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Yao X, Li H, Nie J, Liu H, Guo Y, Lv L, Yang Z, Sui X. Disruption of the amino acid transporter CsAAP2 inhibits auxin-mediated root development in cucumber. THE NEW PHYTOLOGIST 2023. [PMID: 37129077 DOI: 10.1111/nph.18947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
Amino acid transporters are the principal mediators of organic nitrogen distribution within plants and are essential for plant growth and development. Despite this importance, relatively few amino acid transporter genes have been explored and elucidated in cucumber (Cucumis sativus). Here, a total of 86 amino acid transporter genes were identified in the cucumber genome. We further identified Amino Acid Permease (AAP) subfamily members that exhibited distinct expression patterns in different tissues. We found that the CsAAP2 as a candidate gene encoding a functional amino acid transporter is highly expressed in cucumber root vascular cells. CsAAP2 knockout lines exhibited arrested development of root meristem, which then caused the delayed initiation of lateral root and the inhibition of root elongation. What is more, the shoot growth of aap2 mutants was strongly retarded due to defects in cucumber root development. Moreover, aap2 mutants exhibited higher concentrations of amino acids and lignin in roots. We found that the mutant roots had a stronger ability to acidize medium. Furthermore, in the aap2 mutants, polar auxin transport was disrupted in the root tip, leading to high auxin levels in roots. Interestingly, slightly alkaline media rescued their severely reduced root growth by stimulating auxin pathway.
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Affiliation(s)
- Xuehui Yao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Hujian Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Nie
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Huan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yicong Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lijun Lv
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhen Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaolei Sui
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
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Cohen M, Hertweck K, Itkin M, Malitsky S, Dassa B, Fischer AM, Fluhr R. Enhanced proteostasis, lipid remodeling, and nitrogen remobilization define barley flag leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6816-6837. [PMID: 35918065 DOI: 10.1093/jxb/erac329] [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: 08/24/2021] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. We characterized flag leaf senescence at 7, 14, and 21 d past anthesis in two near-isogenic barley lines varying in the allelic state of the HvNAM1 transcription factor gene, which influences senescence timing. Metabolomics and microscopy indicated that, as senescence progressed, thylakoid lipids were transiently converted to neutral lipids accumulating in lipid droplets. Senescing leaves also exhibited an accumulation of sugars including glucose, while nitrogen compounds (nucleobases, nucleotides, and amino acids) decreased. RNA-Seq analysis suggested lipid catabolism via β-oxidation and the glyoxylate cycle, producing carbon skeletons and feeding respiration as a replacement of the diminished carbon supply from photosynthesis. Comparison of the two barley lines highlighted a more prominent up-regulation of heat stress transcription factor- and chaperone-encoding genes in the late-senescing line, suggesting a role for these genes in the control of leaf longevity. While numerous genes with putative roles in nitrogen remobilization were up-regulated in both lines, several peptidases, nucleases, and nitrogen transporters were more highly induced in the early-senescing line; this finding identifies processes and specific candidates which may affect nitrogen remobilization from senescing barley leaves, downstream of the HvNAM1 transcription factor.
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Affiliation(s)
- Maja Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kendra Hertweck
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas M Fischer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Robert Fluhr
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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3
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Marín-Sanz M, Barro F. RNAi silencing of wheat gliadins alters the network of transcription factors that regulate the synthesis of seed storage proteins toward maintaining grain protein levels. FRONTIERS IN PLANT SCIENCE 2022; 13:935851. [PMID: 36003813 PMCID: PMC9395171 DOI: 10.3389/fpls.2022.935851] [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: 05/04/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reduction of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated, respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are regulated independently of the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling.
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Yang Y, Wang X, Zheng J, Men Y, Zhang Y, Liu L, Han Y, Hou S, Sun Z. Amino acid transporter (AAT) gene family in Tartary buckwheat (Fagopyrum tataricum L. Gaertn.): Characterization, expression analysis and functional prediction. Int J Biol Macromol 2022; 217:330-344. [PMID: 35839952 DOI: 10.1016/j.ijbiomac.2022.07.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022]
Abstract
Tartary buckwheat (Fagopyrum tataricum L. Gaertn., TB) is an ancient minor crop and an important food source for humans to supplement nutrients such as flavonoids and essential amino acids. Amino acid transporters (AATs) play critical roles in plant growth and development through the transport of amino acids. In this study, 104 AATs were identified in TB genome and divided into 11 subfamilies by phylogenetic relationships. Tandem and segmental duplications promoted the expansion of FtAAT gene family, and the variations of gene sequence, protein structure and expression pattern were the main reasons for the functional differentiation of FtAATs. Based on RNA-seq and qRT-PCR, the expression patterns of FtAATs in different tissues and under different abiotic stresses were analyzed, and several candidate FtAATs that might affect grain development and response to abiotic stresses were identified, such as FtAAP12 and FtCAT7. Finally, combined with the previous studies, the expression patterns and phylogenetic relationships of AATs in multiple species, the functions of multiple high-confidence FtAAT genes were predicted, and the schematic diagram of FtAATs in TB was initially drawn. Overall, this work provided a framework for further functional analysis of FtAAT genes and important clues for the improvement of TB quality and stress resistance.
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Affiliation(s)
- Yang Yang
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China
| | - Xinfang Wang
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China
| | - Jie Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yihan Men
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China
| | - Yijuan Zhang
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
| | - Yuanhuai Han
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China
| | - Siyu Hou
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China.
| | - Zhaoxia Sun
- College of Agriculture, Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Effciency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan 030031, Shanxi, China.
