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Xia X, Mi X, Jin L, Guo R, Zhu J, Xie H, Liu L, An Y, Zhang C, Wei C, Liu S. CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis). BMC PLANT BIOLOGY 2021; 21:243. [PMID: 34049485 PMCID: PMC8164267 DOI: 10.1186/s12870-021-03044-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Branch angle is a pivotal component of tea plant architecture. Tea plant architecture not only affects tea quality and yield but also influences the efficiency of automatic tea plant pruning. However, the molecular mechanism controlling the branch angle, which is an important aspect of plant architecture, is poorly understood in tea plants. RESULTS In the present study, three CsLAZY genes were identified from tea plant genome data through sequence homology analysis. Phylogenetic tree displayed that the CsLAZY genes had high sequence similarity with LAZY genes from other plant species, especially those in woody plants. The expression patterns of the three CsLAZYs were surveyed in eight tissues. We further verified the expression levels of the key CsLAZY1 transcript in different tissues among eight tea cultivars and found that CsLAZY1 was highly expressed in stem. Subcellular localization analysis showed that the CsLAZY1 protein was localized in the plasma membrane. CsLAZY1 was transferred into Arabidopsis thaliana to investigate its potential role in regulating shoot development. Remarkably, the CsLAZY1 overexpressed plants responded more effectively than the wild-type plants to a gravity inversion treatment under light and dark conditions. The results indicate that CsLAZY1 plays an important role in regulating shoot gravitropism in tea plants. CONCLUSIONS The results provide important evidence for understanding the functions of CsLAZY1 in regulating shoot gravitropism and influencing the stem branch angle in tea plants. This report identifies CsLAZY1 as a promising gene resource for the improvement of tea plant architecture.
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Affiliation(s)
- Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Ling Jin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Hui Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Lu Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Cao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China.
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China.
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Sharma M, Singh D, Saksena HB, Sharma M, Tiwari A, Awasthi P, Botta HK, Shukla BN, Laxmi A. Understanding the Intricate Web of Phytohormone Signalling in Modulating Root System Architecture. Int J Mol Sci 2021; 22:ijms22115508. [PMID: 34073675 PMCID: PMC8197090 DOI: 10.3390/ijms22115508] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Root system architecture (RSA) is an important developmental and agronomic trait that is regulated by various physical factors such as nutrients, water, microbes, gravity, and soil compaction as well as hormone-mediated pathways. Phytohormones act as internal mediators between soil and RSA to influence various events of root development, starting from organogenesis to the formation of higher order lateral roots (LRs) through diverse mechanisms. Apart from interaction with the external cues, root development also relies on the complex web of interaction among phytohormones to exhibit synergistic or antagonistic effects to improve crop performance. However, there are considerable gaps in understanding the interaction of these hormonal networks during various aspects of root development. In this review, we elucidate the role of different hormones to modulate a common phenotypic output, such as RSA in Arabidopsis and crop plants, and discuss future perspectives to channel vast information on root development to modulate RSA components.
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53
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A single-cell analysis of the Arabidopsis vegetative shoot apex. Dev Cell 2021; 56:1056-1074.e8. [PMID: 33725481 DOI: 10.1016/j.devcel.2021.02.021] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/06/2020] [Accepted: 02/19/2021] [Indexed: 01/13/2023]
Abstract
The shoot apical meristem allows for reiterative formation of new aerial structures throughout the life cycle of a plant. We use single-cell RNA sequencing to define the cellular taxonomy of the Arabidopsis vegetative shoot apex at the transcriptome level. We find that the shoot apex is composed of highly heterogeneous cells, which can be partitioned into 7 broad populations with 23 transcriptionally distinct cell clusters. We delineate cell-cycle continuums and developmental trajectories of epidermal cells, vascular tissue, and leaf mesophyll cells and infer transcription factors and gene expression signatures associated with cell fate decisions. Integrative analysis of shoot and root apical cell populations further reveals common and distinct features of epidermal and vascular tissues. Our results, thus, offer a valuable resource for investigating the basic principles underlying cell division and differentiation in plants at single-cell resolution.
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Sun C, Zhang C, Wang X, Zhao X, Chen F, Zhang W, Hu M, Fu S, Yi B, Zhang J. Genome-Wide Identification and Characterization of the IGT Gene Family in Allotetraploid Rapeseed ( Brassica napus L.). DNA Cell Biol 2021; 40:441-456. [PMID: 33600242 DOI: 10.1089/dna.2020.6227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
IGT family genes function critically to regulate lateral organ orientation in plants. However, little information is available about this family of genes in Brassica napus. In this study, 27 BnIGT genes were identified on 16 chromosomes and divided into seven clades, namely LAZY1∼LAZY6 and TAC1 (Tiller Angle Control 1), based on their phylogenetic relationships. Duplication analysis revealed that 91.1% of the gene pairs were derived from whole-genome duplication. Most BnIGT genes had a similar structural pattern with one or two very short exons followed by a long and a shorter exon. Common and specific motifs were identified among the seven clades, and motif 1, containing the family-specific GφL(A/T)IGT sequence, was observed in all clades except LAZY5. Three types of cis-elements pertinent to transcription factor binding, light responses, and hormone signaling were detected in the BnIGT promoters. Intriguingly, more than half of the BnIGT genes exhibited no or very low expression in various tissues, and the LAZY1 and TAC1 clade members showed distinct tissue expression preferences. Coexpression analysis revealed that the LAZY1 members had strong associations with cell wall biosynthesis genes. This analysis provides a deeper understanding of the BnIGT gene family and will facilitate further deduction of their role in regulating plant architecture in B. napus.
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Affiliation(s)
- Chengming Sun
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,National Key Laboratory of Crop Genetic Improvement/College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chun Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,National Key Laboratory of Crop Genetics and Germplasm Innovation, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Xiadong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaozhen Zhao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,National Key Laboratory of Crop Genetics and Germplasm Innovation, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Feng Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Sanxiong Fu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,National Key Laboratory of Crop Genetics and Germplasm Innovation, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
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Uga Y. Challenges to design-oriented breeding of root system architecture adapted to climate change. BREEDING SCIENCE 2021; 71:3-12. [PMID: 33762871 PMCID: PMC7973499 DOI: 10.1270/jsbbs.20118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 05/12/2023]
Abstract
Roots are essential organs for capturing water and nutrients from the soil. In particular, root system architecture (RSA) determines the extent of the region of the soil where water and nutrients can be gathered. As global climate change accelerates, it will be important to improve belowground plant parts, as well as aboveground ones, because roots are front-line organs in the response to abiotic stresses such as drought, flooding, and salinity stress. However, using conventional breeding based on phenotypic selection, it is difficult to select breeding lines possessing promising RSAs to adapted to abiotic stress because roots remain hidden underground. Therefore, new breeding strategies that do not require phenotypic selection are necessary. Recent advances in molecular biology and biotechnology can be applied to the design-oriented breeding of RSA without phenotypic selection. Here I summarize recent progress in RSA ideotypes as "design" and RSA-related gene resources as "materials" that will be needed in leveraging these technologies for the RSA breeding. I also highlight the future challenges to design-oriented breeding of RSA and explore solutions to these challenges.
