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Li Q, Wang Y, Sun Z, Li H, Liu H. The Biosynthesis Process of Small RNA and Its Pivotal Roles in Plant Development. Int J Mol Sci 2024; 25:7680. [PMID: 39062923 PMCID: PMC11276867 DOI: 10.3390/ijms25147680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
In the realm of plant biology, small RNAs (sRNAs) are imperative in the orchestration of gene expression, playing pivotal roles across a spectrum of developmental sequences and responses to environmental stressors. The biosynthetic cascade of sRNAs is characterized by an elaborate network of enzymatic pathways that meticulously process double-stranded RNA (dsRNA) precursors into sRNA molecules, typically 20 to 30 nucleotides in length. These sRNAs, chiefly microRNAs (miRNAs) and small interfering RNAs (siRNAs), are integral in guiding the RNA-induced silencing complex (RISC) to selectively target messenger RNAs (mRNAs) for post-transcriptional modulation. This regulation is achieved either through the targeted cleavage or the suppression of translational efficiency of the mRNAs. In plant development, sRNAs are integral to the modulation of key pathways that govern growth patterns, organ differentiation, and developmental timing. The biogenesis of sRNA itself is a fine-tuned process, beginning with transcription and proceeding through a series of processing steps involving Dicer-like enzymes and RNA-binding proteins. Recent advances in the field have illuminated the complex processes underlying the generation and function of small RNAs (sRNAs), including the identification of new sRNA categories and the clarification of their involvement in the intercommunication among diverse regulatory pathways. This review endeavors to evaluate the contemporary comprehension of sRNA biosynthesis and to underscore the pivotal role these molecules play in directing the intricate performance of plant developmental processes.
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Affiliation(s)
| | | | | | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (Q.L.); (Y.W.); (Z.S.)
| | - Huan Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (Q.L.); (Y.W.); (Z.S.)
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Li Y, Liu X, Xu X, Zhu G, Xiang D, Liu P. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 2024; 25:670. [PMID: 38965476 PMCID: PMC11223397 DOI: 10.1186/s12864-024-10347-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed. RESULTS The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes. CONCLUSION We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyang Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyuan Xu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Guishuang Zhu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Dianjun Xiang
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Peng Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
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Sun X, Liu Z, Liu R, Bucher J, Zhao J, Visser RGF, Bonnema G. Transcriptomic analyses to summarize gene expression patterns that occur during leaf initiation of Chinese cabbage. HORTICULTURE RESEARCH 2024; 11:uhae059. [PMID: 38689699 PMCID: PMC11059812 DOI: 10.1093/hr/uhae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
In Chinese cabbage, rosette leaves expose their adaxial side to the light converting light energy into chemical energy, acting as a source for the growth of the leafy head. In the leafy head, the outer heading leaves expose their abaxial side to the light while the inner leaves are shielded from the light and have become a sink organ of the growing Chinese cabbage plant. Interestingly, variation in several ad/abaxial polarity genes is associated with the typical leafy head morphotype. The initiation of leaf primordia and the establishment of leaf ad/abaxial polarity are essential steps in the initiation of marginal meristem activity leading to leaf formation. Understanding the molecular genetic mechanisms of leaf primordia formation, polar differentiation, and leaf expansion is thus relevant to understand leafy head formation. As Brassica's are mesa-hexaploids, many genes have multiple paralogues, complicating analysis of the genetic regulation of leaf development. In this study, we used laser dissection of Chinese cabbage leaf primordia and the shoot apical meristem (SAM) to compare gene expression profiles between both adaxial and abaxial sides and the SAM aiming to capture transcriptome changes underlying leaf primordia development. We highlight genes with roles in hormone pathways and transcription factors. We also assessed gene expression gradients along expanded leaf blades from the same plants to analyze regulatory links between SAM, leaf primordia and the expanding rosette leaf. The catalogue of differentially expressed genes provides insights in gene expression patterns involved in leaf development and form a starting point to unravel leafy head formation.
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Affiliation(s)
- XiaoXue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Zihan Liu
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Rui Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Johan Bucher
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Liu Z, Alemán-Báez J, Visser RGF, Bonnema G. Cabbage ( Brassica oleracea var. capitata) Development in Time: How Differential Parenchyma Tissue Growth Affects Leafy Head Formation. PLANTS (BASEL, SWITZERLAND) 2024; 13:656. [PMID: 38475502 DOI: 10.3390/plants13050656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
This study aims to categorize the morphological changes during cabbage (B. oleracea ssp. capitata) development, seedling, rosette, folding, and heading, and to elucidate the cellular mechanisms of the leaf curvature, essential for the formation of the leafy head. We followed the growth of two cabbage cultivars with distinct head shapes (round and pointed) and one non-heading collard cultivar; we phenotyped the size and volume of the whole plant as well as the size, shape, and curvature of the leaves during growth. By integrating these phenotypic data, we determined the four vegetative stages for both cabbages. The histological phenotypes of microtome sections from five distinct leaf positions of the rosette, folding, and heading leaves at two timepoints during leaf growth were quantified and revealed variations in cellular parameters among leaf types, between leaf positions, and between the adaxial and abaxial sides. We identified two synergistic cellular mechanisms contributing to the curvature of heading leaves: differential growth across the leaf blade, with increased growth at the leaf's center relative to the margins; and the increased expansion of the spongy parenchyma layer compared to the palisade parenchyma layer, resulting in the direction of the curvature, which is inwards. These two processes together contribute to the typical leafy heads of cabbages.
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Affiliation(s)
- Zihan Liu
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Jorge Alemán-Báez
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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Ahn JY, Subburaj S, Yan F, Yao J, Chandrasekaran A, Ahn KG, Lee GJ. Molecular Evaluation of the Effects of FLC Homologs and Coordinating Regulators on the Flowering Responses to Vernalization in Cabbage ( Brassica oleracea var. capitata) Genotypes. Genes (Basel) 2024; 15:154. [PMID: 38397144 PMCID: PMC10887945 DOI: 10.3390/genes15020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and BoVIN3 of early (CAB1), middle (CAB3), and late (CAB5) flowering cabbage genotypes. Analysis of allele-specifically amplified genomic DNA and various sequence alignments demonstrated that maximal insertions and deletions influenced cabbage flowering behavior, notably in CAB3 and CAB5. Phylogenetic studies showed that BoFLC1, 2, and 3 in the CAB1, 3, and 5 genotypes had the highest homologies to other Brassica species, with CAB3 and 5 the most similar. Although CAB3 and CAB5 have comparable genetic patterns, flowering repressors and flowering regulators were investigated individually with and without vernalization to determine their minor flowering differences. The expression investigation revealed that vernalized CAB5 downregulated all BoFLC genes compared to CAB3 and, in contrast, CAB3 exhibited upregulated BoCOOLAIR. We hypothesized that the CAB3 BoFLC locus' additional insertions may have led to BoCOOLAIR overexpression and BoFLC downregulation. This study sheds light on cabbage genotypes-particularly those of CAB1 and CAB5-and suggests that structural variations in BoFLC2 and 3 bind flowering regulators, such as COOLAIR, which may affect cabbage flowering time.
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Affiliation(s)
- Ju-Young Ahn
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Fanzhuang Yan
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Jian Yao
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Ajithan Chandrasekaran
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Kyoung-Gu Ahn
- Joen Seed Co., Ltd., Goesan 28051, Republic of Korea;
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
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Tabusam J, Liu M, Luo L, Zulfiqar S, Shen S, Ma W, Zhao J. Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L. J Adv Res 2023; 53:49-59. [PMID: 36581197 PMCID: PMC10658314 DOI: 10.1016/j.jare.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies. AIM OF REVIEW Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development. KEY SCIENTIFIC CONCEPTS OF REVIEW Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.