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5
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Sayre-Chavez B, Bettenhausen H, Windes S, Aron P, Cistué L, Fisk S, Helgerson L, Heuberger AL, Tynan S, Hayes P, Muñoz-Amatriaín M. Genetic basis of barley contributions to beer flavor. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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6
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De La Torre AR, Sekhwal MK, Neale DB. Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia. Genes (Basel) 2021; 12:1826. [PMID: 34828432 PMCID: PMC8621000 DOI: 10.3390/genes12111826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype-environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Manoj K. Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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7
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Yang Y, Chai Y, Liu J, Zheng J, Zhao Z, Amo A, Cui C, Lu Q, Chen L, Hu YG. Amino acid transporter (AAT) gene family in foxtail millet (Setaria italica L.): widespread family expansion, functional differentiation, roles in quality formation and response to abiotic stresses. BMC Genomics 2021; 22:519. [PMID: 34238217 PMCID: PMC8268433 DOI: 10.1186/s12864-021-07779-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Background Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response. Results A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted. Conclusion This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07779-9.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongmao Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jie Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Aduragbemi Amo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunge Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiumei Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China. .,Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, Shaanxi, China.
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8
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Meng X, Wang X, Zhang Z, Xiong S, Wei Y, Guo J, Zhang J, Wang L, Ma X, Tegeder M. Transcriptomic, proteomic, and physiological studies reveal key players in wheat nitrogen use efficiency under both high and low nitrogen supply. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4435-4456. [PMID: 33829261 DOI: 10.1093/jxb/erab153] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
The effective use of available nitrogen (N) to improve crop grain yields provides an important strategy to reduce environmental N pollution and promote sustainable agriculture. However, little is known about the common genetic basis of N use efficiency (NUE) at varying N availability. Two wheat (Triticum aestivum L.) cultivars were grown in the field with high, moderate, and low N supply. Cultivar Zhoumai 27 outperformed Aikang 58 independent of the N supply and showed improved growth, canopy leaf area index, flag leaf surface area, grain number, and yield, and enhanced NUE due to both higher N uptake and utilization efficiency. Further, transcriptome and proteome analyses were performed using flag leaves that provide assimilates for grain growth. The results showed that many genes or proteins that are up- or down-regulated under all N regimes are associated with N and carbon metabolism and transport. This was reinforced by cultivar differences in photosynthesis, assimilate phloem transport, and grain protein/starch yield. Overall, our study establishes that improving NUE at both high and low N supply requires distinct adjustments in leaf metabolism and assimilate partitioning. Identified key genes/proteins may individually or concurrently regulate NUE and are promising targets for maximizing crop NUE irrespective of the N supply.
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Affiliation(s)
- Xiaodan Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
- School of Biological Sciences, Washington State University, Pullman, WAUSA
| | - Xiaochun Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
| | - Zhiyong Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Shuping Xiong
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Yihao Wei
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jianbiao Guo
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jie Zhang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Lulu Wang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Xinming Ma
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WAUSA
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9
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Miryeganeh M. Senescence: The Compromised Time of Death That Plants May Call on Themselves. Genes (Basel) 2021; 12:143. [PMID: 33499161 PMCID: PMC7912376 DOI: 10.3390/genes12020143] [Citation(s) in RCA: 7] [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: 01/03/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/03/2023] Open
Abstract
Plants synchronize their life history events with proper seasonal conditions, and as the fitness consequences of each life stage depend on previous and/or subsequent one, changes in environmental cues create cascading effects throughout their whole life cycle. For monocarpic plants, proper senescence timing is very important as the final production of plants depends on it. Citing available literatures, this review discusses how plants not only may delay senescence until after they reproduce successfully, but they may also bring senescence time forward, in order to reproduce in favored conditions. It demonstrates that even though senescence is part of aging, it does not necessarily mean plants have to reach a certain age to senesce. Experiments using different aged plants have suggested that in interest of their final outcome and fitness, plants carefully weigh out environmental cues and transit to next developmental phase at proper time, even if that means transiting to terminal senescence phase earlier and shortening their lifespan. How much plants have control over senescence timing and how they balance internal and external signals for that is not well understood. Future studies are needed to identify processes that trigger senescence timing in response to environment and investigate genetic/epigenetic mechanisms behind it.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
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10
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Tian R, Yang Y, Chen M. Genome-wide survey of the amino acid transporter gene family in wheat (Triticum aestivum L.): Identification, expression analysis and response to abiotic stress. Int J Biol Macromol 2020; 162:1372-1387. [PMID: 32781128 DOI: 10.1016/j.ijbiomac.2020.07.302] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/30/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Amino acid transporters (AATs), which transport amino acids across cell membranes, play important roles in alleviating plant damage under stresses and in plant growth. To data, little is known about the AAT genes in wheat because of its complex genome. In this study, a total of 296 AAT genes were identified from the latest wheat genome sequence (IWGSC v1.1) and classified into 12 distinct subfamilies based upon their sequence composition and phylogenetic relationship. The expansion of the wheat AAT family was mainly the results of whole-genome duplication (WGD) and tandem events. The unequal expansion of different subfamilies brought new features to TaAATs. TaAATs were highly expressed and exhibited distinct expression patterns in different tissues. On the basis of homology and expression pattern analysis, we identified several wheat AAT family members that may affect grain quality. In addition, TaAAP3, TaATLa2 and TaATLb13 exhibited sustained expression in response to drought and high-temperature stress. These genes are involved in the response of wheat to abiotic stress by regulating the transport and distribution of amino acids. Overall, our results help to understand the complexity of TaAATs and provide a theoretical basis for further identification and utilization of AATs in wheat and other crop species.