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Affiliation(s)
- Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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56
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Waite JM, Dardick C. The roles of the IGT gene family in plant architecture: past, present, and future. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101983. [PMID: 33422965 DOI: 10.1016/j.pbi.2020.101983] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 05/03/2023]
Abstract
Genetic improvement of architectural traits offers tremendous opportunities to dramatically improve crop densities, productivity, and ultimately sustainability. Among these, the orientation, or gravitropic set point angle (GSA), of plant organs is critical to optimize crop profiles, light capture, and nutrient acquisition. Mutant GSA phenotypes have been studied in plants since the 1930's but only recently have the underlying genes been identified. Many of these genes have turned out to fall within the IGT (LAZY1/DRO1/TAC1) family, which initially was not previously recognized due to the lack of sequence conservation of homologous genes across species. Here we discuss recent progress on IGT family genes in various plant species over the past century, review possible functional mechanisms, and provide further analysis of their evolution in land plants and their past and future roles in crop domestication.
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Affiliation(s)
- Jessica Marie Waite
- USDA Tree Fruit Research Laboratory, 1104 N Western Avenue, Wenatchee, WA, USA
| | - Christopher Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA.
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57
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Zhong Y, Lu X, Deng Z, Lu Z, Fu M. A 1232 bp upstream sequence of glutamine synthetase 1b from Eichhornia crassipes is a root-preferential promoter sequence. BMC PLANT BIOLOGY 2021; 21:66. [PMID: 33514320 PMCID: PMC7845104 DOI: 10.1186/s12870-021-02832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Glutamine synthetase (GS) acts as a key enzyme in plant nitrogen (N) metabolism. It is important to understand the regulation of GS expression in plant. Promoters can initiate the transcription of its downstream gene. Eichhornia crassipes is a most prominent aquatic invasive plant, which has negative effects on environment and economic development. It also can be used in the bioremediation of pollutants present in water and the production of feeding and energy fuel. So identification and characterization of GS promoter in E. crassipes can help to elucidate its regulation mechanism of GS expression and further to control its N metabolism. RESULTS A 1232 bp genomic fragment upstream of EcGS1b sequence from E. crassipes (EcGS1b-P) has been cloned, analyzed and functionally characterized. TSSP-TCM software and PlantCARE analysis showed a TATA-box core element, a CAAT-box, root specific expression element, light regulation elements including chs-CMA1a, Box I, and Sp1 and other cis-acting elements in the sequence. Three 5'-deletion fragments of EcGS1b upstream sequence with 400 bp, 600 bp and 900 bp length and the 1232 bp fragment were used to drive the expression of β-glucuronidase (GUS) in tobacco. The quantitative test revealed that GUS activity decreased with the decreasing of the promoter length, which indicated that there were no negative regulated elements in the EcGS1-P. The GUS expressions of EcGS1b-P in roots were significantly higher than those in leaves and stems, indicating EcGS1b-P to be a root-preferential promoter. Real-time Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) analysis of EcGS1b gene also showed higher expression in the roots of E.crassipes than in stems and leaves. CONCLUSIONS EcGS1b-P is a root-preferential promoter sequence. It can specifically drive the transcription of its downstream gene in root. This study will help to elucidate the regulatory mechanisms of EcGS1b tissue-specific expression and further study its other regulatory mechanisms in order to utilize E.crassipes in remediation of eutrophic water and control its overgrowth from the point of nutrient metabolism.
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Affiliation(s)
- Yanshan Zhong
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Xiaodan Lu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Zhiwei Deng
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Ziqing Lu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Minghui Fu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006.
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Zheng C, Shen F, Wang Y, Wu T, Xu X, Zhang X, Han Z. Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics 2020; 21:852. [PMID: 33261554 PMCID: PMC7709433 DOI: 10.1186/s12864-020-07257-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Results Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°. Conclusions Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.
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Affiliation(s)
- Caixia Zheng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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59
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Su SH, Keith MA, Masson PH. Gravity Signaling in Flowering Plant Roots. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1290. [PMID: 33003550 PMCID: PMC7601833 DOI: 10.3390/plants9101290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/28/2022]
Abstract
Roots typically grow downward into the soil where they anchor the plant and take up water and nutrients necessary for plant growth and development. While the primary roots usually grow vertically downward, laterals often follow a gravity set point angle that allows them to explore the surrounding environment. These responses can be modified by developmental and environmental cues. This review discusses the molecular mechanisms that govern root gravitropism in flowering plant roots. In this system, the primary site of gravity sensing within the root cap is physically separated from the site of curvature response at the elongation zone. Gravity sensing involves the sedimentation of starch-filled plastids (statoliths) within the columella cells of the root cap (the statocytes), which triggers a relocalization of plasma membrane-associated PIN auxin efflux facilitators to the lower side of the cell. This process is associated with the recruitment of RLD regulators of vesicular trafficking to the lower membrane by LAZY proteins. PIN relocalization leads to the formation of a lateral gradient of auxin across the root cap. Upon transmission to the elongation zone, this auxin gradient triggers a downward curvature. We review the molecular mechanisms that control this process in primary roots and discuss recent insights into the regulation of oblique growth in lateral roots and its impact on root-system architecture, soil exploration and plant adaptation to stressful environments.
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Affiliation(s)
| | | | - Patrick H. Masson
- Laboratory of Genetics, University of Wisconsin-Madison, 425G Henry Mall, Madison, WI 53706, USA; (S.-H.S.); (M.A.K.)
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Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci U S A 2020; 117:21242-21250. [PMID: 32817523 PMCID: PMC7474696 DOI: 10.1073/pnas.2005911117] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 (DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.
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Light modulates the gravitropic responses through organ-specific PIFs and HY5 regulation of LAZY4 expression in Arabidopsis. Proc Natl Acad Sci U S A 2020; 117:18840-18848. [PMID: 32690706 DOI: 10.1073/pnas.2005871117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light and gravity are two key environmental factors that control plant growth and architecture. However, the molecular basis of the coordination of light and gravity signaling in plants remains obscure. Here, we report that two classes of transcription factors, PHYTOCHROME INTERACTING FACTORS (PIFs) and ELONGATED HYPOCOTYL5 (HY5), can directly bind and activate the expression of LAZY4, a positive regulator of gravitropism in both shoots and roots in Arabidopsis In hypocotyls, light promotes degradation of PIFs to reduce LAZY4 expression, which inhibits the negative gravitropism of hypocotyls. LAZY4 overexpression can partially rescue the negative gravitropic phenotype of pifq in the dark without affecting amyloplast development. Our identification of the PIFs-LAZY4 regulatory module suggests the presence of another role for PIF proteins in gravitropism, in addition to a previous report demonstrating that PIFs positively regulate amyloplast development to promote negative gravitropism in hypocotyls. In roots, light promotes accumulation of HY5 proteins to activate expression of LAZY4, which promotes positive gravitropism in roots. Together, our data indicate that light exerts opposite regulation of LAZY4 expression in shoots and roots by mediating the protein levels of PIFs and HY5, respectively, to inhibit the negative gravitropism of shoots and promote positive gravitropism of roots in Arabidopsis.