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Affiliation(s)
- Javaria Tabusam
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Lei Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Sumer Zulfiqar
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Wei Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
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Zhao Y, Huang S, Zhang Y, Tan C, Feng H. Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:170. [PMID: 37420138 DOI: 10.1007/s00122-023-04411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Yonghui Zhao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yun Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chong Tan
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
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Lu H, Chen L, Du M, Lu H, Liu J, Ye S, Tao B, Li R, Zhao L, Wen J, Yi B, Tu J, Fu T, Shen J. miR319 and its target TCP4 involved in plant architecture regulation in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111531. [PMID: 36343867 DOI: 10.1016/j.plantsci.2022.111531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Plant architecture is a collection of genetically controlled crop productivity and adaptation. MicroRNAs (miRNAs) have been proved to function in various biological processes, but little is known about how miRNA regulates plant architecture in rapeseed (Brassica napus L.). In this study, four small RNA libraries and two degradome libraries from shoot apex of normal and rod-like plants were sequenced. A total of 639 miRNA precursors and 16 differentially expressed miRNAs were identified in this study. In addition, 322 targets were identified through degradome sequencing. Among them, 14 targets were further validated via RNA ligase-mediated 5' rapid amplification of cDNA ends. Transgenic approach showed that increased TCP4 activity in Arabidopsis resulted in premature onset of maturation and reduced plant size along with early flowering and shortened flowering time. miR319-OE lines in Brassica napus exhibited serrated leaves and abnormal development of shoot apical meristem (SAM), which led to the deformed growth of stem and reduced plant height. In conclusion, our study lays the foundation for elucidating miRNA regulate plant architecture and provides new insight into the miR319/TCP4 module regulates plant architecture in rapeseed.
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Affiliation(s)
- Hongchen Lu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China; School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
| | - Mengjie Du
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Haiqin Lu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Shenhua Ye
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Baolong Tao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Rihui Li
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China.
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Overexpression of Mtr-miR319a Contributes to Leaf Curl and Salt Stress Adaptation in Arabidopsis thaliana and Medicago truncatula. Int J Mol Sci 2022; 24:ijms24010429. [PMID: 36613873 PMCID: PMC9820427 DOI: 10.3390/ijms24010429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering.
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Liu DK, Zhang C, Zhao X, Ke S, Li Y, Zhang D, Zheng Q, Li MH, Lan S, Liu ZJ. Genome-wide analysis of the TCP gene family and their expression pattern in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2022; 13:1068969. [PMID: 36570938 PMCID: PMC9772009 DOI: 10.3389/fpls.2022.1068969] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
TCP gene family are specific transcription factors for plant, and considered to play an important role in development and growth. However, few related studies investigated the TCP gene trait and how it plays a role in growth and development of Orchidaceae. In this study, we obtained 14 TCP genes (CgTCPs) from the Spring Orchid Cymbidium goeringii genome. The classification results showed that 14 CgTCPs were mainly divided into two clades as follows: four PCF genes (Class I), nine CIN genes and one CYC gene (Class II). The sequence analysis showed that the TCP proteins of C. goeringii contain four conserved regions (basic Helix-Loop-Helix) in the TCP domain. The exon-intron structure varied in the clade according to a comparative investigation of the gene structure, and some genes had no introns. There are fewer CgTCP homologous gene pairs compared with Dendrobium catenatum and Phalaenopsis equestris, suggesting that the TCP genes in C. goeringii suffered more loss events. The majority of the cis-elements revealed to be enriched in the function of light responsiveness, followed by MeJA and ABA responsiveness, demonstrating their functions in regulating by light and phytohormones. The collinearity study revealed that the TCPs in D. catenatum, P. equestris and C. goeringii almost 1:1. The transcriptomic data and real-time reverse transcription-quantitative PCR (RT-qPCR) expression profiles showed that the flower-specific expression of the TCP class II genes (CgCIN2, CgCIN5 and CgCIN6) may be related to the regulation of florescence. Altogether, this study provides a comprehensive analysis uncovering the underlying function of TCP genes in Orchidaceae.
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Affiliation(s)
- Ding-Kun Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-He Li
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Hao N, Cao J, Wang C, Zhu Y, Du Y, Wu T. Understanding the molecular mechanism of leaf morphogenesis in vegetable crops conduces to breeding process. FRONTIERS IN PLANT SCIENCE 2022; 13:971453. [PMID: 36570936 PMCID: PMC9773389 DOI: 10.3389/fpls.2022.971453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Leaf morphology can affect the development and yield of plants by regulating plant architecture and photosynthesis. Several factors can determine the final leaf morphology, including the leaf complexity, size, shape, and margin type, which suggests that leaf morphogenesis is a complex regulation network. The formation of diverse leaf morphology is precisely controlled by gene regulation on translation and transcription levels. To further reveal this, more and more genome data has been published for different kinds of vegetable crops and advanced genotyping approaches have also been applied to identify the causal genes for the target traits. Therefore, the studies on the molecular regulation of leaf morphogenesis in vegetable crops have also been largely improved. This review will summarize the progress on identified genes or regulatory mechanisms of leaf morphogenesis and development in vegetable crops. These identified markers can be applied for further molecular-assisted selection (MAS) in vegetable crops. Overall, the review will contribute to understanding the leaf morphology of different crops from the perspective of molecular regulation and shortening the breeding cycle for vegetable crops.
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Affiliation(s)
- Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Yipeng Zhu
- Guiyang Productivity Promotion Center, Guiyang Science and Technology Bureau, Guiyang, China
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
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12
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Preusche M, Vahl M, Riediger J, Ulbrich A, Schulz M. Modulating Expression Levels of TCP Transcription Factors by Mentha x piperita Volatiles-An Allelopathic Tool to Influence Leaf Growth? PLANTS (BASEL, SWITZERLAND) 2022; 11:3078. [PMID: 36432807 PMCID: PMC9697212 DOI: 10.3390/plants11223078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Peppermint (Mentha x piperita) is a species with inhibitory allelopathic properties due to its high amounts of terpenes. Recent studies have disclosed dosage dependent growth promotion or defense reactions in plants when facing appropriate amounts of Mentha bouquet terpenes. These positive effects could be of interest for agricultural applications. To obtain more insights into leaf growth modulations, the expression of Arabidopsis and Brassica rapa TCP transcription factors were studied after fumigation with M. x piperita bouquets (Arabidopsis), with M. x piperita essential oil or with limonene (Arabidopsis and Chinese cabbage). According to qPCR studies, expression of TCP3, TCP24, and TCP20 were downregulated by all treatments in Arabidopsis, leading to altered leaf growth. Expressions of B. rapa TCPs after fumigation with the essential oil or limonene were less affected. Extensive greenhouse and polytunnel trials with white cabbage and Mentha plants showed that the developmental stage of the leaves, the dosage, and the fumigation time are of crucial importance for changed fresh and dry weights. Although further research is needed, the study may contribute to a more intensive utilization of ecologically friendly and species diversity conservation and positive allelopathic interactions in future agricultural systems.