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Affiliation(s)
- Ruizheng Tian
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China
| | - Yang Yang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Yangling 712100, China
| | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China.
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11
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Yao X, Nie J, Bai R, Sui X. Amino Acid Transporters in Plants: Identification and Function. PLANTS 2020; 9:plants9080972. [PMID: 32751984 PMCID: PMC7466100 DOI: 10.3390/plants9080972] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/25/2020] [Accepted: 07/29/2020] [Indexed: 12/04/2022]
Abstract
Amino acid transporters are the main mediators of nitrogen distribution throughout the plant body, and are essential for sustaining growth and development. In this review, we summarize the current state of knowledge on the identity and biological functions of amino acid transporters in plants, and discuss the regulation of amino acid transporters in response to environmental stimuli. We focus on transporter function in amino acid assimilation and phloem loading and unloading, as well as on the molecular identity of amino acid exporters. Moreover, we discuss the effects of amino acid transport on carbon assimilation, as well as their cross-regulation, which is at the heart of sustainable agricultural production.
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12
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Miryeganeh M. Synchronization of senescence and desynchronization of flowering in Arabidopsis thaliana. AOB PLANTS 2020; 12:plaa018. [PMID: 32577195 PMCID: PMC7299267 DOI: 10.1093/aobpla/plaa018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
In a recent publication, we proposed that adjusting lifespan in order to synchronize senescence is important for timing of reproduction, and we quantified the synchrony of reproductive timing relative to germination timing. Here, in a second sequential seeding experiment (SSE), the germination timing of Arabidopsis thaliana accessions was manipulated and plants were then grown under two different temperature regimes. Life stage traits of plants in each temperature regime were analysed and it was evaluated whether the cohorts were grouped according to age and/or environmental conditions. While flowering-related traits showed desynchrony among cohorts, striking synchrony in the timing of senescence among cohorts for each group was found. A quantitative trait locus (QTL) analysis using a genotyped population of 'Cvi/Ler' recombinant inbred lines (RILs) was then conducted. Novel and known loci were assigned to flowering and senescence timing. However, senescence synchrony resulted in low variation in senescence time and weak QTL detection for flowering termination. Overlapping flowering and senescence genes with loci affecting either of those traits were found and suggest a potential interdependency of reproductive traits.
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Affiliation(s)
- Matin Miryeganeh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Japan
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13
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Taranto F, D'Agostino N, Rodriguez M, Pavan S, Minervini AP, Pecchioni N, Papa R, De Vita P. Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm. Front Genet 2020; 11:217. [PMID: 32373150 PMCID: PMC7187681 DOI: 10.3389/fgene.2020.00217] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/24/2020] [Indexed: 01/31/2023] Open
Abstract
The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
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Affiliation(s)
- Francesca Taranto
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Sassari, Italy.,CBV - Interdepartmental Centre for Plant Biodiversity Conservation and Enhancement Sassari University, Alghero, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Anna P Minervini
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
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Aliyu H, Gorte O, Zhou X, Neumann A, Ochsenreither K. In silico Proteomic Analysis Provides Insights Into Phylogenomics and Plant Biomass Deconstruction Potentials of the Tremelalles. Front Bioeng Biotechnol 2020; 8:226. [PMID: 32318549 PMCID: PMC7147457 DOI: 10.3389/fbioe.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
Basidiomycetes populate a wide range of ecological niches but unlike ascomycetes, their capabilities to decay plant polymers and their potential for biotechnological approaches receive less attention. Particularly, identification and isolation of CAZymes is of biotechnological relevance and has the potential to improve the cache of currently available commercial enzyme cocktails toward enhanced plant biomass utilization. The order Tremellales comprises phylogenetically diverse fungi living as human pathogens, mycoparasites, saprophytes or associated with insects. Here, we have employed comparative genomics approaches to highlight the phylogenomic relationships among thirty-five Tremellales and to identify putative enzymes of biotechnological interest encoded on their genomes. Evaluation of the predicted proteomes of the thirty-five Tremellales revealed 6,918 putative carbohydrate-active enzymes (CAZYmes) and 7,066 peptidases. Two soil isolates, Saitozyma podzolica DSM 27192 and Cryptococcus sp. JCM 24511, show higher numbers harboring an average of 317 compared to a range of 267-121 CAZYmes for the rest of the strains. Similarly, the proteomes of the two soil isolates along with two plant associated strains contain higher number of peptidases sharing an average of 234 peptidases compared to a range of 226-167 for the rest of the strains. Despite these huge differences and the apparent enrichment of these enzymes among the soil isolates, the data revealed a diversity of the various enzyme families that does not reflect specific habitat type. Growth experiment on various carbohydrates to validate the predictions provides support for this view. Overall, the data indicates that the Tremellales could serve as a rich source of both CAZYmes and peptidases with wide range of potential biotechnological relevance.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Olga Gorte
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xinhai Zhou
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Dissecting the Regulatory Network of Leaf Premature Senescence in Maize ( Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant. Genes (Basel) 2019; 10:genes10110944. [PMID: 31752425 PMCID: PMC6895817 DOI: 10.3390/genes10110944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/03/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Leaf premature senescence largely determines maize (Zea mays L.) grain yield and quality. A natural recessive premature-senescence mutant was selected from the breeding population, and near-isogenic lines were constructed using Jing24 as the recurrent parent. In the near-isogenic lines, the dominant homozygous material was wild-type (WT), and the recessive material of early leaf senescence was the premature-senescence-type ZmELS5. To identify major genes and regulatory mechanisms involved in leaf senescence, a transcriptome analysis of the ZmELS5 and WT near-isogenic lines (NILs) was performed. A total of 8796 differentially expressed transcripts were identified between ZmELS5 and WT, including 3811 up-regulated and 4985 down-regulated transcripts. By combining gene ontology, Kyoto Encyclopedia of Genes and Genomes, gene set, and transcription factor enrichment analyses, key differentially expressed genes were screened. The senescence regulatory network was predicted based on these key differentially expressed genes, which indicated that the senescence process is mainly regulated by bHLH, WRKY, and AP2/EREBP family transcription factors, leading to the accumulations of jasmonic acid and ethylene. This causes stress responses and reductions in the chlorophyll a/b-binding protein activity level. Then, decreased ATP synthase activity leads to increased photosystem II photodamage, ultimately leading to leaf senescence.
