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Liu B, Shen CC, Xia SW, Song SS, Su LH, Li Y, Hao Q, Liu YJ, Guan DL, Wang N, Wang WJ, Zhao X, Li HX, Li XX, Lai YS. A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation. PLANT PHYSIOLOGY 2024; 195:970-985. [PMID: 38478469 DOI: 10.1093/plphys/kiae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 06/02/2024]
Abstract
The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.
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Affiliation(s)
- Bin Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, 830091 Urumqi, China
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cheng-Cheng Shen
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Shi-Wei Xia
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Shan-Shan Song
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Li-Hong Su
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Qian Hao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yan-Jun Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Dai-Lu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ning Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Wen-Jiao Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Xiang Zhao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Huan-Xiu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Xi-Xiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100080 Beijing, China
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
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Xie Q, Zhang Y, Wu M, Chen Y, Wang Y, Zeng Q, Han Y, Zhang S, Zhang J, Chen T, Cai M. Identification and Functional Analysis of KH Family Genes Associated with Salt Stress in Rice. Int J Mol Sci 2024; 25:5950. [PMID: 38892138 PMCID: PMC11172612 DOI: 10.3390/ijms25115950] [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: 03/17/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Salinity stress has a great impact on crop growth and productivity and is one of the major factors responsible for crop yield losses. The K-homologous (KH) family proteins play vital roles in regulating plant development and responding to abiotic stress in plants. However, the systematic characterization of the KH family in rice is still lacking. In this study, we performed genome-wide identification and functional analysis of KH family genes and identified a total of 31 KH genes in rice. According to the homologs of KH genes in Arabidopsis thaliana, we constructed a phylogenetic tree with 61 KH genes containing 31 KH genes in Oryza sativa and 30 KH genes in Arabidopsis thaliana and separated them into three major groups. In silico tissue expression analysis showed that the OsKH genes are constitutively expressed. The qRT-PCR results revealed that eight OsKH genes responded strongly to salt stresses, and OsKH12 exhibited the strongest decrease in expression level, which was selected for further study. We generated the Oskh12-knockout mutant via the CRISPR/Cas9 genome-editing method. Further stress treatment and biochemical assays confirmed that Oskh12 mutant was more salt-sensitive than Nip and the expression of several key salt-tolerant genes in Oskh12 was significantly reduced. Taken together, our results shed light on the understanding of the KH family and provide a theoretical basis for future abiotic stress studies in rice.
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Affiliation(s)
- Qinyu Xie
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yutong Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Youheng Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingwei Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Qinzong Zeng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuliang Han
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Siqi Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Juncheng Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Maohong Cai
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
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Song Z, Chen H, Lai X, Wang L, Yao Y, Qin J, Pang X, Zhu H, Chen W, Li X, Zhu X. The Zinc Finger Protein MaCCCH33-Like2 Positively Regulates Banana Fruit Ripening by Modulating Genes in Starch and Cell Wall Degradation. PLANT & CELL PHYSIOLOGY 2024; 65:49-67. [PMID: 37767757 DOI: 10.1093/pcp/pcad115] [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: 07/12/2023] [Revised: 08/31/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023]
Abstract
As zinc finger protein transcription factors (TFs), the molecular mechanism of Cys-Cys-Cys-His (CCCH) TFs in regulating plant development, growth and stress response has been well studied. However, the roles of CCCH TFs in fruit ripening are still obscure. Herein, we report that MaCCCH33-like2 TF and its associated proteins modulate the fruit softening of 'Fenjiao' bananas. MaCCCH33-like2 interacts directly with the promoters of three genes: isoamylase2 (MaISA2), sugar transporter14-like (MaSUR14-like) and β-d-xylosidase23 (MaXYL23), all of which are responsible for encoding proteins involved in the degradation of starch and cell wall components. Additionally, MaCCCH33-like2 forms interactions with abscisic acid-insensitive 5 (ABI5)-like and ethylene F-box protein 1 (MaEBF1), resulting in enhanced binding and activation of promoters of genes related to starch and cell wall degradation. When MaCCCH33-like2 is transiently and ectopically overexpressed in 'Fenjiao' banana and tomato fruit, it facilitates softening and ripening processes by promoting the degradation of cell wall components and starch and the production of ethylene. Conversely, the temporary silencing of MaCCCH33-like2 using virus-induced gene silencing (VIGS) inhibits softening and ripening in the 'Fenjiao' banana by suppressing ethylene synthesis, as well as starch and cell wall degradation. Furthermore, the promoter activity of MaCCCH33-like2 is regulated by MaABI5-like. Taken together, we have uncovered a novel MaCCCH33-like2/MaEBF1/MaABI5-like module that participates in fruit softening regulation in bananas.