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Affiliation(s)
- Matthias Preusche
- Department of Horticultural Production, University of Applied Science, 49090 Osnabrück, Germany
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53127 Bonn, Germany
| | - Marvin Vahl
- Department of Horticultural Production, University of Applied Science, 49090 Osnabrück, Germany
| | - Johanna Riediger
- Department of Horticultural Production, University of Applied Science, 49090 Osnabrück, Germany
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53127 Bonn, Germany
| | - Andreas Ulbrich
- Department of Horticultural Production, University of Applied Science, 49090 Osnabrück, Germany
| | - Margot Schulz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53127 Bonn, Germany
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13
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An G, Yu C, Yan C, Wang M, Zhang W, Jia Y, Shi C, Larkin RM, Chen J, Lavelle D, Michelmore RW, Kuang H. Loss-of-function of SAWTOOTH 1 affects leaf dorsiventrality genes to promote leafy heads in lettuce. THE PLANT CELL 2022; 34:4329-4347. [PMID: 35916734 PMCID: PMC9614500 DOI: 10.1093/plcell/koac234] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The mechanisms underlying leafy heads in vegetables are poorly understood. Here, we cloned a quantitative trait locus (QTL) controlling leafy heads in lettuce (Lactuca sativa). The QTL encodes a transcription factor, SAWTOOTH 1 (LsSAW1), which has a BEL1-like homeodomain and is a homolog of Arabidopsis thaliana. A 1-bp deletion in Lssaw1 contributes to the development of leafy heads. Laser-capture microdissection and RNA-sequencing showed that LsSAW1 regulates leaf dorsiventrality and loss-of-function of Lssaw1 downregulates the expression of many adaxial genes but upregulates abaxial genes. LsSAW1 binds to the promoter region of the adaxial gene ASYMMETRIC LEAVES 1 (LsAS1) to upregulate its expression. Overexpression of LsAS1 compromised the effects of Lssaw1 on heading. LsSAW1 also binds to the promoter region of the abaxial gene YABBY 1 (LsYAB1), but downregulates its expression. Overexpression of LsYAB1 led to bending leaves in LsSAW1 genotypes. LsSAW1 directly interacts with KNOTTED 1 (LsKN1), which is necessary for leafy heads in lettuce. RNA-seq data showed that LsSAW1 and LsKN1 exert antagonistic effects on the expression of thousands of genes. LsSAW1 compromises the ability of LsKN1 to repress LsAS1. Our results suggest that downregulation or loss-of-function of adaxial genes and upregulation of abaxial genes allow for the development of leafy heads.
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Affiliation(s)
- Guanghui An
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenghuan Yan
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Menglu Wang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dean Lavelle
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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14
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Cao B, Wang H, Bai J, Wang X, Li X, Zhang Y, Yang S, He Y, Yu X. miR319-Regulated TCP3 Modulates Silique Development Associated with Seed Shattering in Brassicaceae. Cells 2022; 11:cells11193096. [PMID: 36231057 PMCID: PMC9563637 DOI: 10.3390/cells11193096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Seed shattering is an undesirable trait that leads to crop yield loss. Improving silique resistance to shattering is critical for grain and oil crops. In this study, we found that miR319-targeted TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR (TCPs) inhibited the process of post-fertilized fruits (silique) elongation and dehiscence via regulation of FRUITFULL (FUL) expression in Arabidopsis thaliana and Brassica napus. AtMIR319a activation resulted in a longer silique with thickened and lignified replum, whereas overexpression of an miR319a-resistant version of AtTCP3 (mTCP3) led to a short silique with narrow and less lignified replum. Further genetic and expressional analysis suggested that FUL acted downstream of TCP3 to negatively regulate silique development. Moreover, hyper-activation of BnTCP3.A8, a B. napus homolog of AtTCP3, in rapeseed resulted in an enhanced silique resistance to shattering due to attenuated replum development. Taken together, our findings advance our knowledge of TCP-regulated silique development and provide a potential target for genetic manipulation to reduce silique shattering in Brassica crops.
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Affiliation(s)
- Biting Cao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Hongfeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266101, China
| | - Jinjuan Bai
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Xuan Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Xiaorong Li
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Yanfeng Zhang
- Hybrid Rape Research Center of Shaanxi Province, Yangling 712100, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Changchun 130102, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Science, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- Correspondence: (Y.H.); (X.Y.)
| | - Xiang Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (Y.H.); (X.Y.)
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15
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Alemán-Báez J, Qin J, Cai C, Zou C, Bucher J, Paulo MJ, Voorrips RE, Bonnema G. Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3611-3628. [PMID: 36057748 PMCID: PMC9519658 DOI: 10.1007/s00122-022-04205-w] [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: 05/02/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.
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Affiliation(s)
- Jorge Alemán-Báez
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Jian Qin
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chunmei Zou
- Centre for Crop Systems Analysis, Wageningen University and Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Roeland E. Voorrips
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
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16
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He M, Kong X, Jiang Y, Qu H, Zhu H. MicroRNAs: emerging regulators in horticultural crops. TRENDS IN PLANT SCIENCE 2022; 27:936-951. [PMID: 35466027 DOI: 10.1016/j.tplants.2022.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 05/24/2023]
Abstract
Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.
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Affiliation(s)
- Meiying He
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjin Kong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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17
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OCTOPUS regulates BIN2 to control leaf curvature in Chinese cabbage. Proc Natl Acad Sci U S A 2022; 119:e2208978119. [PMID: 35969746 PMCID: PMC9407555 DOI: 10.1073/pnas.2208978119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heading is one of the most important agronomic traits for Chinese cabbage crops. During the heading stage, leaf axial growth is an essential process. In the past, most genes predicted to be involved in the heading process have been based on leaf development studies in Arabidopsis. No genes that control leaf axial growth have been mapped and cloned via forward genetics in Chinese cabbage. In this study, we characterize the inward curling mutant ic1 in Brassica rapa ssp. pekinensis and identify a mutation in the OCTOPUS (BrOPS) gene by map-based cloning. OPS is involved in phloem differentiation in Arabidopsis, a functionalization of regulating leaf curvature that is differentiated in Chinese cabbage. In the presence of brassinosteroid (BR) at the early heading stage in ic1, the mutation of BrOPS fails to sequester brassinosteroid insensitive 2 (BrBIN2) from the nucleus, allowing BrBIN2 to phosphorylate and inactivate BrBES1, which in turn relieves the repression of BrAS1 and results in leaf inward curving. Taken together, the results of our findings indicate that BrOPS positively regulates BR signaling by antagonizing BrBIN2 to promote leaf epinastic growth at the early heading stage in Chinese cabbage.
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18
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Xin Y, Tan C, Wang C, Wu Y, Huang S, Gao Y, Wang L, Wang N, Liu Z, Feng H. BrAN contributes to leafy head formation by regulating leaf width in Chinese cabbage ( Brassica rapa L. ssp. pekinensis). HORTICULTURE RESEARCH 2022; 9:uhac167. [PMID: 36204207 PMCID: PMC9531340 DOI: 10.1093/hr/uhac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 06/16/2023]
Abstract
Leafy head is an important agronomic trait that determines the yield and quality of Chinese cabbage. The molecular mechanism underlying heading in Chinese cabbage has been the focus of research, and wide leaves are a prerequisite for leafy head formation. In our study, two allelic leafy heading-deficient mutants (lhd1 and lhd2) with narrow leaf phenotypes were screened in an ethyl methanesulfonate mutagenized population from a heading Chinese cabbage double haploid line 'FT'. Genetic analysis revealed that the mutant trait was controlled by a recessive nuclear gene, which was found to be BraA10g000480.3C by MutMap and Kompetitive allele-specific PCR analyses. As BraA10g000480.3C was the ortholog of ANGUSTIFOLIA in Arabidopsis, which has been found to regulate leaf width by controlling cortical microtubule arrangement and pavement cell shape, we named it BrAN. BrAN in mutant lhd1 carried an SNP (G to A) on intron 2 that co-segregated with the mutant phenotype, and disrupted the exon-intron splice junction generating intron retention and a putative truncated protein. BrAN in mutant lhd2 carried an SNP (G to A) on exon 4 leading to a premature stop codon. The ectopic overexpression of BrAN restored normal leaf phenotype due to abnormal cortical microtubule arrangement and pavement cell shape in the Arabidopsis an-t1 mutant. However, transformation of Bran did not rescue the an-t1 phenotype. These results indicate that BrAN contributes to leafy head formation of Chinese cabbage.