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Frank S, Hollmann J, Mulisch M, Matros A, Carrión CC, Mock HP, Hensel G, Krupinska K. Barley cysteine protease PAP14 plays a role in degradation of chloroplast proteins. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6057-6069. [PMID: 31403664 PMCID: PMC6859807 DOI: 10.1093/jxb/erz356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/31/2019] [Indexed: 05/18/2023]
Abstract
Chloroplast protein degradation is known to occur both inside chloroplasts and in the vacuole. Genes encoding cysteine proteases have been found to be highly expressed during leaf senescence. However, it remains unclear where they participate in chloroplast protein degradation. In this study HvPAP14, which belongs to the C1A family of cysteine proteases, was identified in senescing barley (Hordeum vulgare L.) leaves by affinity enrichment using the mechanism-based probe DCG-04 targeting cysteine proteases and subsequent mass spectrometry. Biochemical analyses and expression of a HvPAP14:RFP fusion construct in barley protoplasts was used to identify the subcellular localization and putative substrates of HvPAP14. The HvPAP14:RFP fusion protein was detected in the endoplasmic reticulum and in vesicular bodies. Immunological studies showed that HvPAP14 was mainly located in chloroplasts, where it was found in tight association with thylakoid membranes. The recombinant enzyme was activated by low pH, in accordance with the detection of HvPAP14 in the thylakoid lumen. Overexpression of HvPAP14 in barley revealed that the protease can cleave LHCB proteins and PSBO as well as the large subunit of Rubisco. HvPAP14 is involved in the normal turnover of chloroplast proteins and may have a function in bulk protein degradation during leaf senescence.
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Affiliation(s)
- Susann Frank
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Solana Research, Eichenallee 9, Windeby, Germany
| | - Maria Mulisch
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Central Microscopy, Christian-Albrechts-University of Kiel, Olshausenstraße 40, Kiel, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Cristian C Carrión
- Instituto de Fisiología Vegetal, INFIVE, CONICET-UNLP, cc 327, 1900 La Plata, Argentina
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Correspondence:
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Ma C, Li B, Wang L, Xu ML, Lizhu E, Jin H, Wang Z, Ye JR. Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development. BMC PLANT BIOLOGY 2019; 19:197. [PMID: 31088353 PMCID: PMC6515667 DOI: 10.1186/s12870-019-1808-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/26/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND During maize early kernel development, the dramatic transcriptional reprogramming determines the rate of developmental progression, and phytohormone plays critical role in these important processes. To investigate the phytohormone levels and transcriptome reprogramming profiles during maize early kernel development, two maize inbreds with similar genetic background but different mature kernel sizes (ILa and ILb) were used. RESULTS The levels of indole-3-acetic acid (IAA) were increased continuously in maize kernels from 5 days after pollination (DAP) to 10 DAP. ILa had smaller mature kernels than ILb, and ILa kernels had significantly lower IAA levels and significantly higher SA levels than ILb at 10 DAP. The different phytohormone profiles correlated with different transcriptional reprogramming in the two kernels. The global transcriptomes in ILa and ILb kernels were strikingly different at 5 DAP, and their differences peaked at 8 DAP. Functional analysis showed that the biggest transcriptome difference between the two kernels is those response to biotic and abiotic stresses. Further analyses indicated that the start of dramatic transcriptional reprogramming and the onset of significantly enriched functional categories, especially the "plant hormone signal transduction" and "starch and sucrose metabolism", was earlier in ILa than in ILb, whereas more significant enrichment of those functional categories occurred at later stage of kernel development in ILb. CONCLUSIONS These results indicate that later onset of the significantly enriched functional categories, coincide with their stronger activities at a later developmental stage and higher IAA level, are necessary for young kernels to undergo longer mitotic activity and finally develop a larger kernel size. The different onset times and complex interactions of the important functional categories, especially phytohormone signal, and carbohydrate metabolism, form the most important molecular regulators mediating maize early kernel development.
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Affiliation(s)
- Chuanyu Ma
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Bo Li
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Lina Wang
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Ming-liang Xu
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - E. Lizhu
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Hongyu Jin
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Zhicheng Wang
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Jian-rong Ye
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
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18
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Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat. Sci Rep 2018; 8:7082. [PMID: 29728590 PMCID: PMC5935732 DOI: 10.1038/s41598-018-25430-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/18/2018] [Indexed: 02/03/2023] Open
Abstract
Plants deploy several ammonium transporter (AMT) and nitrate transporter (NRT) genes to acquire NH4+ and NO3− from the soil into the roots and then transport them to other plant organs. Coding sequences of wheat genes obtained from ENSEMBL were aligned to known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous genes. Bayesian phylogenetic relationships among these genes showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2). Inter-species gene duplication analysis showed that eight AMT and 77 NRT genes were orthologous to the AMT and NRT genes of aforementioned plant species. Expression patterns of these genes were studied via whole transcriptome sequencing of 21-day old seedlings of five spring wheat lines. Eight AMT and 52 NRT genes were differentially expressed between root and shoot; and 131 genes did not express neither in root nor in shoot of 21-day old seedlings. Homeologous genes in the A, B, and D genomes, characterized by high sequence homology, revealed that their counterparts exhibited different expression patterns. This complement and evolutionary relationship of wheat AMT and NRT genes is expected to help in development of wheat germplasm with increased efficiency in nitrogen uptake and usage.