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Affiliation(s)
- Zunyang Song
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Hangcong Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiuhua Lai
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Lihua Wang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yulin Yao
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiajia Qin
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xuequn Pang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hong Zhu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weixin Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xueping Li
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
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Yang J, Xue H, Li Z, Zhang Y, Shi T, He X, Barrett SCH, Wang Q, Chen J. Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica. THE NEW PHYTOLOGIST 2023; 240:2058-2071. [PMID: 37717220 DOI: 10.1111/nph.19264] [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: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.
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Affiliation(s)
- Jingshan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Zhizhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiangyan He
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
| | - Qingfeng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
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5
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Coe K, Bostan H, Rolling W, Turner-Hissong S, Macko-Podgórni A, Senalik D, Liu S, Seth R, Curaba J, Mengist MF, Grzebelus D, Van Deynze A, Dawson J, Ellison S, Simon P, Iorizzo M. Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots. NATURE PLANTS 2023; 9:1643-1658. [PMID: 37770615 PMCID: PMC10581907 DOI: 10.1038/s41477-023-01526-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.
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Affiliation(s)
- Kevin Coe
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - William Rolling
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | | | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Douglas Senalik
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | - Su Liu
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Romit Seth
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Molla Fentie Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, CA, USA
| | - Julie Dawson
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shelby Ellison
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Philipp Simon
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA.
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA.
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA.
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Jun SE, Shim JS, Park HJ. Beyond NPK: Mineral Nutrient-Mediated Modulation in Orchestrating Flowering Time. PLANTS (BASEL, SWITZERLAND) 2023; 12:3299. [PMID: 37765463 PMCID: PMC10535918 DOI: 10.3390/plants12183299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Flowering time in plants is a complex process regulated by environmental conditions such as photoperiod and temperature, as well as nutrient conditions. While the impact of major nutrients like nitrogen, phosphorus, and potassium on flowering time has been well recognized, the significance of micronutrient imbalances and their deficiencies should not be neglected because they affect the floral transition from the vegetative stage to the reproductive stage. The secondary major nutrients such as calcium, magnesium, and sulfur participate in various aspects of flowering. Micronutrients such as boron, zinc, iron, and copper play crucial roles in enzymatic reactions and hormone biosynthesis, affecting flower development and reproduction as well. The current review comprehensively explores the interplay between microelements and flowering time, and summarizes the underlying mechanism in plants. Consequently, a better understanding of the interplay between microelements and flowering time will provide clues to reveal the roles of microelements in regulating flowering time and to improve crop reproduction in plant industries.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea;
| | - Jae Sun Shim
- School of Biological Science and Technology, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hee Jin Park
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:12888. [PMID: 37629069 PMCID: PMC10454627 DOI: 10.3390/ijms241612888] [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: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.
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Affiliation(s)
- Zeyi Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Zhijiang Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xinyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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8
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Xiong X, Li J, Su P, Duan H, Sun L, Xu S, Sun Y, Zhao H, Chen X, Ding D, Zhang X, Tang J. Genetic dissection of maize (Zea mays L.) chlorophyll content using multi-locus genome-wide association studies. BMC Genomics 2023; 24:384. [PMID: 37430212 DOI: 10.1186/s12864-023-09504-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The chlorophyll content (CC) is a key factor affecting maize photosynthetic efficiency and the final yield. However, its genetic basis remains unclear. The development of statistical methods has enabled researchers to design and apply various GWAS models, including MLM, MLMM, SUPER, FarmCPU, BLINK and 3VmrMLM. Comparative analysis of their results can lead to more effective mining of key genes. RESULTS The heritability of CC was 0.86. Six statistical models (MLM, BLINK, MLMM, FarmCPU, SUPER, and 3VmrMLM) and 1.25 million SNPs were used for the GWAS. A total of 140 quantitative trait nucleotides (QTNs) were detected, with 3VmrMLM and MLM detecting the most (118) and fewest (3) QTNs, respectively. The QTNs were associated with 481 genes and explained 0.29-10.28% of the phenotypic variation. Additionally, 10 co-located QTNs were detected by at least two different models or methods, three co-located QTNs were identified in at least two different environments, and six co-located QTNs were detected by different models or methods in different environments. Moreover, 69 candidate genes within or near these stable QTNs were screened based on the B73 (RefGen_v2) genome. GRMZM2G110408 (ZmCCS3) was identified by multiple models and in multiple environments. The functional characterization of this gene indicated the encoded protein likely contributes to chlorophyll biosynthesis. In addition, the CC differed significantly between the haplotypes of the significant QTN in this gene, and CC was higher for haplotype 1. CONCLUSION This study's results broaden our understanding of the genetic basis of CC, mining key genes related to CC and may be relevant for the ideotype-based breeding of new maize varieties with high photosynthetic efficiency.