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Waidmann S, Kleine‐Vehn J. Asymmetric cytokinin signaling opposes gravitropism in roots. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:882-886. [PMID: 32233010 PMCID: PMC7383806 DOI: 10.1111/jipb.12929] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/24/2020] [Indexed: 05/03/2023]
Abstract
Plants depend on gravity to provide the constant landmark for downward root growth and upward shoot growth. The phytohormone auxin and its cell-to-cell transport machinery are central determinants ensuring gravitropic growth. Statolith sedimentation toward gravity is sensed in specialized cells. This positional cue is translated into the polar distribution of PIN auxin efflux carriers at the plasma membrane, leading to asymmetric auxin distribution and consequently, differential growth and organ bending. While we have started to understand the general principles of how primary organs execute gravitropism, we currently lack basic understanding of how lateral plant organs can defy gravitropic responses. Here we briefly review the establishment of the oblique gravitropic set point angle in lateral roots and particularly discuss the emerging role of asymmetric cytokinin signaling as a central anti-gravitropic signal. Differential cytokinin signaling is co-opted in gravitropic lateral and hydrotropic primary roots to counterbalance gravitropic root growth.
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Affiliation(s)
- Sascha Waidmann
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life Sciences (BOKU)Muthgasse 18Vienna1190Austria
| | - Jürgen Kleine‐Vehn
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life Sciences (BOKU)Muthgasse 18Vienna1190Austria
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63
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Waite JM, Collum TD, Dardick C. AtDRO1 is nuclear localized in root tips under native conditions and impacts auxin localization. PLANT MOLECULAR BIOLOGY 2020; 103:197-210. [PMID: 32130643 PMCID: PMC7170825 DOI: 10.1007/s11103-020-00984-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/20/2020] [Indexed: 05/19/2023]
Abstract
DEEPER ROOTING 1 (DRO1) contributes to the downward gravitropic growth trajectory of roots upstream of lateral auxin transport in monocots and dicots. Loss of DRO1 function leads to horizontally oriented lateral roots and altered gravitropic set point angle, while loss of all three DRO family members results in upward, vertical root growth. Here, we attempt to dissect the roles of AtDRO1 by analyzing expression, protein localization, auxin gradient formation, and auxin responsiveness in the atdro1 mutant. Current evidence suggests AtDRO1 is predominantly a membrane-localized protein. Here we show that VENUS-tagged AtDRO1 driven by the native AtDRO1 promoter complemented an atdro1 Arabidopsis mutant and the protein was localized in root tips and detectable in nuclei. atdro1 primary and lateral roots showed impairment in establishing an auxin gradient upon gravistimulation as visualized with DII-VENUS, a sensor for auxin signaling and proxy for relative auxin distribution. Additionally, PIN3 domain localization was not significantly altered upon gravistimulation in atdro1 primary and lateral roots. RNA-sequencing revealed differential expression of known root development-related genes in atdro1 mutants. atdro1 lateral roots were able to respond to exogenous auxin and AtDRO1 gene expression levels in root tips were unaffected by the addition of auxin. Collectively, the data suggest that nuclear localization may be important for AtDRO1 function and suggests a more nuanced role for DRO1 in regulating auxin-mediated changes in lateral branch angle. KEY MESSAGE: DEEPER ROOTING 1 (DRO1) when expressed from its native promoter is predominately localized in Arabidopsis root tips, detectable in nuclei, and impacts auxin gradient formation.
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Affiliation(s)
- Jessica M Waite
- Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA, 98801, USA
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Tamara D Collum
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Chris Dardick
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA.
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Opposing influences of TAC1 and LAZY1 on Lateral Shoot Orientation in Arabidopsis. Sci Rep 2020; 10:6051. [PMID: 32269265 PMCID: PMC7142156 DOI: 10.1038/s41598-020-62962-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
TAC1 and LAZY1 are members of a gene family that regulates lateral shoot orientation in plants. TAC1 promotes outward orientations in response to light, while LAZY1 promotes upward shoot orientations in response to gravity via altered auxin transport. We performed genetic, molecular, and biochemical assays to investigate possible interactions between these genes. In Arabidopsis they were expressed in similar tissues and double mutants revealed the wide-angled lazy1 branch phenotype, indicating it is epistatic to the tac1 shoot phenotype. Surprisingly, the lack of TAC1 did not influence gravitropic shoot curvature responses. Combined, these results suggest TAC1 might negatively regulate LAZY1 to promote outward shoot orientations. However, additional results revealed that TAC1- and LAZY1 influence on shoot orientation is more complex than a simple direct negative regulatory pathway. Transcriptomes of Arabidopsis tac1 and lazy1 mutants compared to wild type under normal and gravistimulated conditions revealed few overlapping differentially expressed genes. Overexpression of each gene did not result in major branch angle differences. Shoot tip hormone levels were similar between tac1, lazy1, and Col, apart from exceptionally elevated levels of salicylic acid in lazy1. The data presented here provide a foundation for future study of TAC1 and LAZY1 regulation of shoot architecture.
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65
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Furutani M, Hirano Y, Nishimura T, Nakamura M, Taniguchi M, Suzuki K, Oshida R, Kondo C, Sun S, Kato K, Fukao Y, Hakoshima T, Morita MT. Polar recruitment of RLD by LAZY1-like protein during gravity signaling in root branch angle control. Nat Commun 2020; 11:76. [PMID: 31900388 PMCID: PMC6941992 DOI: 10.1038/s41467-019-13729-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 11/13/2019] [Indexed: 01/07/2023] Open
Abstract
In many plant species, roots maintain specific growth angles relative to the direction of gravity, known as gravitropic set point angles (GSAs). These contribute to the efficient acquisition of water and nutrients. AtLAZY1/LAZY1-LIKE (LZY) genes are involved in GSA control by regulating auxin flow toward the direction of gravity in Arabidopsis. Here, we demonstrate that RCC1-like domain (RLD) proteins, identified as LZY interactors, are essential regulators of polar auxin transport. We show that interaction of the CCL domain of LZY with the BRX domain of RLD is important for the recruitment of RLD from the cytoplasm to the plasma membrane by LZY. A structural analysis reveals the mode of the interaction as an intermolecular β-sheet in addition to the structure of the BRX domain. Our results offer a molecular framework in which gravity signal first emerges as polarized LZY3 localization in gravity-sensing cells, followed by polar RLD1 localization and PIN3 relocalization to modulate auxin flow.