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Jehanzeb M, Zheng X, Miao Y. The Role of the S40 Gene Family in Leaf Senescence. Int J Mol Sci 2017; 18:ijms18102152. [PMID: 29035318 PMCID: PMC5666833 DOI: 10.3390/ijms18102152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 01/03/2023] Open
Abstract
Senescence affect different traits of plants, such as the ripening of fruit, number, quality and timing of seed maturation. While senescence is induced by age, growth hormones and different environmental stresses, a highly organized genetic mechanism related to substantial changes in gene expression regulates the process. Only a few genes associated to senescence have been identified in crop plants despite the vital significance of senescence for crop yield. The S40 gene family has been shown to play a role in leaf senescence. The barley HvS40 gene is one of the senescence marker genes which shows expression during age-dependent as well as dark-induced senescence. Like barley HvS40, the Arabidopsis AtS40-3 gene is also induced during natural senescence as well as in response to treatment with abscisic acid, salicylic acid, darkness and pathogen attack. It is speculated that rice OsS40 has a similar function in the leaf senescence of rice.
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Affiliation(s)
- Muhammad Jehanzeb
- The Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, China.
| | - Xiangzi Zheng
- The Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, China.
| | - Ying Miao
- The Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, China.
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20
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Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Sci Rep 2017; 7:5461. [PMID: 28710348 PMCID: PMC5511167 DOI: 10.1038/s41598-017-04473-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
Amino acid transporters have roles in amino acid uptake from soil, long-distance transport, remobilization from vegetative tissues and accumulation in grain. Critically, the majority of wheat grain nitrogen is derived from amino acids remobilized from vegetative organs. However, no systematic analysis of wheat AAT genes has been reported to date. Here, 283 full length wheat AAT genes representing 100 distinct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC CSS chromosome sorted reads to fill any gaps. Gene expression profiling was performed using public RNA-seq data from root, leaf, stem, spike, grain and grain cells (transfer cell (TC), aleurone cell (AL), and starchy endosperm (SE)). AATs highly expressed in roots are good candidates for amino acid uptake from soil whilst AATs highly expressed in senescing leaves and stems may be involved in translocation to grain. AATs in TC (TaAAP2 and TaAAP19) and SE (TaAAP13) may play important roles in determining grain protein content and grain yield. The expression levels of AAT homeologs showed unequal contributions in response to abiotic stresses and development, which may aid wheat adaptation to a wide range of environments.
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21
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Wan Y, King R, Mitchell RAC, Hassani-Pak K, Hawkesford MJ. Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Sci Rep 2017. [PMID: 28710348 DOI: 10.1038/s41598-017-04473-4473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Amino acid transporters have roles in amino acid uptake from soil, long-distance transport, remobilization from vegetative tissues and accumulation in grain. Critically, the majority of wheat grain nitrogen is derived from amino acids remobilized from vegetative organs. However, no systematic analysis of wheat AAT genes has been reported to date. Here, 283 full length wheat AAT genes representing 100 distinct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC CSS chromosome sorted reads to fill any gaps. Gene expression profiling was performed using public RNA-seq data from root, leaf, stem, spike, grain and grain cells (transfer cell (TC), aleurone cell (AL), and starchy endosperm (SE)). AATs highly expressed in roots are good candidates for amino acid uptake from soil whilst AATs highly expressed in senescing leaves and stems may be involved in translocation to grain. AATs in TC (TaAAP2 and TaAAP19) and SE (TaAAP13) may play important roles in determining grain protein content and grain yield. The expression levels of AAT homeologs showed unequal contributions in response to abiotic stresses and development, which may aid wheat adaptation to a wide range of environments.
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Affiliation(s)
- Yongfang Wan
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Robert King
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Rowan A C Mitchell
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Keywan Hassani-Pak
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
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22
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Ma H, Cao X, Shi S, Li S, Gao J, Ma Y, Zhao Q, Chen Q. Genome-wide survey and expression analysis of the amino acid transporter superfamily in potato (Solanum tuberosum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:164-177. [PMID: 27289266 DOI: 10.1016/j.plaphy.2016.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 05/18/2023]
Abstract
Amino acid transporters (AATs) are integral membrane proteins responsible for the transmembrane transport of amino acids and play important roles in various physiological processes of plants. However, there has not yet been a genome-wide overview of the StAAT gene family to date and only StAAP1 has been previously studied in potato. In this paper, a total of 72 StAATs were identified using a series of bioinformatics searches and classified into 12 subfamilies based on their phylogenetic relationship with known Arabidopsis and rice AATs. Chromosomal localization revealed their distribution on all 12 chromosomes. Nearly one-third of StAAT genes (23 of 72) were derived from gene duplication, among which tandem duplication made the greatest contribution to the expansion of the StAAT family. Motif analysis showed that the same subfamily had similar conserved motifs in both numbers and varieties. Moreover, high-throughput sequencing data was used to analyze the expression patterns of StAAT genes and was verified by quantitative real-time RT-PCR. The expression of StAAT genes exhibited both abundant and tissue-specific expression patterns, which might be connected to their functional roles in long- and short-distance transport. This study provided a comprehensive survey of the StAAT gene family, and could serve as a theoretical foundation for the further functional identification and utilization of family members.