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Affiliation(s)
| | | | - Che Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yanji Wu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Shengnan Huang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Gao
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lu Wang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Nan Wang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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19
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Gao Y, Qu G, Huang S, Liu Z, Fu W, Zhang M, Feng H. BrCPS1 Function in Leafy Head Formation Was Verified by Two Allelic Mutations in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:889798. [PMID: 35903226 PMCID: PMC9315314 DOI: 10.3389/fpls.2022.889798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
The formation of the leafy heads of Chinese cabbage is an important agricultural factor because it directly affects yield. In this study, we identified two allelic non-heading mutants, nhm4-1 and nhm4-2, from an ethyl methanesulfonate mutagenic population of a heading Chinese cabbage double haploid line "FT." Using MutMap, Kompetitive Allele-Specific PCR genotyping, and map-based cloning, we found that BraA09g001440.3C was the causal gene for the mutants. BraA09g001440.3C encodes an ent-copalyl diphosphate synthase 1 involved in gibberellin biosynthesis. A single non-synonymous SNP in the seventh and fourth exons of BraA09g001440.3C was responsible for the nhm4-1 and nhm4-2 mutant phenotypes, respectively. Compared with the wild-type "FT," the gibberellin content in the mutant leaves was significantly reduced. Both mutants showed a tendency to form leafy heads after exogenous GA3 treatment. The two non-heading mutants and the work presented herein demonstrate that gibberellin is related to leafy head formation in Chinese cabbage.
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Affiliation(s)
- Yue Gao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Gaoyang Qu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Shengnan Huang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Wei Fu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Meidi Zhang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hui Feng
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, Shenyang, China
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Huang S, Gao Y, Xue M, Xu J, Liao R, Shang S, Yang X, Zhao Y, Li C, Liu Z, Feng H. BrKAO2 mutations disrupt leafy head formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2453-2468. [PMID: 35726066 DOI: 10.1007/s00122-022-04126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The role of BrKAO2 in leafy head formation was confirmed by using two allelic Chinese cabbage mutants. Chinese cabbage yield and quality are determined by leafy head formation. Cloning and characterising the key genes regulating leafy head formation are essential for its varietal improvement. We used an EMS-mutagenised population of the heading type 'FT' Chinese cabbage line and identified two allelic non-heading mutants, i.e. nhm3-1 and nhm3-2. Genetic analysis showed that the mutant trait was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping revealed that BraA05g012440.3C was the candidate gene, which encodes ent-kaurenoic acid oxidase 2 in gibberellin (GA) biosynthetic pathway. It was named BrKAO2. Two non-synonymous mutations in the second BrKAO2 exon, respectively, accounted for the mutant phenotypes of nhm3-1 and nhm3-2. BrKAO2 was expressed during all leaf development stages, and there were no significant differences between the wild type and mutants in terms of BrKAO2 expression. The mutant phenotypes were restored to the wild type via exogenous GA3 application. RNA-Seq was performed on wild-type 'FT', nhm3-1, and nhm3-1 + GA3 rosette leaves, and several key genes involved in GA biosynthesis, signal transduction, and leafy head development were identified. These findings indicate that BrKAO2 is responsible for the leafy head formation in nhm3 mutants.
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Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Meihui Xue
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Junjie Xu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Ruiqi Liao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shayu Shang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Xiaofei Yang
- Integrated Department, Wafangdian Agriculture Technology and Popularization Center, Dalian, 116300, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chengyu Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China.
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21
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Yue X, Su T, Xin X, Li P, Wang W, Yu Y, Zhang D, Zhao X, Wang J, Sun L, Jin G, Yu S, Zhang F. The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 13:918112. [PMID: 35755702 PMCID: PMC9224592 DOI: 10.3389/fpls.2022.918112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.
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Affiliation(s)
- Xiaozhen Yue
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiao Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Liling Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Guihua Jin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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22
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Tang Y, Gao X, Cui Y, Xu H, Yu J. 植物TCP转录因子研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Zhang K, Yang Y, Wu J, Liang J, Chen S, Zhang L, Lv H, Yin X, Zhang X, Zhang Y, Zhang L, Zhang Y, Freeling M, Wang X, Cheng F. A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:688-706. [PMID: 35118736 PMCID: PMC9314147 DOI: 10.1111/tpj.15695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 05/10/2023]
Abstract
Leaf heading is an important and economically valuable horticultural trait in many vegetables. The formation of a leafy head is a specialized leaf morphogenesis characterized by the emergence of the enlarged incurving leaves. However, the transcriptional regulation mechanisms underlying the transition to leaf heading remain unclear. We carried out large-scale time-series transcriptome assays covering the major vegetative growth phases of two headingBrassica crops, Chinese cabbage and cabbage, with the non-heading morphotype Taicai as the control. A regulatory transition stage that initiated the heading process is identified, accompanied by a developmental switch from rosette leaf to heading leaf in Chinese cabbages. This transition did not exist in the non-heading control. Moreover, we reveal that the heading transition stage is also conserved in the cabbage clade. Chinese cabbage acquired through domestication a leafy head independently from the origins of heading in other cabbages; phylogenetics supports that the ancestor of all cabbages is non-heading. The launch of the transition stage is closely associated with the ambient temperature. In addition, examination of the biological activities in the transition stage identified the ethylene pathway as particularly active, and we hypothesize that this pathway was targeted for selection for domestication to form the heading trait specifically in Chinese cabbage. In conclusion, our findings on the transcriptome transition that initiated the leaf heading in Chinese cabbage and cabbage provide a new perspective for future studies of leafy head crops.
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Affiliation(s)
- Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Shumin Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Xiaona Yin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yiyue Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Michael Freeling
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCAUSA
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
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24
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Guo X, Liang J, Lin R, Zhang L, Wu J, Wang X. Series-Spatial Transcriptome Profiling of Leafy Head Reveals the Key Transition Leaves for Head Formation in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 12:787826. [PMID: 35069646 PMCID: PMC8770947 DOI: 10.3389/fpls.2021.787826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 05/12/2023]
Abstract
Chinese cabbage is an important leaf heading vegetable crop. At the heading stage, its leaves across inner to outer show significant morphological differentiation. However, the genetic control of this complex leaf morphological differentiation remains unclear. Here, we reported the transcriptome profiling of Chinese cabbage plant at the heading stage using 24 spatially dissected tissues representing different regions of the inner to outer leaves. Genome-wide transcriptome analysis clearly separated the inner leaf tissues from the outer leaf tissues. In particular, we identified the key transition leaf by the spatial expression analysis of key genes for leaf development and sugar metabolism. We observed that the key transition leaves were the first inwardly curved ones. Surprisingly, most of the heading candidate genes identified by domestication selection analysis obviously showed a corresponding expression transition, supporting that key transition leaves are related to leafy head formation. The key transition leaves were controlled by a complex signal network, including not only internal hormones and protein kinases but also external light and other stimuli. Our findings provide new insights and the rich resource to unravel the genetic control of heading traits.
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25
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Xu P, Zhu Y, Zhang Y, Jiang J, Yang L, Mu J, Yu X, He Y. Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed. Front Genet 2021; 12:741858. [PMID: 34594365 PMCID: PMC8476912 DOI: 10.3389/fgene.2021.741858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.
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Affiliation(s)
- Pengfei Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yantao Zhu
- Hybrid Rape Research Center of Shaanxi Province, Yangling, China
| | - Yanfeng Zhang
- Hybrid Rape Research Center of Shaanxi Province, Yangling, China
| | - Jianxia Jiang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liyong Yang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianxin Mu
- Hybrid Rape Research Center of Shaanxi Province, Yangling, China
| | - Xiang Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
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26
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Wang R, Yang X, Guo S, Wang Z, Zhang Z, Fang Z. MiR319-targeted OsTCP21 and OsGAmyb regulate tillering and grain yield in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1260-1272. [PMID: 33838011 DOI: 10.1111/jipb.13097] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/08/2021] [Indexed: 05/21/2023]
Abstract
Multiple genes and microRNAs (miRNAs) improve grain yield by promoting tillering. MiR319s are known to regulate several aspects of plant development; however, whether miR319s are essential for tillering regulation remains unclear. Here, we report that miR319 is highly expressed in the basal part of rice plant at different development stages. The miR319 knockdown line Short Tandem Target Mimic 319 (STTM319) showed higher tiller bud length in seedlings under low nitrogen (N) condition and higher tiller bud number under high N condition compared with the miR319a-overexpression line. Through targets prediction, we identified OsTCP21 and OsGAmyb as downstream targets of miR319. Moreover, OsTCP21 and OsGAmyb overexpression lines and STTM319 had increased tiller bud length and biomass, whereas both were decreased in OsTCP21 and OsGAmyb knockout lines and OE319a. These data suggest that miR319 regulates rice tiller bud development and tillering through targeting OsTCP21 and OsGAmyb. Notably, the tiller number and grain yield increased in STTM319 and overexpression lines of OsTCP21 and OsGAmyb but decreased in OE319a and knockout lines of OsTCP21 and OsGAmyb. Taken together, our findings indicate that miR319s negatively affect tiller number and grain yield by targeting OsTCP21 and OsGAmyb, revealing a novel function for miR319 in rice.
