrays the marker density along the barely genome is still insufficient to cover all associations in a whole genome scan. Therefore, the candidate gene-based approach will further play an important role in barley association studies.
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Affiliation(s)
- Grit Haseneyer
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- University of Hohenheim, Institute for Plant Breeding, Seed Science and Population Genetics (350), 70593 Stuttgart, Germany
- Plant Breeding, Centre of Life and Food Sciences Weihenstephan, Technische Universitaet Muenchen, Am Hochanger 4, 85350 Freising, Germany
| | - Silke Stracke
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- Department of Crop Sciences, Quality of Plant Products, University of Goettingen, Carl-Sprengel-Weg 1, 37075 Goettingen, Germany
| | - Hans-Peter Piepho
- University of Hohenheim, Institute for Crop Production and Grassland Research (340), Bioinformatics, 70593 Stuttgart, Germany
| | - Sascha Sauer
- Max-Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany
| | - Hartwig H Geiger
- University of Hohenheim, Institute for Plant Breeding, Seed Science and Population Genetics (350), 70593 Stuttgart, Germany
| | - Andreas Graner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
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Ravel C, Martre P, Romeuf I, Dardevet M, El-Malki R, Bordes J, Duchateau N, Brunel D, Balfourier F, Charmet G. Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. PLANT PHYSIOLOGY 2009; 151:2133-44. [PMID: 19828671 PMCID: PMC2785959 DOI: 10.1104/pp.109.146076] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/10/2009] [Indexed: 05/19/2023]
Abstract
Storage protein activator (SPA) is a key regulator of the transcription of wheat (Triticum aestivum) grain storage protein genes and belongs to the Opaque2 transcription factor subfamily. We analyzed the sequence polymorphism of the three homoeologous Spa genes in hexaploid wheat. The level of polymorphism in these genes was high particularly in the promoter. The deduced protein sequences of each homoeolog and haplotype show greater than 93% identity. Two major haplotypes were studied for each Spa gene. The three Spa homoeologs have similar patterns of expression during grain development, with a peak in expression around 300 degree days after anthesis. On average, Spa-B is 10 and seven times more strongly expressed than Spa-A and Spa-D, respectively. The haplotypes are associated with significant quantitative differences in Spa expression, especially for Spa-A and Spa-D. Significant differences were found in the quantity of total grain nitrogen allocated to the gliadin protein fractions for the Spa-A haplotypes, whereas the synthesis of glutenins is not modified. Genetic association analysis between Spa and dough viscoelasticity revealed that Spa polymorphisms are associated with dough tenacity, extensibility, and strength. Except for Spa-A, these associations can be explained by differences in grain hardness. No association was found between Spa markers and the average single grain dry mass or grain protein concentration. These results demonstrate that in planta Spa is involved in the regulation of grain storage protein synthesis. The associations between Spa and dough viscoelasticity and grain hardness strongly suggest that Spa has complex pleiotropic functions during grain development.
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Affiliation(s)
- Catherine Ravel
- INRA, UMR1095, Genetics, Diversity, and Ecophysiology of Cereals, F-63100 Clermont-Ferrand, France.
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Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, Balfourier F. Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1523-37. [PMID: 19756470 DOI: 10.1007/s00122-009-1153-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 08/30/2009] [Indexed: 05/21/2023]
Abstract
A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT-ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920-1959), modern varieties (1960-2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT-ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0-5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.
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Affiliation(s)
- Aniko Horvath
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
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22
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Chebotar S, Sourdille P, Paux E, Balfourier F, Feuillet C, Bernard M. Evaluation of the genetic variability of homoeologous group 3 SSRS in bread wheat. CYTOL GENET+ 2009. [DOI: 10.3103/s0095452709020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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