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Affiliation(s)
- Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoli Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shandang Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Silu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junpeng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China; Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China; Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qin Zhao
- College of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi 712000, China
| | - Qin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Zou H, Tzarfati R, Hübner S, Krugman T, Fahima T, Abbo S, Saranga Y, Korol AB. Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars. BMC Genomics 2015; 16:777. [PMID: 26462652 PMCID: PMC4603339 DOI: 10.1186/s12864-015-1996-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/03/2015] [Indexed: 12/02/2022] Open
Abstract
Background Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. Methods A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. Results Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. Conclusions The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongda Zou
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Raanan Tzarfati
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Sariel Hübner
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Shahal Abbo
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
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Schippers JHM, Schmidt R, Wagstaff C, Jing HC. Living to Die and Dying to Live: The Survival Strategy behind Leaf Senescence. PLANT PHYSIOLOGY 2015; 169:914-30. [PMID: 26276844 PMCID: PMC4587445 DOI: 10.1104/pp.15.00498] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Senescence represents the final developmental act of the leaf, during which the leaf cell is dismantled in a coordinated manner to remobilize nutrients and to secure reproductive success. The process of senescence provides the plant with phenotypic plasticity to help it adapt to adverse environmental conditions. Here, we provide a comprehensive overview of the factors and mechanisms that control the onset of senescence. We explain how the competence to senesce is established during leaf development, as depicted by the senescence window model. We also discuss the mechanisms by which phytohormones and environmental stresses control senescence as well as the impact of source-sink relationships on plant yield and stress tolerance. In addition, we discuss the role of senescence as a strategy for stress adaptation and how crop production and food quality could benefit from engineering or breeding crops with altered onset of senescence.
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Affiliation(s)
- Jos H M Schippers
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S., R.S.);Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, Berkshire RG6 6AP, United Kingdom (C.W.); andKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (H.-C.J.)
| | - Romy Schmidt
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S., R.S.);Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, Berkshire RG6 6AP, United Kingdom (C.W.); andKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (H.-C.J.)
| | - Carol Wagstaff
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S., R.S.);Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, Berkshire RG6 6AP, United Kingdom (C.W.); andKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (H.-C.J.)
| | - Hai-Chun Jing
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S., R.S.);Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, Berkshire RG6 6AP, United Kingdom (C.W.); andKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (H.-C.J.)
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Kohl S, Hollmann J, Erban A, Kopka J, Riewe D, Weschke W, Weber H. Metabolic and transcriptional transitions in barley glumes reveal a role as transitory resource buffers during endosperm filling. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1397-411. [PMID: 25617470 PMCID: PMC4339599 DOI: 10.1093/jxb/eru492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
During grain filling in barley (Hordeum vulgare L. cv. Barke) reserves are remobilized from vegetative organs. Glumes represent the vegetative tissues closest to grains, senesce late, and are involved in the conversion of assimilates. To analyse glume development and metabolism related to grain filling, parallel transcript and metabolite profiling in glumes and endosperm were performed, showing that glume metabolism and development adjusts to changing grain demands, reflected by specific signatures of metabolite and transcript abundances. Before high endosperm sink strength is established by storage product accumulation, glumes form early, intermediary sink organs, shifting then to remobilizing and exporting source organs. Metabolic and transcriptional transitions occur at two phases: first, at the onset of endosperm filling, as a consequence of endosperm sink activity and assimilate depletion in endosperm and vascular tissues; second, at late grain filling, by developmental ageing and senescence. Regulation of and transition between phases are probably governed by specific NAC and WRKY transcription factors, and both abscisic and jasmonic acid, and are accompanied by changed expression of specific nitrogen transporters. Expression and metabolite profiling suggest glume-specific mechanisms of assimilate conversion and translocation. In summary, grain filling and endosperm sink strength coordinate phase changes in glumes via metabolic, hormonal, and transcriptional control. This study provides a comprehensive view of barley glume development and metabolism, and identifies candidate genes and associated pathways, potentially important for breeding improved grain traits.
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Affiliation(s)
- Stefan Kohl
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Julien Hollmann
- Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - David Riewe
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Winfriede Weschke
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Hans Weber
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
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Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley. Proc Natl Acad Sci U S A 2014; 111:13403-8. [PMID: 25197090 DOI: 10.1073/pnas.1414335111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.
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Palmer NA, Donze-Reiner T, Horvath D, Heng-Moss T, Waters B, Tobias C, Sarath G. Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics. Funct Integr Genomics 2014; 15:1-16. [PMID: 25173486 DOI: 10.1007/s10142-014-0393-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
Abstract
Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had increased expression of genes for chlorophyll biosynthesis and those needed for full leaf function. Phase 3 coincided with the most active phase for leaf C and N assimilation. Phase 4 was associated with the onset of senescence, as observed by declining leaf chlorophyll content, a significant up-regulation in transcripts coding for enzymes involved with chlorophyll degradation, and in a large number of senescence-associated genes. Of considerable interest were switchgrass NAC transcription factors with significantly higher expression in senescing flag leaves. Two of these transcription factors were closely related to a wheat NAC gene that impacts mineral remobilization. The third switchgrass NAC factor was orthologous to an Arabidopsis gene with a known role in leaf senescence. Other genes coding for nitrogen and mineral utilization, including ureide, ammonium, nitrate, and molybdenum transporters, shared expression profiles that were significantly co-regulated with the expression profiles of the three NAC transcription factors. These data provide a good starting point to link shoot senescence to the onset of dormancy in field-grown switchgrass.