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Affiliation(s)
- Rongna Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Xiuyan Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China
| | - Shuang Guo
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhaohui Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhongming Fang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China
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27
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Bhatia N, Runions A, Tsiantis M. Leaf Shape Diversity: From Genetic Modules to Computational Models. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:325-356. [PMID: 34143649 DOI: 10.1146/annurev-arplant-080720-101613] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the importance of the genetic control of the amount, duration, and direction of cellular growth for the emergence of leaf form. We highlight how the combined use of live imaging and computational frameworks can help conceptualize how regulated cellular growth is translated into different leaf shapes. In particular, we focus on the morphogenetic differences between simple and complex leaves and how carnivorous plants form three-dimensional insect traps. We discuss how evolution has shaped leaf diversity in the case of complex leaves, by tinkering with organ-wide growth and local growth repression, and in carnivorous plants, by modifying the relative growth of the lower and upper sides of the leaf primordium to create insect-digesting traps.
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Affiliation(s)
- Neha Bhatia
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Adam Runions
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Current affiliation: Department of Computer Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
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28
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Kawakatsu Y, Sakamoto T, Nakayama H, Kaminoyama K, Igarashi K, Yasugi M, Kudoh H, Nagano AJ, Yano K, Kubo N, Notaguchi M, Kimura S. Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan. HORTICULTURE RESEARCH 2021; 8:132. [PMID: 34059655 PMCID: PMC8167115 DOI: 10.1038/s41438-021-00569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/09/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna.
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Affiliation(s)
- Yaichi Kawakatsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Hokuto Nakayama
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kaori Kaminoyama
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Kaori Igarashi
- School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Masaki Yasugi
- Faculty of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi, 321-8585, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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29
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Dong W, Ren W, Wang X, Mao Y, He Y. MicroRNA319a regulates plant resistance to Sclerotinia stem rot. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3540-3553. [PMID: 33606883 DOI: 10.1093/jxb/erab070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
MicroRNA319a (miR319a) controls cell division arrest in plant leaves by inhibiting the expression of TCP (TEOSINTE BRANCHED 1/CYCLOIDEA/PCF) family genes. However, it is unclear whether miR319a influences infection by necrotrophic pathogens and host susceptibility. In this study, we revealed that miR319a affects plant resistance to stem rot disease caused by Sclerotinia sclerotiorum. In Brassica rapa plants infected with S. sclerotiorum, miR319a levels increased while the expression levels of several BraTCP genes significantly decreased compared with those of uninfected plants. Overexpression of BraMIR319a in B. rapa increased the susceptibility of the plants to S. sclerotiorum and aggravated stem rot disease, whereas overexpression of BraTCP4-1 promoted plant resistance. RNA sequencing data revealed a potential relationship between miR319a and pathogen-related WRKY genes. Chromatin immunoprecipitation, electrophoretic mobility shift, and reporter transaction assays showed that BraTCP4-1 could bind to the promoters of WRKY75, WRKY70, and WRKY33 and directly activate these pathogen-related genes. Moreover, the expression levels of WRKY75, WRKY70, and WRKY33 in plants overexpressing BraMIR319a decreased significantly, whereas those of plants overexpressing BraTCP4-1 increased significantly, relative to the wild type. These results suggest that miR319a and its target gene BraTCP4 control stem rot resistance through pathways of WRKY genes.
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Affiliation(s)
- Weiguo Dong
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Ren
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanfei Mao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuke He
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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30
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Sun X, Gao Y, Lu Y, Zhang X, Luo S, Li X, Liu M, Feng D, Gu A, Chen X, Xuan S, Wang Y, Shen S, Bonnema G, Zhao J. Genetic analysis of the "head top shape" quality trait of Chinese cabbage and its association with rosette leaf variation. HORTICULTURE RESEARCH 2021; 8:106. [PMID: 33931629 PMCID: PMC8087666 DOI: 10.1038/s41438-021-00541-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
The agricultural and consumer quality of Chinese cabbage is determined by its shape. The shape is defined by the folding of the heading leaves, which defines the head top shape (HTS). The overlapping HTS, in which the heading leaves curve inward and overlap at the top, is the shape preferred by consumers. To understand the genetic regulation of HTS, we generated a large segregating F2 population from a cross between pak choi and Chinese cabbage, with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading leaves. HTS was correlated with plant height, outer/rosette leaf length, and petiole length. A high-density genetic map was constructed. Quantitative trait locus (QTL) analysis resulted in the identification of 22 QTLs for leafy head-related traits, which included five HTS QTLs. Bulked segregant analysis (BSA) was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide polymorphisms. Interestingly, the HTS QTLs colocalized with QTLs for plant height, outer/rosette leaf, and petiole length, consistent with the observed phenotypic correlations. Combined QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.
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Affiliation(s)
- Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xing Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Guusje Bonnema
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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31
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Karamat U, Sun X, Li N, Zhao J. Genetic regulators of leaf size in Brassica crops. HORTICULTURE RESEARCH 2021; 8:91. [PMID: 33931619 PMCID: PMC8087820 DOI: 10.1038/s41438-021-00526-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/03/2021] [Accepted: 02/24/2021] [Indexed: 05/06/2023]
Abstract
Leaf size influences plant development and biomass and is also an important agricultural trait in Brassica crops, in which leaves are the main organ produced for consumption. Leaf size is determined by the coordinated regulation of cell proliferation and cell expansion during leaf development, and these processes are strictly controlled by various integrated signals from the intrinsic regulatory network and the growth environment. Understanding the molecular mechanism of leaf size control is a prerequisite for molecular breeding for crop improvement purposes. Although research on leaf size control is just beginning in Brassica, recent studies have identified several genes and QTLs that are important in leaf size regulation. These genes have been proposed to influence leaf growth through different pathways and mechanisms, including phytohormone biosynthesis and signaling, transcription regulation, small RNAs, and others. In this review, we summarize the current findings regarding the genetic regulators of leaf size in Brassica and discuss future prospects for this research.
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Affiliation(s)
- Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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32
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Zhang Y, Liang J, Cai X, Chen H, Wu J, Lin R, Cheng F, Wang X. Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology. HORTICULTURE RESEARCH 2021; 8:68. [PMID: 33790228 PMCID: PMC8012600 DOI: 10.1038/s41438-021-00504-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/28/2020] [Accepted: 01/17/2021] [Indexed: 05/26/2023]
Abstract
The leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and breeding. BREVIS RADIX (BRX) has been suggested to control root elongation, shoot growth, and tiller angle in Arabidopsis and rice. In Brassica rapa, three BrBRX homoeologs have been identified, but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions, indicating their functional diversification in leafy head formation. Here, we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications, motif compositions and expression patterns. Moreover, although the expression of these three BrBRX genes differed, compared with BrBRX.3, BrBRX.1, and BrBRX.2 displayed similar expression patterns. Arabidopsis mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype, whereas BrBRX.2 and BrBRX.3 could not. However, overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes, including epinastic leaf morphology, with an increase in leaf number and leaf petiole length and a reduction in leaf angle. These leaf traits are associated with leafy head formation. Further testing of a SNP (T/C) in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of B. rapa. Our results revealed that all three BrBRX genes may be involved in the leaf-heading trait, but they may have functionally diverged on the basis of their differential expression.
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Affiliation(s)
- Yuanyuan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China.