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Affiliation(s)
- Masahiko Furutani
- 0000 0004 1760 2876grid.256111.0College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China ,0000 0004 1760 2876grid.256111.0FAFU-UCR Joint Center, Fujian Provincial Key Laboratory of Haixia Applied Plant System Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China ,0000 0001 0943 978Xgrid.27476.30Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Yoshinori Hirano
- 0000 0000 9227 2257grid.260493.aGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0101 Japan ,0000 0001 2151 536Xgrid.26999.3dGraduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Takeshi Nishimura
- 0000 0004 0618 8593grid.419396.0Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki 444-8556 Japan
| | - Moritaka Nakamura
- 0000 0004 0618 8593grid.419396.0Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki 444-8556 Japan
| | - Masatoshi Taniguchi
- 0000 0001 0943 978Xgrid.27476.30Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Kanako Suzuki
- 0000 0001 0943 978Xgrid.27476.30Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Ryuichiro Oshida
- 0000 0001 0943 978Xgrid.27476.30Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Chiemi Kondo
- 0000 0001 0943 978Xgrid.27476.30Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Song Sun
- 0000 0004 1760 2876grid.256111.0College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China ,0000 0004 1760 2876grid.256111.0FAFU-UCR Joint Center, Fujian Provincial Key Laboratory of Haixia Applied Plant System Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Kagayaki Kato
- 0000 0004 0618 8593grid.419396.0Laboratory of Biological Diversity, National Institute for Basic Biology, Myodaiji, Okazaki 444-8556 Japan ,0000 0000 9137 6732grid.250358.9Bioimage Informatics Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Myodaiji, Okazaki 444-8585 Japan
| | - Yoichiro Fukao
- 0000 0000 8863 9909grid.262576.2Department of Bioinformatics, Ritsumeikan University, Kusatsu, 525-8577 Japan
| | - Toshio Hakoshima
- 0000 0000 9227 2257grid.260493.aGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0101 Japan
| | - Miyo Terao Morita
- 0000 0004 0618 8593grid.419396.0Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki 444-8556 Japan
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Chen Y, Xu S, Tian L, Liu L, Huang M, Xu X, Song G, Wu P, Sato S, Jiang H, Wu G. LAZY3 plays a pivotal role in positive root gravitropism in Lotus japonicus. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:168-177. [PMID: 31559427 PMCID: PMC6913700 DOI: 10.1093/jxb/erz429] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 09/12/2019] [Indexed: 05/14/2023]
Abstract
LAZY1 family genes play important roles in both shoot and root gravitropism in plants. Here we report a Lotus japonicus mutant that displays negative gravitropic response in primary and lateral roots. Map-based cloning identified the mutant gene LAZY3 as a functional ortholog of the LAZY1 gene. Mutation of the LAZY3 gene reduced rootward polar auxin transport (PAT) in the primary root, which was also insensitive to the PAT inhibitor N-1-naphthylphthalamic acid. Moreover, immunolocalization of enhanced green fluorescent protein-tagged LAZY3 in L. japonicus exhibited polar localization of LAZY3 on the plasma membrane in root stele cells. We therefore suggest that the polar localization of LAZY3 in stele cells might be required for PAT in L. japonicus root. LAZY3 transcripts displayed asymmetric distribution at the root tip within hours of gravistimulation, while overexpression of LAZY3 under a constitutive promoter in lazy3 plants rescued the gravitropic response in roots. These data indicate that root gravitropism depends on the presence of LAZY3 but not on its asymmetric expression in root tips. Expression of other LAZY genes in a lazy3 background did not rescue the growth direction of roots, suggesting that the LAZY3 gene plays a distinct role in root gravitropism in L. japonicus.
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Affiliation(s)
- Yaping Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shaoming Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Leru Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingchao Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinlan Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guanying Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Huawu Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Corresponding author. or
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Corresponding author. or
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67
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Li Y, Liu X, Chen R, Tian J, Fan Y, Zhou X. Genome-scale mining of root-preferential genes from maize and characterization of their promoter activity. BMC PLANT BIOLOGY 2019; 19:584. [PMID: 31878892 PMCID: PMC6933907 DOI: 10.1186/s12870-019-2198-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/12/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Modification of root architecture and improvement of root resistance to stresses can increase crop productivity. Functional analyses of root-specific genes are necessary for root system improvement, and root-specific promoters enable research into the regulation of root development and genetic manipulation of root traits. Maize is an important crop species; however, little systematic mining of root-specific genes and promoters has been performed to date. RESULTS Genomic-scale mining based on microarray data sets followed by transcript detection resulted in the identification of 222 root-specific genes. Gene Ontology enrichment analyses revealed that these 222 root-specific genes were mainly involved in responses to chemical, biotic, and abiotic stresses. Of the 222 genes, 33 were verified by quantitative reverse transcription polymerase chain reaction, and 31 showed root-preferential activity. About 2 kb upstream 5 of the 31 identified root-preferential genes were cloned from the maize genome as putative promoters and named p8463, p5023, p1534, p8531 and p6629. GUS staining of transgenic maize-derived promoter-GUS constructs revealed that the five promoters drove GUS expression in a root-preferential manner. CONCLUSIONS We mined root-preferential genes and their promoters in maize and verified p8463, p5023, p1534, p8531 and p6629 as root-preferential promoters. Our research enables the identification of other tissue-specific genes and promoters in maize and other species. In addition, the five promoters may enable enhancement of target gene(s) of maize in a root-preferential manner to generate novel maize cultivars with resistance to water, fertilizer constraints, or biotic stresses.
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Affiliation(s)
- Ye Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Rumei Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China.
| | - Xiaojin Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China.
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68
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Nakamura M, Nishimura T, Morita MT. Bridging the gap between amyloplasts and directional auxin transport in plant gravitropism. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:54-60. [PMID: 31446250 DOI: 10.1016/j.pbi.2019.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/14/2019] [Accepted: 07/09/2019] [Indexed: 05/25/2023]
Abstract
Gravitropism is the directional control of plant organ growth in response to gravity. Specialized gravity-sensing cells contain amyloplasts that can change their position according to the direction of gravity. Gravity signaling, which is elicited by the relocation of amyloplasts, is a key process that redirects auxin transport from gravity-sensing cells to the lower flank of gravity-responsive organs. Despite the long history of research on plant gravitropism, a molecular detail of gravity signaling remained unexplained. Recent studies have characterized the Arabidopsis LAZY1 family genes to be key factors of gravity signaling. Furthermore, studies regarding Arabidopsis AGCVIII kinases have demonstrated the requirement of auxin transporter PIN-FORMED3 (PIN3) phosphorylation in plant gravitropism.
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Affiliation(s)
- Moritaka Nakamura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Takeshi Nishimura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan; Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Miyo Terao Morita
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan; Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan.
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69
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Abstract
Roots provide the primary mechanism that plants use to absorb water and nutrients from their environment. These functions are dependent on developmental mechanisms that direct root growth and branching into regions of soil where these resources are relatively abundant. Water is the most limiting factor for plant growth, and its availability is determined by the weather, soil structure, and salinity. In this review, we define the developmental pathways that regulate the direction of growth and branching pattern of the root system, which together determine the expanse of soil from which a plant can access water. The ability of plants to regulate development in response to the spatial distribution of water is a focus of many recent studies and provides a model for understanding how biological systems utilize positional cues to affect signaling and morphogenesis. A better understanding of these processes will inform approaches to improve crop water use efficiency to more sustainably feed a growing population.