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Affiliation(s)
- Nathan A Palmer
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583-0937, USA
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28
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Hollmann J, Gregersen PL, Krupinska K. Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3963-73. [PMID: 24700620 PMCID: PMC4106439 DOI: 10.1093/jxb/eru094] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The transcriptomes of senescing flag leaves collected from barley field plots with standard or high nitrogen supply were compared to identify genes specifically associated with nitrogen remobilization during leaf senescence under agronomically relevant conditions. In flag leaves collected in field plots with high nitrogen supply, the decline in chlorophyll content was delayed. By comparing changes in gene expression for the two nitrogen levels, it was possible to discriminate genes related to nitrogen remobilization during senescence and genes involved in other processes associated with the late development of leaves under field conditions. Predominant genes that were more strongly upregulated during senescence of flag leaves from plants with standard nitrogen supply included genes encoding the transcription factor HvNAC026, serine type protease SCPL51, and the autophagy factors APG7 and ATG18F. Elevated expression of these genes in senescing leaves from plants with standard nitrogen supply indicates important roles of the corresponding proteins in nitrogen remobilization. In comparison, the genes upregulated in both flag leaf samples might have roles in general senescence processes associated with late leaf development. Among these genes were the transcription factor genes HvNAC001, HvNAC005, HvNAC013, HvWRKY12 and MYB, genes encoding the papain-like cysteine peptidases HvPAP14 and HvPAP20, as well as a subtilase gene.
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Affiliation(s)
- Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, AU-Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
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29
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Distelfeld A, Avni R, Fischer AM. Senescence, nutrient remobilization, and yield in wheat and barley. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3783-98. [PMID: 24470467 DOI: 10.1093/jxb/ert477] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cereals including wheat and barley are of primary importance to ensure food security for the 21st century. A combination of lab- and field-based approaches has led to a considerably improved understanding of the importance of organ and particularly of whole-plant (monocarpic) senescence for wheat and barley yield and quality. A delicate balance between senescence timing, grain nutrient content, nutrient-use efficiency, and yield needs to be considered to (further) improve cereal varieties for a given environment and end use. The recent characterization of the Gpc-1 (NAM-1) genes in wheat and barley demonstrates the interdependence of these traits. Lines or varieties with functional Gpc-1 genes demonstrate earlier senescence and enhanced grain protein and micronutrient content but, depending on the environment, somewhat reduced yields. A major effort is needed to dissect regulatory networks centred on additional wheat and barley transcription factors and signalling pathways influencing the senescence process. Similarly, while important molecular details of nutrient (particularly nitrogen) remobilization from senescing organs to developing grains have been identified, important knowledge gaps remain. The genes coding for the major proteases involved in senescence-associated plastidial protein degradation are largely unknown. Membrane transport proteins involved in the different transport steps occurring between senescing organ (such as leaf mesophyll) cells and protein bodies in the endosperm of developing grains remain to be identified or further characterized. Existing data suggest that an improved understanding of all these steps will reveal additional, important targets for continued cereal improvement.
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Affiliation(s)
- Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978, Israel
| | - Raz Avni
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978, Israel
| | - Andreas M Fischer
- Department of Plant Sciences and Plant Pathology, 119 Plant BioScience Building, Montana State University, Bozeman, MT 59717-3150, USA
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30
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Sekhon RS, Hirsch CN, Childs KL, Breitzman MW, Kell P, Duvick S, Spalding EP, Buell CR, de Leon N, Kaeppler SM. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination. PLANT PHYSIOLOGY 2014; 165:658-669. [PMID: 24710068 PMCID: PMC4044855 DOI: 10.1104/pp.114.235424] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals.
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Affiliation(s)
- Rajandeep S Sekhon
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Candice N Hirsch
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Kevin L Childs
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Matthew W Breitzman
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Paul Kell
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Susan Duvick
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Edgar P Spalding
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - C Robin Buell
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Natalia de Leon
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
| | - Shawn M Kaeppler
- Department of Energy Great Lakes Bioenergy Research Center (R.S.S., M.W.B., N.d.L., S.M.K.), Department of Agronomy (R.S.S., M.W.B., P.K., N.d.L., S.M.K.), and Department of Botany (E.P.S.), University of Wisconsin, Madison, Wisconsin 53706;Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (C.N.H.);Department of Energy Great Lakes Bioenergy Research Center (K.L.C., C.R.B.) and Department of Plant Biology (K.L.C., C.R.B.), Michigan State University, East Lansing, Michigan 48824; andUnited States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.D.)