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33
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Fang Y, Zheng Y, Lu W, Li J, Duan Y, Zhang S, Wang Y. Roles of miR319-regulated TCPs in plant development and response to abiotic stress. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.cj.2020.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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Yu C, Yan C, Liu Y, Liu Y, Jia Y, Lavelle D, An G, Zhang W, Zhang L, Han R, Larkin RM, Chen J, Michelmore RW, Kuang H. Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce. Proc Natl Acad Sci U S A 2020; 117:33668-33678. [PMID: 33288708 PMCID: PMC7776633 DOI: 10.1073/pnas.2019698117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.
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Affiliation(s)
- Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Chenghuan Yan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yuling Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yali Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Dean Lavelle
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Guanghui An
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Lei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Rongkui Han
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China;
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35
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Li Y, Liu GF, Ma LM, Liu TK, Zhang CW, Xiao D, Zheng HK, Chen F, Hou XL. A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. HORTICULTURE RESEARCH 2020; 7:212. [PMID: 33372175 PMCID: PMC7769993 DOI: 10.1038/s41438-020-00449-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/28/2020] [Accepted: 12/09/2020] [Indexed: 05/12/2023]
Abstract
Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gao-Feng Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li-Ming Ma
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang-Wei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Fei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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36
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Gao Y, Huang S, Qu G, Fu W, Zhang M, Liu Z, Feng H. The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURE RESEARCH 2020; 7:178. [PMID: 33328441 PMCID: PMC7603516 DOI: 10.1038/s41438-020-00399-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/23/2020] [Accepted: 08/30/2020] [Indexed: 05/26/2023]
Abstract
The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage. A non-heading mutant (nhm1) was identified in an ethyl methanesulfonate mutagenesis population of the heading Chinese cabbage double haploid line FT. Segregation analysis revealed that a single recessive gene, Brnhm1, controlled the mutant phenotype. Using MutMap, Kompetitive allele-specific PCR, and cloning analyses, we demonstrated that BraA07g042410.3C, which encodes an ent-kaurene synthase involved in the gibberellin biosynthesis pathway, is the nhm1 mutant candidate gene. A single-nucleotide mutation (C to T) in the fourth exon of BraA07g042410.3C caused an amino acid substitution from histidine to tyrosine. Compared to that of the wild-type FT, BraA07g042410.3C in the leaves of the nhm1 mutant had lower levels of expression. In addition, gibberellin contents were lower in the mutant than in the wild type, and the mutant plant phenotype could be restored to that of the wild type after exogenous GA3 treatment. These results indicate that BraA07g042410.3C caused the non-heading mutation. This is the first study to demonstrate a relationship between gibberellin content in the leaves and leafy head formation in Chinese cabbage. These findings facilitate the understanding of the mechanisms underlying leafy head development in Chinese cabbage.
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Affiliation(s)
- Yue Gao
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Shengnan Huang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Gaoyang Qu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Wei Fu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Meidi Zhang
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Zhiyong Liu
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China
| | - Hui Feng
- Liaoning Key Laboratory of Genetics and Breeding for Cruciferous Vegetable Crops, College of Horticulture, Shenyang Agricultural University, 110866, Shenyang, China.
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37
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Fine mapping of a leaf flattening gene Bralcm through BSR-Seq in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Sci Rep 2020; 10:13924. [PMID: 32811880 PMCID: PMC7435182 DOI: 10.1038/s41598-020-70975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/03/2020] [Indexed: 11/09/2022] Open
Abstract
Leaf flattening influences plant photosynthesis, thereby affecting product yield and quality. Here, we obtained a stably inherited leaf crinkled mutant (lcm), derived from the Chinese cabbage doubled haploid (DH) ‘FT’ line using EMS mutagenesis combined with isolated microspore culture. The crinkled phenotype was controlled by a single recessive nuclear gene, namely Bralcm, which was preliminarily mapped to chromosome A01 by bulked segregant analysis RNA-seq, and further between markers SSRS-1 and IndelD-20 using 1,575 recessive homozygous individuals in F2 population by a map-based cloning method. The target region physical distance was 126.69 kb, containing 23 genes; the marker SSRMG-4 co-segregated with the crinkled trait. Further, we found SSRMG-4 to be located on BraA01g007510.3C, a homolog of AHA2, which encodes H+-ATPase2, an essential enzyme in plant growth and development. Sequence analysis indicated a C to T transition in exon 7 of BraA01g007510.3C, resulting in a Thr (ACT) to Ile (ATT) amino acid change. Genotyping revealed that the leaf crinkled phenotype fully co-segregated with this SNP within the recombinants. qRT-PCR demonstrated that BraA01g007510.3C expression in lcm mutant leaves was dramatically higher than that in wild-type ‘FT’. Thus, BraA01g007510.3C is a strong candidate gene for Bralcm, and AHA2 is possibly associated with leaf flattening in Chinese cabbage.
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Gao Y, Lu Y, Li X, Li N, Zhang X, Su X, Feng D, Liu M, Xuan S, Gu A, Wang Y, Chen X, Zhao J, Shen S. Development and Application of SSR Markers Related to Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Front Genet 2020; 11:773. [PMID: 32793286 PMCID: PMC7391075 DOI: 10.3389/fgene.2020.00773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
In Chinese cabbage (Brassica rapa L. ssp. pekinensis), leaf adaxial-abaxial (ad-ab) polarity is tightly related to leaf incurvature, an essential factor for the formation of leafy heads. Therefore, identification of the genes responsible for leaf ad-ab polarity and studying their genetic variation may clarify the mechanism of leafy head formation. By comparing the sequences of the genes regulating leaf ad-ab polarity development in Arabidopsis thaliana (A. thaliana), 41 candidate genes distributed on 10 chromosomes were found to be responsible for the establishment of ad-ab polarity in Chinese cabbage. Orthologous genes, including 10 single copies, 14 double copies, and one triple copies, were detected in the Chinese cabbage. The gene structure and conserved domain analyses showed that the number of exons of the 41 candidate genes range from one to 25, and that most genes share the conserved motifs 1, 6, and 10. Based on the 41 candidate genes, 341 simple sequence repeats (SSRs) were detected, including five replicated types: single, double, triple, quintuple, and sextuple nucleotide replications. Among these sequence repeat (SSR) loci, 323 loci were used to design 969 specific primers, and 362 primer pairs were selected randomly and evaluated using 12 Chinese cabbage accessions with different heading types. 23 primer pairs resulting with clear, polymorphic bands, combined with other 127 markers, was used to construct a linkage map by using an F2 population containing 214 lines derived from the hybrid of the overlapping heading Chinese cabbage “14Q-141” and the outward curling heading Chinese cabbage “14Q-279.” The result showed that the sequences of markers in the genetic linkage map and the physical map was consistent in general. Our study could help to accelerate the breeding process of leafy head quality in Chinese cabbage.
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Affiliation(s)
- Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China.,Agriculture and Rural Affairs Bureau of Xindu District, Xingtai, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaoguang Li
- Institute of Forestry and Fruits, Xingtai Academy of Agricultural Sciences, Xingtai, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiangjie Su
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
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The Regulation of CIN-like TCP Transcription Factors. Int J Mol Sci 2020; 21:ijms21124498. [PMID: 32599902 PMCID: PMC7349945 DOI: 10.3390/ijms21124498] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 01/07/2023] Open
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1 and 2 (TCP) family proteins are the plant-specific transcription factors extensively participating in diverse developmental processes by integrating external cues with internal signals. The roles of CINCINNATA (CIN)-like TCPs are conserved in control of the morphology and size of leaves, petal development, trichome formation and plant flowering. The tight regulation of CIN-like TCP activity at transcriptional and post-transcriptional levels are central for plant developmental plasticity in response to the ever-changing environmental conditions. In this review, we summarize recent progresses with regard to the function and regulation of CIN-like TCPs. CIN-like TCPs are regulated by abiotic and biotic cues including light, temperature and pathogens. They are also finely controlled by microRNA319 (miRNA319), chromatin remodeling complexes and auxin homeostasis. The protein degradation plays critical roles in tightly controlling the activity of CIN-like TCPs as well.