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Affiliation(s)
- Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Pingping Su
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haidong Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyang Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
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9
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Xu J, Huang Z, Du H, Tang M, Fan P, Yu J, Zhou Y. SEC1-C3H39 module fine-tunes cold tolerance by mediating its target mRNA degradation in tomato. THE NEW PHYTOLOGIST 2023; 237:870-884. [PMID: 36285381 DOI: 10.1111/nph.18568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Plants adapt to cold stress at the physiological and biochemical levels, thus enabling them to maintain growth and development. However, the molecular mechanism of fine-tuning cold signals remains largely unknown. We addressed the function of SlSEC1-SlC3H39 module in cold tolerance by using SlSEC1 and SlC3H39 knockout and overexpression tomato lines. A tandem CCCH zinc-finger protein SlC3H39 negatively modulates cold tolerance in tomato. SlC3H39 binds to AU-rich elements in the 3'-untranslated region (UTR) to induce mRNA degradation and regulates gene expression post-transcriptionally. We further validate that SlC3H39 participates in post-transcriptional regulation of a variety of cold-responsive genes. An O-linked N-acetylglucosamine transferase SlSEC1 physically interacts with SlC3H39 proteins and negatively regulates cold tolerance in tomato. Further study shows that SlSEC1 is essential for SlC3H39 protein stability and maintains SlC3H39 function in cold tolerance. Genetic analysis shows that SlC3H39 is epistatic to SlSEC1 in cold tolerance. The findings indicate that SlC3H39 negatively modulates plant cold tolerance through post-transcriptional regulation by binding to cold-responding mRNA 3'-UTR and reducing those transcripts. SlSEC1 promotes the O-GlcNAclation status of SlC3H39 and maintains SlC3H39 function in cold tolerance. Taken together, we propose a SlSEC1-SlC3H39 module, which allows plants to balance defense responses and growth processes.
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Affiliation(s)
- Jin Xu
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zelan Huang
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hongyu Du
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mingjia Tang
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Pengxiang Fan
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Yanhong Zhou
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, China
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10
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Li S, Xie H, Zhou L, Dong D, Liu Y, Jia C, Han L, Chao Y, Chen Y. Overexpression of MsSAG113 gene promotes leaf senescence in alfalfa via participating in the hormone regulatory network. FRONTIERS IN PLANT SCIENCE 2022; 13:1085497. [PMID: 36570962 PMCID: PMC9774027 DOI: 10.3389/fpls.2022.1085497] [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: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Introduction Alfalfa (Medicago sativa) is a kind of high quality leguminous forage species, which was widely cultivated in the world. Leaf senescence is an essential process in plant development and life cycle. Here, we reported the isolation and functional analysis of an alfalfa SENESCENCE-ASSOCIATED GENE113 (MsSAG113), which belongs to the PP2C family and mainly plays a role in promoting plant senescence. Methods In the study, Agrobacterium-mediated, gene expression analysis, next generation sequencing, DNA pull-down, yeast single hybridization and transient expression were used to identify the function of MsSAG113 gene. Results The MsSAG113 gene was isolated from alfalfa, and the transgenic plants were obtained by Agrobacterium-mediated method. Compared with the wildtype, transgenic plants showed premature senescence in leaves, especially when cultivated under dark conditions. Meanwhile, application of exogenous hormones ABA, SA, MeJA, obviously acclerated leaf senescence of transgenic plants. Furthermore, the detached leaves from transgenic plants turned yellow earlier with lower chlorophyll content. Transcriptome analysis identified a total of 1,392 differentially expressed genes (DEGs), involving 13 transcription factor families. Of which, 234 genes were related to phytohormone synthesis, metabolism and transduction. Pull-down assay and yeast one-hybrid assay confirmed that alfalfa zinc finger CCCH domain-containing protein 39 (MsC3H-39) could directly bind the upstream of MsSAG113 gene. In conclusion, the MsSAG113 gene plays a crucial role in promoting leaf senescence in alfalfa via participating in the hormone regulatory network. Discussion This provides an essential basis for further analysis on the regulatory network involving senescence-associated genes in alfalfa.