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31
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Thiel J. Development of endosperm transfer cells in barley. FRONTIERS IN PLANT SCIENCE 2014; 5:108. [PMID: 24723929 PMCID: PMC3972472 DOI: 10.3389/fpls.2014.00108] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/06/2014] [Indexed: 05/18/2023]
Abstract
Endosperm transfer cells (ETCs) are positioned at the intersection of maternal and filial tissues in seeds of cereals and represent a bottleneck for apoplasmic transport of assimilates into the endosperm. Endosperm cellularization starts at the maternal-filial boundary and generates the highly specialized ETCs. During differentiation barley ETCs develop characteristic flange-like wall ingrowths to facilitate effective nutrient transfer. A comprehensive morphological analysis depicted distinct developmental time points in establishment of transfer cell (TC) morphology and revealed intracellular changes possibly associated with cell wall metabolism. Embedded inside the grain, ETCs are barely accessible by manual preparation. To get tissue-specific information about ETC specification and differentiation, laser microdissection (LM)-based methods were used for transcript and metabolite profiling. Transcriptome analysis of ETCs at different developmental stages by microarrays indicated activated gene expression programs related to control of cell proliferation and cell shape, cell wall and carbohydrate metabolism reflecting the morphological changes during early ETC development. Transporter genes reveal distinct expression patterns suggesting a switch from active to passive modes of nutrient uptake with the onset of grain filling. Tissue-specific RNA-seq of the differentiating ETC region from the syncytial stage until functionality in nutrient transfer identified a high number of novel transcripts putatively involved in ETC differentiation. An essential role for two-component signaling (TCS) pathways in ETC development of barley emerged from this analysis. Correlative data provide evidence for abscisic acid and ethylene influences on ETC differentiation and hint at a crosstalk between hormone signal transduction and TCS phosphorelays. Collectively, the data expose a comprehensive view on ETC development, associated pathways and identified candidate genes for ETC specification.
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Affiliation(s)
- Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
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32
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Krupinska K, Oetke S, Desel C, Mulisch M, Schäfer A, Hollmann J, Kumlehn J, Hensel G. WHIRLY1 is a major organizer of chloroplast nucleoids. FRONTIERS IN PLANT SCIENCE 2014; 5:432. [PMID: 25237316 PMCID: PMC4154442 DOI: 10.3389/fpls.2014.00432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/13/2014] [Indexed: 05/20/2023]
Abstract
WHIRLY1 is an abundant protein of chloroplast nucleoids, which has also been named pTAC-1 with regard to its detection in the proteome of transcriptionally active chromosomes (TAC). In barley primary foliage leaves, expression of the WHIRLY1 gene is highest at the base whereas protein accumulation is highest in the middle of the leaf where young developing chloroplasts are found. In order to elucidate the function of WHIRLY1 in chloroplast nucleoids, transgenic barley plants with an RNAi-mediated knock-down of the HvWHIRLY1 gene (RNAi-W1) were generated. The homozygous RNAi-W1-7 plants, barely containing traces of the WHIRLY1 protein, were chosen for detailed analyses of nucleoids. Nucleic acid specific-staining with YO-PRO®-1 revealed that in comparison to wild type chloroplasts, which have multiple small nucleoids attached to thylakoids, chloroplasts of the transgenic plants contain large irregularly formed patches of DNA besides nucleoids that are similar in size and shape to those of wild type chloroplasts. In large electron lucent areas, filamentous structures were detected by conventional transmission electron microscopy. Analyses of ptDNA levels by both DNA dot-blot hybridization and quantitative PCR showed that leaves of the transgenic plants have a two- to three-fold higher level of ptDNA than the wild type. The higher ptDNA level in RNAi-W1 plants coincided with an enhanced expression of the gene encoding a putative organelle targeted DNA polymerase in the mid part of primary foliage leaves. Furthermore, overexpression of the barley WHIRLY1 gene in E. coli cells revealed a higher compaction of bacterial nucleoids. These results suggest that WHIRLY1 belongs to the group of plastid nucleoid associated proteins (ptNAP) having a function in compacting a subpopulation of chloroplast nucleoids thereby affecting DNA replication.
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Affiliation(s)
- Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
- *Correspondence: Karin Krupinska, Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany e-mail:
| | - Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Christine Desel
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Maria Mulisch
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
- Central Microscopy of the Center of Biology, Christian-Albrechts-University of KielKiel, Germany
| | - Anke Schäfer
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland/OT Gatersleben, Germany
| | - Götz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland/OT Gatersleben, Germany
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33
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Schultz JC, Appel HM, Ferrieri AP, Arnold TM. Flexible resource allocation during plant defense responses. FRONTIERS IN PLANT SCIENCE 2013; 4:324. [PMID: 23986767 PMCID: PMC3749688 DOI: 10.3389/fpls.2013.00324] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/31/2013] [Indexed: 05/02/2023]
Abstract
Plants are organisms composed of modules connected by xylem and phloem transport streams. Attack by both insects and pathogens elicits sometimes rapid defense responses in the attacked module. We have also known for some time that proteins are often reallocated away from pathogen-infected tissues, while the same infection sites may draw carbohydrates to them. This has been interpreted as a tug of war in which the plant withdraws critical resources to block microbial growth while the microbes attempt to acquire more resources. Sink-source regulated transport among modules of critical resources, particularly carbon and nitrogen, is also altered in response to attack. Insects and jasmonate can increase local sink strength, drawing carbohydrates that support defense production. Shortly after attack, carbohydrates may also be drawn to the root. The rate and direction of movement of photosynthate or signals in phloem in response to attack is subject to constraints that include branching, degree of connection among tissues, distance between sources and sinks, proximity, strength, and number of competing sinks, and phloem loading/unloading regulators. Movement of materials (e.g., amino acids, signals) to or from attack sites in xylem is less well understood but is partly driven by transpiration. The root is an influential sink and may regulate sink-source interactions and transport above and below ground as well as between the plant and the rhizosphere and nearby, connected plants. Research on resource translocation in response to pathogens or herbivores has focused on biochemical mechanisms; whole-plant research is needed to determine which, if any, of these plant behaviors actually influence plant fitness.
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Affiliation(s)
- Jack C. Schultz
- Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Heidi M. Appel
- Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Abigail P. Ferrieri
- Department of Molecular Ecology, Max Planck Institute for Chemical EcologyJena, Germany
| | - Thomas M. Arnold
- Biochemistry and Molecular Biology Program, Department of Biology, Dickinson College, CarlislePA, USA
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