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Ren W, Wu F, Bai J, Li X, Yang X, Xue W, Liu H, He Y. BcpLH organizes a specific subset of microRNAs to form a leafy head in Chinese cabbage ( Brassica rapa ssp. pekinensis). HORTICULTURE RESEARCH 2020; 7:1. [PMID: 31908804 PMCID: PMC6938484 DOI: 10.1038/s41438-019-0222-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/07/2019] [Accepted: 10/24/2019] [Indexed: 05/18/2023]
Abstract
HYL1 (HYPONASTIC LEAVES 1) in Arabidopsis thaliana encodes a double-stranded RNA-binding protein needed for proper miRNA maturation, and its null mutant hyl1 shows a typical leaf-incurvature phenotype. In Chinese cabbage, BcpLH (Brassica rapa ssp. pekinensis LEAFY HEADS), a close homolog of HYL1, is differentially expressed in juvenile leaves, which are flat, and in adult leaves, which display extreme incurvature. BcpLH lacks protein-protein interaction domains and is much shorter than HYL1. To test whether BcpLH is associated with defects in microRNA (miRNA) biogenesis and leaf flatness, we enhanced and repressed the activity of BcpLH by transgenics and investigated BcpLH-dependent miRNAs and plant morphology. BcpLH promoted miRNA biogenesis by the proper processing of primary miRNAs. BcpLH downregulation via antisense decreased a specific subset of miRNAs and increased the activities of their target genes, causing upward curvature of rosette leaves and early leaf incurvature, concurrent with the enlargement, earliness, and round-to-oval shape transition of leafy heads. Moreover, BcpLH-dependent miRNAs in Chinese cabbage are not the same as HYL1-dependent miRNAs in Arabidopsis. We suggest that BcpLH controls a specific subset of miRNAs in Chinese cabbage and coordinates the direction, extent, and timing of leaf curvature during head formation in Brassica rapa.
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Affiliation(s)
- Wenqing Ren
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
- Graduate School of the Chinese Academy of Sciences, Shanghai, 200032 China
| | - Feijie Wu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Jinjuan Bai
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Xiaorong Li
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Xi Yang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Wanxin Xue
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Heng Liu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Yuke He
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
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Jiu S, Xu Y, Wang J, Wang L, Wang S, Ma C, Guan L, Abdullah M, Zhao M, Xu W, Ma W, Zhang C. Genome-Wide Identification, Characterization, and Transcript Analysis of the TCP Transcription Factors in Vitis vinifera. Front Genet 2019; 10:1276. [PMID: 31921312 PMCID: PMC6934063 DOI: 10.3389/fgene.2019.01276] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/19/2019] [Indexed: 11/16/2022] Open
Abstract
The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) protein, belonging to a plant-specific transcription factors (TFs) family, participates in the control of plant growth and development by regulating cell proliferation. Until now, a comprehensive study of concerning the TCP gene family and their roles in grapevine (Vitis vinifera L.) has not been completed. Using bioinformatics approaches, 17 VvTCP genes were identified and further classified into two classes, designated class I (PCF subclass) and class II (CIN and CYC/TB1 subclass), which was further supported by exon-intron organizations and conserved motif analysis. Promoter analysis demonstrated that VvTCPs have numerous cis-acting elements related to plant growth and development, phytohormone, and abiotic/biotic stress responses. The singleton duplication of grapevine TCP genes contributed to this gene family expansion. The syntenic analyses among Vitis vinifera, Arabidopsis, and Oryza sativa showed that these genes located in corresponding syntenic blocks arose before the divergence of V. vinifera, Arabidopsis, and O. sativa. The expression levels of 17 VvTCPs were determined in different tissues and fruit developmental stages, and abscisic acid (ABA) treatment. Seventeen VvTCPs exhibited distinct tissue-specific expression patterns, potentially illustrating the functional divergence of VvTCPs in all tested tissues. Eleven VvTCPs were down-regulated in five berry developmental stages, while three VvTCPs were up-regulated. Additionally, many members were strongly modulated by ABA treatment, suggesting these VvTCPs have important and diverse regulatory roles in ABA treatment. Our results provide valuable information on the evolution and functions of the VvTCPs, pave the way for further functional verification of these VvTCPs in grapevine.
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Affiliation(s)
- Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Le Guan
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Maoxiang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenli Ma
- Agricultural Technology Extension and Service Center of Ningxia Agricultural Reclamation Management Bureau, Yinchuan, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Li R, Hou Z, Gao L, Xiao D, Hou X, Zhang C, Yan J, Song L. Conjunctive Analyses of BSA-Seq and BSR-Seq to Reveal the Molecular Pathway of Leafy Head Formation in Chinese Cabbage. PLANTS (BASEL, SWITZERLAND) 2019; 8:E603. [PMID: 31847231 PMCID: PMC6963953 DOI: 10.3390/plants8120603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/23/2022]
Abstract
As the storage organ of Chinese cabbage, the leafy head was harvested as a commercial product due to its edible value. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-Seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of leafy head formation in Chinese cabbage. BSA-Seq analysis located four candidate regions containing 40 candidate genes, while BSR-Seq analysis revealed eight candidate regions containing 607 candidate genes. The conjunctive analyses of these two methods identified that Casein kinase gene BrCKL8 (Bra035974) is the common candidate gene related with leafy head formation in Chinese cabbage, and it showed high expression levels at the three segments of heading type plant leaves. The differentially expressed genes (DEGs) between two set pairs of cDNA sequencing bulks were divided into two categories: one category was related with five hormone pathways (Auxin, Ethylene, Abscisic acid, Jasmonic acid and Gibberellin), the other category was composed of genes that associate with the calcium signaling pathway. Moreover, a series of upregulated transcriptional factors (TFs) were also identified by the association analysis of BSR-Seq analysis. The leafy head development was regulated by various biological processes and effected by diverse external environment factors, so our research will contribute to the breeding of perfect leaf-heading types of Chinese cabbage.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Zhongle Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Liwei Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (Z.H.); (L.G.); (D.X.); (X.H.)
| | - Jiyong Yan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
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Song M, Cheng F, Wang J, Wei Q, Fu W, Yu X, Li J, Chen J, Lou Q. A leaf shape mutant provides insight into PINOID Serine/Threonine Kinase function in cucumber (Cucumis sativus L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1000-1014. [PMID: 30421569 DOI: 10.1111/jipb.12739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/08/2018] [Indexed: 05/10/2023]
Abstract
Optimizing leaf shape is a major challenge in efforts to develop an ideal plant type. Cucumber leaf shapes are diverse; however, the molecular regulatory mechanisms underlying leaf shape formation are unknown. In this study, we obtained a round leaf mutant (rl) from an ethyl methanesulfonate-induced mutagenesis population. Genetic analysis revealed that a single recessive gene, rl, is responsible for this mutation. A modified MutMap analysis combined linkage mapping identified a single nucleotide polymorphism within a candidate gene, Csa1M537400, as the mutation underlying the trait. Csa1M537400 encodes a PINOID kinase protein involved in auxin transport. Expression of Csa1M537400 was significantly lower in the rl mutant than in wild type, and it displayed higher levels of IAA (indole-3-acetic acid) in several tissues. Treatment of wild-type plants with an auxin transport inhibitor induced the formation of round leaves, similar to those in the rl mutant. Altered expression patterns of several auxin-related genes in the rl mutant suggest that rl plays a key role in auxin biosynthesis, transport, and response in cucumber. These findings provide insight into the molecular mechanism underlying the regulation of auxin signaling pathways in cucumber, and will be valuable in the development of an ideal plant type.