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Affiliation(s)
- José R. Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
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70
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Dawson IK, Powell W, Hendre P, Bančič J, Hickey JM, Kindt R, Hoad S, Hale I, Jamnadass R. The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition. THE NEW PHYTOLOGIST 2019; 224:37-54. [PMID: 31063598 DOI: 10.1111/nph.15895] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/28/2019] [Indexed: 05/27/2023]
Abstract
Especially in low-income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low-input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'.
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Affiliation(s)
- Ian K Dawson
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- World Agroforestry (ICRAF), Headquarters, PO Box 30677, Nairobi, Kenya
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Prasad Hendre
- World Agroforestry (ICRAF), Headquarters, PO Box 30677, Nairobi, Kenya
| | - Jon Bančič
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- The Roslin Institute, Easter Bush Campus, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - John M Hickey
- The Roslin Institute, Easter Bush Campus, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Roeland Kindt
- World Agroforestry (ICRAF), Headquarters, PO Box 30677, Nairobi, Kenya
| | - Steve Hoad
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Iago Hale
- University of New Hampshire, Durham, NH,, 03824, USA
| | - Ramni Jamnadass
- World Agroforestry (ICRAF), Headquarters, PO Box 30677, Nairobi, Kenya
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71
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Li Z, Liang Y, Yuan Y, Wang L, Meng X, Xiong G, Zhou J, Cai Y, Han N, Hua L, Liu G, Li J, Wang Y. OsBRXL4 Regulates Shoot Gravitropism and Rice Tiller Angle through Affecting LAZY1 Nuclear Localization. MOLECULAR PLANT 2019; 12:1143-1156. [PMID: 31200078 DOI: 10.1016/j.molp.2019.05.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/07/2019] [Accepted: 05/31/2019] [Indexed: 05/03/2023]
Abstract
Rice tiller angle is a key agronomic trait that contributes to ideal plant architecture and grain production. LAZY1 (LA1) was previously shown to control tiller angle via affecting shoot gravitropism, but the underlying molecular mechanism remains largely unknown. In this study, we identified an LA1-interacting protein named Brevis Radix Like 4 (OsBRXL4). We showed that the interaction between OsBRXL4 and LA1 occurs at the plasma membrane and that their interaction determines nuclear localization of LA1. We found that nuclear localization of LA1 is essential for its function, which is different from AtLA1, its Arabidopsis ortholog. Overexpression of OsBRXL4 leads to a prostrate growth phenotype, whereas OsBRXLs RNAi plants, in which the expression levels of OsBRXL1, OsBRXL4, and OsBRXL5 were decreased, display a compact phenotype. Further genetic analysis also supported that OsBRXL4 controls rice tiller angle by affecting nuclear localization of LA1. Consistently, we demonstrated that OsBRXL4 regulates the shoot gravitropism through affecting polar auxin transport as did LA1. Taken together, our study not only identifies OsBRXL4 as a regulatory component of rice tiller angle but also provides new insights into genetic regulation of rice plant architecture.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yundong Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guosheng Xiong
- Plant Phenomics Research Center, Nanjing Agriculture University, Nanjing 210095, China
| | - Jie Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yueyue Cai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ningpei Han
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lekai Hua
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Zhang W, Tan L, Sun H, Zhao X, Liu F, Cai H, Fu Y, Sun X, Gu P, Zhu Z, Sun C. Natural Variations at TIG1 Encoding a TCP Transcription Factor Contribute to Plant Architecture Domestication in Rice. MOLECULAR PLANT 2019; 12:1075-1089. [PMID: 31002981 DOI: 10.1016/j.molp.2019.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/24/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
The modification of plant architecture is a crucial target in rice domestication and modern genetic improvement. Although several genes regulating rice plant architecture have been characterized, the molecular mechanisms underlying rice plant architecture domestication remain largely unclear. Here we show that the inclined tiller growth in wild rice is controlled by a single dominant gene, TILLER INCLINED GROWTH 1 (TIG1), which is located on chromosome 8 and encodes a TCP transcriptional activator. TIG1 is primarily expressed in the adaxial side of the tiller base, promotes cell elongation, and enlarges the tiller angle in wild rice. Variations in the TIG1 promoter of indica cultivars (tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle, leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice domestication. TIG1 positively regulates the expression of EXPA3, EXPB5, and SAUR39 to promote cell elongation and increase the tiller angle. Selective sweep analysis revealed that the tig1 allele was selected in indica cultivars by human beings. The cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.
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Affiliation(s)
- Weifeng Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Lubin Tan
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Hongying Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xinhui Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Hongwei Cai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Yongcai Fu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xianyou Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Ping Gu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Zuofeng Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
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Sauer M, Kleine-Vehn J. PIN-FORMED and PIN-LIKES auxin transport facilitators. Development 2019; 146:146/15/dev168088. [PMID: 31371525 DOI: 10.1242/dev.168088] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The phytohormone auxin influences virtually all aspects of plant growth and development. Auxin transport across membranes is facilitated by, among other proteins, members of the PIN-FORMED (PIN) and the structurally similar PIN-LIKES (PILS) families, which together govern directional cell-to-cell transport and intracellular accumulation of auxin. Canonical PIN proteins, which exhibit a polar localization in the plasma membrane, determine many patterning and directional growth responses. Conversely, the less-studied non-canonical PINs and PILS proteins, which mostly localize to the endoplasmic reticulum, attenuate cellular auxin responses. Here, and in the accompanying poster, we provide a brief summary of current knowledge of the structure, evolution, function and regulation of these auxin transport facilitators.
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Affiliation(s)
- Michael Sauer
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
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74
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Nakamura M, Nishimura T, Morita MT. Gravity sensing and signal conversion in plant gravitropism. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3495-3506. [PMID: 30976802 DOI: 10.1093/jxb/erz158] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/08/2019] [Indexed: 05/17/2023]
Abstract
Plant organs control their growth orientation in response to gravity. Within gravity-sensing cells, the input (gravity sensing) and signal conversion (gravity signalling) progress sequentially. The cells contain a number of high-density, starch-accumulating amyloplasts, which sense gravity when they reposition themselves by sedimentation to the bottom of the cell when the plant organ is re-orientated. This triggers the next step of gravity signalling, when the physical signal generated by the sedimentation of the amyloplasts is converted into a biochemical signal, which redirects auxin transport towards the lower flank of the plant organ. This review focuses on recent advances in our knowledge of the regulatory mechanisms that underlie amyloplast sedimentation and the system by which this is perceived, and on recent progress in characterising the factors that play significant roles in gravity signalling by which the sedimentation is linked to the regulation of directional auxin transport. Finally, we discuss the contribution of gravity signalling factors to the mechanisms that control the gravitropic set-point angle.