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Affiliation(s)
- Mengfei Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingzhen Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyuan Fu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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He Y, Bonnema G, Xiao H, Zhao Y. Editorial: Organ Modification for Edible Parts of Horticultural Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:961. [PMID: 31396254 PMCID: PMC6664054 DOI: 10.3389/fpls.2019.00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Yuke He
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, United States
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Yu J, Gao L, Liu W, Song L, Xiao D, Liu T, Hou X, Zhang C. Transcription Coactivator ANGUSTIFOLIA3 (AN3) Regulates Leafy Head Formation in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2019; 10:520. [PMID: 31114598 PMCID: PMC6502973 DOI: 10.3389/fpls.2019.00520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 04/04/2019] [Indexed: 05/24/2023]
Abstract
Leafy head formation in Chinese cabbage (B. rapa ssp. pekinensis cv. Bre) results from leaf curvature, which is under the tight control of genes involved in the adaxial-abaxial patterning during leaf development. The transcriptional coactivator ANGUSTIFOLIA3 (AN3) binds to the SWI/SNF chromatin remodeling complexes formed around ATPases such as BRAHMA (BRM) in order to regulate transcription in various aspects of leaf development such as cell proliferation, leaf primordia expansion, and leaf adaxial/abaxial patterning in Arabidopsis. However, its regulatory function in Chinese cabbage remains poorly understood. Here, we analyzed the expression patterns of the Chinese cabbage AN3 gene (BrAN3) before and after leafy head formation, and produced BrAN3 gene silencing plants by using the turnip yellow mosaic virus (TYMV)-derived vector in order to explore its potential function in leafy head formation in Chinese cabbage. We found that BrAN3 had distinct expression patterns in the leaves of Chinese cabbage at the rosette and heading stages. We also found silencing of BrAN3 stimulated leafy head formation at the early stage. Transcriptome analysis indicated that silencing of BrAN3 modulated the hormone signaling pathways of auxin, ethylene, GA, JA, ABA, BR, CK, and SA in Chinese cabbage. Our study offers unique insights into the function of BrAN3 in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwei Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Abuyusuf M, Nath UK, Kim HT, Islam MR, Park JI, Nou IS. Molecular markers based on sequence variation in BoFLC1.C9 for characterizing early- and late-flowering cabbage genotypes. BMC Genet 2019; 20:42. [PMID: 31029104 PMCID: PMC6487051 DOI: 10.1186/s12863-019-0740-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cabbage (Brassica oleracea var. capitata) is popular worldwide for consumption as a leafy vegetable. Premature flowering is triggered by low temperature, and deteriorates quality of cabbage as vegetable. In general, growers prefer late-flowering varieties to assure good quality compact head. Here, we report BoFLC1.C9 as a gene with clear sequence variation between cabbage lines with different flowering times, and proposed as molecular marker to characterize early- and late-flowering cabbage lines. RESULTS We identified sequence variation of 67 bp insertions in intron 2, which were contributed in flowering time variation between two inbred lines through rapid down-regulation of the BoFLC1.C9 gene in early-flowering line compared to late-flowering one upon vernalization. One set of primer 'F7R7' proposed as marker, of which was explained with 83 and 80% of flowering time variation in 141 F2 individuals and 20 commercial lines, respectively. CONCLUSIONS This F7R7 marker could be used as genetic tools to characterize flowering time variation and to select as well to develop early- and late-flowering cabbage cultivars.
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Affiliation(s)
- Md Abuyusuf
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Agronomy, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Md Rafiqul Islam
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
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Zhang Q, Zhang Y, Wang S, Hao L, Wang S, Xu C, Jiang F, Li T. Characterization of genome-wide microRNAs and their roles in development and biotic stress in pear. PLANTA 2019; 249:693-707. [PMID: 30368557 DOI: 10.1007/s00425-018-3027-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Using a genome-wide analysis of miRNAs in 'Yali' pear (Pyrus bretschneideri) via the next-generation high-throughput sequencing of small RNAs with a bioinformatics analysis, we found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 and their target genes function in viral defense in 'Duli' and 'Hongbaoshi'. pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319 and their targets function in auxin signaling pathways in 'Zhongai 4' and 'Zhongai 5'. Successful fruit production in pear (Pyrus spp.) depends on the use of optimal combinations of rootstocks and scions. Deciphering plant-pathogen defense mechanisms and hormone signaling pathways is an important step towards developing pear rootstocks and varieties with improved qualities. In the current study, we combined next-generation sequencing of small RNAs with a bioinformatics analysis to systematically identify and characterize 298 miRNAs in the pear scion cultivar 'Yali' (Pyrus bretschneideri). We also analyzed miRNAs in three rootstock varieties ('Duli', 'Zhongai 4', and 'Zhongai 5') and one scion cultivar ('Hongbaoshi'). We found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 are induced following infection with the pear virus Apple stem pitting virus (ASPV), and identified their target genes (pbRPS6, pbNAC, pbTLR, and pbRX-CC, respectively), which participate in viral defense pathways in 'Duli' and 'Hongbaoshi'. Furthermore, we identified pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319, and found that the production of these miRNAs was suppressed under low levels of synthetic auxin. The targets of these miRNAs (pbARF, pbAEC, pbSCL, and pbTCP4) respond to auxin signaling pathways in 'Zhongai 4' and 'Zhongai 5'. Our results lay the foundation for breeding improved pear cultivars.
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Affiliation(s)
- Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Jiang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Li J, Zhang X, Lu Y, Feng D, Gu A, Wang S, Wu F, Su X, Chen X, Li X, Liu M, Fan S, Feng D, Luo S, Xuan S, Wang Y, Shen S, Zhao J. Characterization of Non-heading Mutation in Heading Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2019; 10:112. [PMID: 30809236 PMCID: PMC6379458 DOI: 10.3389/fpls.2019.00112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/23/2019] [Indexed: 05/26/2023]
Abstract
Heading is a key agronomic trait of Chinese cabbage. A non-heading mutant with flat growth of heading leaves (fg-1) was isolated from an EMS-induced mutant population of the heading Chinese cabbage inbred line A03. In fg-1 mutant plants, the heading leaves are flat similar to rosette leaves. The epidermal cells on the adaxial surface of these leaves are significantly smaller, while those on the abaxial surface are much larger than in A03 plants. The segregation of the heading phenotype in the F2 and BC1 population suggests that the mutant trait is controlled by a pair of recessive alleles. Phytohormone analysis at the early heading stage showed significant decreases in IAA, ABA, JA and SA, with increases in methyl IAA and trans-Zeatin levels, suggesting they may coordinate leaf adaxial-abaxial polarity, development and morphology in fg-1. RNA-sequencing analysis at the early heading stage showed a decrease in expression levels of several auxin transport (BrAUX1, BrLAXs, and BrPINs) and responsive genes. Transcript levels of important ABA responsive genes, including BrABF3, were up-regulated in mid-leaf sections suggesting that both auxin and ABA signaling pathways play important roles in regulating leaf heading. In addition, a significant reduction in BrIAMT1 transcripts in fg-1 might contribute to leaf epinastic growth. The expression profiles of 19 genes with known roles in leaf polarity were significantly different in fg-1 leaves compared to wild type, suggesting that these genes might also regulate leaf heading in Chinese cabbage. In conclusion, leaf heading in Chinese cabbage is controlled through a complex network of hormone signaling and abaxial-adaxial patterning pathways. These findings increase our understanding of the molecular basis of head formation in Chinese cabbage.
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Affiliation(s)
- Jingrui Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaomeng Zhang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Lu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Dongxiao Feng
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Aixia Gu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shan Wang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Fang Wu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiangjie Su
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xing Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Mengyang Liu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxi Fan
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Daling Feng
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxia Luo
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxin Xuan
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yanhua Wang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
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Sun X, Basnet RK, Yan Z, Bucher J, Cai C, Zhao J, Bonnema G. Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage ( Brassica rapa). HORTICULTURE RESEARCH 2019; 6:130. [PMID: 31814983 PMCID: PMC6885048 DOI: 10.1038/s41438-019-0212-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 10/19/2019] [Indexed: 05/10/2023]
Abstract
Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.
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Affiliation(s)
- XiaoXue Sun
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Ram Kumar Basnet
- Quantitative genetics department, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS The Netherlands
| | - Zhichun Yan
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Guusje Bonnema
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
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