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Affiliation(s)
- Moritaka Nakamura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, Japan
| | - Takeshi Nishimura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Miyo Terao Morita
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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75
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Fromm H. Root Plasticity in the Pursuit of Water. PLANTS (BASEL, SWITZERLAND) 2019; 8:E236. [PMID: 31336579 PMCID: PMC6681320 DOI: 10.3390/plants8070236] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/22/2023]
Abstract
One of the greatest challenges of terrestrial vegetation is to acquire water through soil-grown roots. Owing to the scarcity of high-quality water in the soil and the environment's spatial heterogeneity and temporal variability, ranging from extreme flooding to drought, roots have evolutionarily acquired tremendous plasticity regarding their geometric arrangement of individual roots and their three-dimensional organization within the soil. Water deficiency has also become an increasing threat to agriculture and dryland ecosystems due to climate change. As a result, roots have become important targets for genetic selection and modification in an effort to improve crop resilience under water-limiting conditions. This review addresses root plasticity from different angles: Their structures and geometry in response to the environment, potential genetic control of root traits suitable for water-limiting conditions, and contemporary and future studies of the principles underlying root plasticity post-Darwin's 'root-brain' hypothesis. Our increasing knowledge of different disciplines of plant sciences and agriculture should contribute to a sustainable management of natural and agricultural ecosystems for the future of mankind.
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Affiliation(s)
- Hillel Fromm
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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76
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Wedger MJ, Topp CN, Olsen KM. Convergent evolution of root system architecture in two independently evolved lineages of weedy rice. THE NEW PHYTOLOGIST 2019; 223:1031-1042. [PMID: 30883803 DOI: 10.1111/nph.15791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 05/13/2023]
Abstract
Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de-domesticated form of rice, to study the evolution of weed-associated RSA traits and the extent to which they evolve through shared or different genetic mechanisms. We characterised 98 two-dimensional and three-dimensional RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains. The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a 'weedy' RSA phenotype. Notably, comparative QTL mapping revealed little evidence for shared underlying genetic mechanisms. Our findings suggest that despite the double bottlenecks of domestication and de-domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below-ground contact as a competitive strategy.
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Affiliation(s)
- Marshall J Wedger
- Biology Department, Campus Box 1137, Washington University in St Louis, 1 Brookings Dr., St Louis, MO, 63130, USA
| | - Christopher N Topp
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Kenneth M Olsen
- Biology Department, Campus Box 1137, Washington University in St Louis, 1 Brookings Dr., St Louis, MO, 63130, USA
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77
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Motte H, Vanneste S, Beeckman T. Molecular and Environmental Regulation of Root Development. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:465-488. [PMID: 30822115 DOI: 10.1146/annurev-arplant-050718-100423] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In order to optimally establish their root systems, plants are endowed with several mechanisms to use at distinct steps during their development. In this review, we zoom in on the major processes involved in root development and detail important new insights that have been generated in recent studies, mainly using the Arabidopsis root as a model. First, we discuss new insights in primary root development with the characterization of tissue-specific transcription factor complexes and the identification of non-cell-autonomous control mechanisms in the root apical meristem. Next, root branching is discussed by focusing on the earliest steps in the development of a new lateral root and control of its postemergence growth. Finally, we discuss the impact of phosphate, nitrogen, and water availability on root development and summarize current knowledge about the major molecular mechanisms involved.
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Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
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78
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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79
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Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements. PLoS One 2019; 14:e0214145. [PMID: 30947257 PMCID: PMC6448822 DOI: 10.1371/journal.pone.0214145] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Root growth angle (RGA) in response to gravity controlled by auxin is a pertinent target trait for obtainment of higher yield in cereals. But molecular basis of this root architecture trait remain obscure in wheat and barley. We selected four cultivars two each for wheat and barley to unveil the molecular genetic mechanism of Deeper Rooting 1-like gene which controls RGA in rice leading to higher yield under drought imposition. Morphological analyses revealed a deeper and vertically oriented root growth in “NARC 2009” variety of wheat than “Galaxy” and two other barley cultivars “Scarlet” and “ISR42-8”. Three new homoeologs designated as TaANDRO1-like, TaBNDRO1-like and TaDNDRO1-like corresponding to A, B and D genomes of wheat could be isolated from “NARC 2009”. Due to frameshift and intronization/exonization events the gene structures of these paralogs exhibit variations in size. DRO1-like genes with five distinct domains prevail in diverse plant phyla from mosses to angiosperms but in lower plants their differentiation from LAZY, NGR and TAC1 (root and shoot angle genes) is enigmatic. Instead of IGT as denominator motif of this family, a new C-terminus motif WxxTD in the V-domain is proposed as family specific motif. The EAR-like motif IVLEM at the C-terminus of the TaADRO1-like and TaDDRO1-like that diverged to KLHTLIPNK in TaBDRO1-like and HvDRO1-like is the hallmark of these proteins. Split-YFP and yeast two hybrid assays complemented the interaction of TaDRO1-like with TOPLESS—a repressor of auxin regulated root promoting genes in plants—through IVLEM/KLHTLIPNK motif. Quantitative RT-PCR revealed abundance of DRO1-like RNA in root tips and spikelets while transcript signals were barely detectable in shoot and leaf tissues. Interestingly, wheat exhibited stronger expression of TaBDRO1-like than barley (HvDRO1-like), but TaBDRO1-like was the least expressing among three paralogs. The underlying cause of this expression divergence seems to be the presence of AuxRE motif TGTCTC and core TGTC with a coupling AuxRE-like motif ATTTTCTT proximal to the transcriptional start site in TaBDRO1-like and HvDRO1-like promoters. This is evident from binding of ARF1 to TGTCTC and TGTC motifs of TaBDRO1-like as revealed by yeast one-hybrid assay. Thus, evolution of DRO1-like wheat homoeologs might incorporate the C-terminus mutations as well as gain and loss of AuxREs and other cis-regulatory elements during expression divergence. Since root architecture is an important target trait for wheat crop improvement, therefore DRO1-like genes have potential applications in plant breeding for enhancement of plant productivity by the use of modern genome editing approaches.
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80
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Kobayashi A, Kim HJ, Tomita Y, Miyazawa Y, Fujii N, Yano S, Yamazaki C, Kamada M, Kasahara H, Miyabayashi S, Shimazu T, Fusejima Y, Takahashi H. Circumnutational movement in rice coleoptiles involves the gravitropic response: analysis of an agravitropic mutant and space-grown seedlings. PHYSIOLOGIA PLANTARUM 2019; 165:464-475. [PMID: 30159898 DOI: 10.1111/ppl.12824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Plants exhibit helical growth movements known as circumnutation in growing organs. Some studies indicate that circumnutation involves the gravitropic response, but this notion is a matter of debate. Here, using the agravitropic rice mutant lazy1 and space-grown rice seedlings, we found that circumnutation was reduced or lost during agravitropic growth in coleoptiles. Coleoptiles of wild-type rice exhibited circumnutation in the dark, with vigorous oscillatory movements during their growth. The gravitropic responses in lazy1 coleoptiles differed depending on the growth stage, with gravitropic responses detected during early growth and agravitropism during later growth. The nutation-like movements observed in lazy1 coleoptiles at the early stage of growth were no longer detected with the disappearance of the gravitropic response. To verify the relationship between circumnutation and gravitropic responses in rice coleoptiles, we conducted spaceflight experiments in plants under microgravity conditions on the International Space Station. Wild-type rice seeds were germinated, and the resulting seedlings were grown under microgravity or a centrifuge-generated 1 g environment in space. We began filming the seedlings 2 days after seed imbibition and obtained images of seedling growth every 15 min. The seed germination rate in space was 92-100% under both microgravity and 1 g conditions. LED-synchronized flashlight photography induced an attenuation of coleoptile growth and circumnutational movement due to cumulative light exposure. Nevertheless, wild-type rice coleoptiles still showed circumnutational oscillations under 1 g but not microgravity conditions. These results support the idea that the gravitropic response is involved in plant circumnutation.
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Affiliation(s)
- Akie Kobayashi
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Hye-Jeong Kim
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Yuta Tomita
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Yutaka Miyazawa
- Faculty of Science, Yamagata University, Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Sachiko Yano
- JEM Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency, Sengen, Tsukuba 305-8505, Japan
| | - Chiaki Yamazaki
- Space Utilization Promotion Department, Japan Space Forum, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Motoshi Kamada
- Future Development Division, Advanced Engineering Services Corporation, Ltd., Takezono, Tsukuba 305-0032, Japan
| | - Haruo Kasahara
- JEM Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency, Sengen, Tsukuba 305-8505, Japan
| | - Sachiko Miyabayashi
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Toru Shimazu
- Space Utilization Promotion Department, Japan Space Forum, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yasuo Fusejima
- Space Utilization Promotion Department, Japan Space Forum, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hideyuki Takahashi
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
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81
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Hill JL, Hollender CA. Branching out: new insights into the genetic regulation of shoot architecture in trees. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:73-80. [PMID: 30339931 DOI: 10.1016/j.pbi.2018.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 05/03/2023]
Abstract
Directional growth in all plants involves both phototropic and gravitropic responses. Accordingly, mechanisms controlling shoot architecture throughout the plant kingdom are likely similar. However, as forms vary between species due in part to gene copy number and functional divergence, some aspects of how plants predetermine and regulate architecture can differ. This is especially true when comparing annual herbaceous species (e.g. model plants) to woody perennials such as trees. In the past decade, inexpensive genomic sequencing and technological advances enabled gene discovery and functional analyses in trees. This led to the identification of genes associated with tree shoot architecture control. Here, we present recent discoveries on the regulation of shoot architectures for which causative genes have been identified, including dwarf, weeping, columnar, and pillar growth habits. We also discuss potential applications of these findings.
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Affiliation(s)
- Joseph L Hill
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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82
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Alaguero-Cordovilla A, Gran-Gómez FJ, Tormos-Moltó S, Pérez-Pérez JM. Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth. Int J Mol Sci 2018; 19:E3888. [PMID: 30563085 PMCID: PMC6321557 DOI: 10.3390/ijms19123888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato 'Micro-Tom' mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species.
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Affiliation(s)
| | | | - Sergio Tormos-Moltó
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain.
- OQOTECH Process Validation System, 03801 Alcoy, Spain.
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83
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Waite JM, Dardick C. TILLER ANGLE CONTROL 1 modulates plant architecture in response to photosynthetic signals. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4935-4944. [PMID: 30099502 DOI: 10.1093/jxb/ery253] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/02/2018] [Indexed: 05/11/2023]
Abstract
Light serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under continuous dark or far-red growth conditions, but did not drop to these low levels during a diurnal time course. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon red/far-red or blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1). Overexpression of TAC1 partially prevented the narrowing of branch angles in the dark or under far-red light. Treatment with the carotenoid biosynthesis inhibitor norflurazon or the PSII inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) led to loss of TAC1 expression similar to dark or far-red conditions, but expression increased in response to the PSI inhibitor paraquat. Treatment of adult plants with norflurazon resulted in upward growth angle of branch tips. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.
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Affiliation(s)
- Jessica M Waite
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, Kearneysville, WV, USA
| | - Chris Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, Kearneysville, WV, USA
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84
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Pauwels L, De Clercq R, Goossens J, Iñigo S, Williams C, Ron M, Britt A, Goossens A. A Dual sgRNA Approach for Functional Genomics in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2018; 8:2603-2615. [PMID: 29884615 PMCID: PMC6071589 DOI: 10.1534/g3.118.200046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/30/2018] [Indexed: 12/25/2022]
Abstract
Reverse genetics uses loss-of-function alleles to interrogate gene function. The advent of CRISPR/Cas9-based gene editing now allows the generation of knock-out alleles for any gene and entire gene families. Even in the model plant Arabidopsis thaliana, gene editing is welcomed as T-DNA insertion lines do not always generate null alleles. Here, we show efficient generation of heritable mutations in Arabidopsis using CRISPR/Cas9 with a workload similar to generating overexpression lines. We obtain for several different genes Cas9 null-segregants with bi-allelic mutations in the T2 generation. While somatic mutations were predominantly generated by the canonical non-homologous end joining (cNHEJ) pathway, we observed inherited mutations that were the result of synthesis-dependent microhomology-mediated end joining (SD-MMEJ), a repair pathway linked to polymerase θ (PolQ). We also demonstrate that our workflow is compatible with a dual sgRNA approach in which a gene is targeted by two sgRNAs simultaneously. This paired nuclease method results in more reliable loss-of-function alleles that lack a large essential part of the gene. The ease of the CRISPR/Cas9 workflow should help in the eventual generation of true null alleles of every gene in the Arabidopsis genome, which will advance both basic and applied plant research.
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Affiliation(s)
- Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Rebecca De Clercq
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jonas Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Sabrina Iñigo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Clara Williams
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mily Ron
- UC Davis, Department of Plant Biology, Davis, CA 95616, US
| | - Anne Britt
- UC Davis, Department of Plant Biology, Davis, CA 95616, US
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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85
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Huang G, Liang W, Sturrock CJ, Pandey BK, Giri J, Mairhofer S, Wang D, Muller L, Tan H, York LM, Yang J, Song Y, Kim YJ, Qiao Y, Xu J, Kepinski S, Bennett MJ, Zhang D. Rice actin binding protein RMD controls crown root angle in response to external phosphate. Nat Commun 2018; 9:2346. [PMID: 29892032 PMCID: PMC5995806 DOI: 10.1038/s41467-018-04710-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/01/2018] [Indexed: 11/12/2022] Open
Abstract
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
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Affiliation(s)
- Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Craig J Sturrock
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Bipin K Pandey
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
| | - Jitender Giri
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
| | - Stefan Mairhofer
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Daoyang Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lukas Muller
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Larry M York
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Jing Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK
| | - Yu Song
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu-Jin Kim
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yang Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough Leicstershire, LE12 5RD, Nottingham, UK.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- University of Adelaide-SJTU Joint Centre for Agriculture and Health, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, 5064, SA, Australia.
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86
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Petri C, Alburquerque N, Faize M, Scorza R, Dardick C. Current achievements and future directions in genetic engineering of European plum (Prunus domestica L.). Transgenic Res 2018; 27:225-240. [PMID: 29651659 PMCID: PMC5986827 DOI: 10.1007/s11248-018-0072-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/06/2018] [Indexed: 01/05/2023]
Abstract
In most woody fruit species, transformation and regeneration are difficult. However, European plum (Prunus domestica) has been shown to be amenable to genetic improvement technologies from classical hybridization, to genetic engineering, to rapid cycle crop breeding ('FasTrack' breeding). Since the first report on European plum transformation with marker genes in the early 90 s, numerous manuscripts have been published reporting the generation of new clones with agronomically interesting traits, such as pests, diseases and/or abiotic stress resistance, shorter juvenile period, dwarfing, continuous flowering, etc. This review focuses on the main advances in genetic transformation of European plum achieved to date, and the lines of work that are converting genetic engineering into a contemporary breeding tool for this species.
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Affiliation(s)
- Cesar Petri
- Departamento de Producción Vegetal, Instituto de Biotecnología Vegetal, UPCT, Campus Muralla del Mar, 30202, Cartagena, Murcia, Spain.
| | - Nuria Alburquerque
- Departamento de Mejora Vegetal, CEBAS-CSIC, Campus de Espinardo, 30100, Espinardo, Murcia, Spain
| | - Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, 24000, El Jadida, Morocco
| | - Ralph Scorza
- Ag Biotech and Plant Breeding Consulting Services, Ralph Scorza LLC, Shepherdstown, WV, 25443, USA
| | - Chris Dardick
- USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
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87
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Hollender CA, Pascal T, Tabb A, Hadiarto T, Srinivasan C, Wang W, Liu Z, Scorza R, Dardick C. Loss of a highly conserved sterile alpha motif domain gene ( WEEP) results in pendulous branch growth in peach trees. Proc Natl Acad Sci U S A 2018; 115:E4690-E4699. [PMID: 29712856 PMCID: PMC5960274 DOI: 10.1073/pnas.1704515115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325, having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP, was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.
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Affiliation(s)
- Courtney A Hollender
- Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, Kearneysville, WV 25430
- Department of Horticulture, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824
| | - Thierry Pascal
- Unité Génétique et Amélioration de Fruits et Légumes, Institut National de la Recherche Agronomique, 84140 Montfavet, France
| | - Amy Tabb
- Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, Kearneysville, WV 25430
| | - Toto Hadiarto
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (BB Biogen), Bogor, Indonesia
| | - Chinnathambi Srinivasan
- Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, Kearneysville, WV 25430
| | - Wanpeng Wang
- Department of Cell Biology and Molecular Genetics, College of Mathematics and Natural Sciences, University of Maryland, College Park, MD 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, College of Mathematics and Natural Sciences, University of Maryland, College Park, MD 20742
| | - Ralph Scorza
- Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, Kearneysville, WV 25430
| | - Chris Dardick
- Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, Kearneysville, WV 25430;
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88
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Hollender CA, Waite JM, Tabb A, Raines D, Chinnithambi S, Dardick C. Alteration of TAC1 expression in Prunus species leads to pleiotropic shoot phenotypes. HORTICULTURE RESEARCH 2018; 5:26. [PMID: 29736251 PMCID: PMC5928093 DOI: 10.1038/s41438-018-0034-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/20/2017] [Accepted: 03/08/2018] [Indexed: 05/11/2023]
Abstract
Prunus persica (peach) trees carrying the "Pillar" or "Broomy" trait (br) have vertically oriented branches caused by loss-of-function mutations in a gene called TILLER ANGLE CONTROL 1 (TAC1). TAC1 encodes a protein in the IGT gene family that includes LAZY1 and DEEPER ROOTING 1 (DRO1), which regulate lateral branch and root orientations, respectively. Here we found that some of the native TAC1 alleles in the hexaploid plum species Prunus domestica, which has a naturally more upright stature, contained a variable length trinucleotide repeat within the same exon 3 region previously found to be disrupted in pillar peach trees. RNAi silencing of TAC1 in plum resulted in trees with severely vertical branch orientations similar to those in pillar peaches but with an even narrower profile. In contrast, PpeTAC1 overexpression in plum led to trees with wider branch angles and more horizontal branch orientations. Pillar peach trees and transgenic plum lines exhibited pleiotropic phenotypes, including differences in trunk and branch diameter, stem growth, and twisting branch phenotypes. Expression profiling of pillar peach trees revealed differential expression of numerous genes associated with biotic and abiotic stress, hormone responses, plastids, reactive oxygen, secondary, and cell wall metabolism. Collectively, the data provide important clues for understanding TAC1 function and show that alteration of TAC1 expression may have broad applicability to agricultural and ornamental tree industries.
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Affiliation(s)
- Courtney A. Hollender
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV 25430 USA
- Present Address: Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Jessica M. Waite
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV 25430 USA
| | - Amy Tabb
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV 25430 USA
| | - Doug Raines
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV 25430 USA
| | | | - Chris Dardick
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV 25430 USA
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89
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Ruiz Rosquete M, Waidmann S, Kleine-Vehn J. PIN7 Auxin Carrier Has a Preferential Role in Terminating Radial Root Expansion in Arabidopsis thaliana. Int J Mol Sci 2018; 19:E1238. [PMID: 29671782 PMCID: PMC5979548 DOI: 10.3390/ijms19041238] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 12/17/2022] Open
Abstract
Directional growth of lateral roots is critical for radial expansion and soil coverage. Despite its importance, almost nothing is known about its molecular determinants. Initially, young lateral roots (LRs) grow away from the parental root, maintaining the angle acquired shortly after emergence. A second downwards bending response to gravity terminates the so-called plateau phase and thereby limits radial root expansion. Here, we show that the exit from the plateau phase correlates with an increase in auxin signalling at the tip of the LRs. Moreover, the increase in auxin levels induces the termination of the plateau phase, which requires PIN-FORMED (PIN) auxin efflux carriers. Our data suggests that the developmental increase in auxin triggers the preferential derepression of PIN7 in gravity-sensing columella cells. The subsequent polarization of PIN7 heralds the bending towards gravity and, hence, the exit from the plateau phase. This developmental framework reveals the distinct roles of PIN auxin efflux carriers in controlling the radial growth of root systems.
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Affiliation(s)
- Michel Ruiz Rosquete
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna 1190, Austria.
| | - Sascha Waidmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna 1190, Austria.
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna 1190, Austria.
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90
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Kulkarni M, Soolanayakanahally R, Ogawa S, Uga Y, Selvaraj MG, Kagale S. Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency. Front Chem 2017; 5:106. [PMID: 29259968 PMCID: PMC5723305 DOI: 10.3389/fchem.2017.00106] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/07/2017] [Indexed: 12/24/2022] Open
Abstract
Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.
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Affiliation(s)
- Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Satoshi Ogawa
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusaku Uga
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Michael G. Selvaraj
- Agrobioversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
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91
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Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol 2017; 79:68-77. [PMID: 28864344 DOI: 10.1016/j.semcdb.2017.08.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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