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Affiliation(s)
- Shuwen Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Hong Xie
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Lingfang Zhou
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yaling Liu
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yinglong Chen
- The University of Western Australia (UWA) Institute of Agriculture, and University of Western Australia School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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11
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Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms232315363. [PMID: 36499688 PMCID: PMC9735588 DOI: 10.3390/ijms232315363] [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: 10/30/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans.
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12
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Liang N, Cheng D, Zhao L, Lu H, Xu L, Bi Y. Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris. Genes (Basel) 2022; 13:genes13122217. [PMID: 36553484 PMCID: PMC9778101 DOI: 10.3390/genes13122217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.
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Affiliation(s)
- Naiguo Liang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
- Correspondence:
| | - Dayou Cheng
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Li Zhao
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Hedong Lu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Lei Xu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Yanhong Bi
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
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13
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López-Ruiz BA, Quezada-Rodríguez EH, Piñeyro-Nelson A, Tovar H, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length. PLANTS (BASEL, SWITZERLAND) 2022; 11:3162. [PMID: 36432890 PMCID: PMC9697774 DOI: 10.3390/plants11223162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elsa H. Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Hugo Tovar
- División de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México 14610, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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14
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Wang W, Wang S, Gong W, Lv L, Xu L, Nie J, Huang L. Valsa mali secretes an effector protein VmEP1 to target a K homology domain-containing protein for virulence in apple. MOLECULAR PLANT PATHOLOGY 2022; 23:1577-1591. [PMID: 35851537 PMCID: PMC9562843 DOI: 10.1111/mpp.13248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The K homology (KH) repeat is an RNA-binding motif that exists in various proteins, some of which participate in plant growth. However, the function of KH domain-containing proteins in plant defence is still unclear. In this study, we found that a KH domain-containing protein in apple (Malus domestica), HEN4-like (MdKRBP4), is involved in the plant immune response. Silencing of MdKRBP4 compromised reactive oxygen species (ROS) production and enhanced the susceptibility of apple to Valsa mali, whereas transient overexpression of MdKRBP4 stimulated ROS accumulation in apple leaves, indicating that MdKRBP4 is a positive immune regulator. Additionally, MdKRBP4 was proven to interact with the VmEP1 effector secreted by V. mali, which led to decreased accumulation of MdKRBP4. Coexpression of MdKRBP4 with VmEP1 inhibited cell death and ROS production induced by MdKRBP4 in Nicotiana benthamiana. These results indicate that MdKRBP4 functions as a novel positive regulatory factor in plant immunity in M. domestica and is a virulence target of the V. mali effector VmEP1.
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Affiliation(s)
- Weidong Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shuaile Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Wan Gong
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Luqiong Lv
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jiajun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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15
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Transcriptome-Wide Identification of CCCH-Type Zinc Finger Proteins Family in Pinus massoniana and RR-TZF Proteins in Stress Response. Genes (Basel) 2022; 13:genes13091639. [PMID: 36140811 PMCID: PMC9498899 DOI: 10.3390/genes13091639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
CCCH-type zinc finger proteins play an important role in multiple biotic and abiotic stresses. More and more reports about CCCH functions in plant development and stress responses have appeared over the past few years, focusing especially on tandem CCCH zinc finger proteins (TZFs). However, this has not been reported in Pinaceae. In this study, we identified 46 CCCH proteins, including 6 plant TZF members in Pinus massoniana, and performed bioinformatic analysis. According to RT-PCR analysis, we revealed the expression patterns of five RR-TZF genes under different abiotic stresses and hormone treatments. Meanwhile, tissue-specific expression analysis suggested that all genes were mainly expressed in needles. Additionally, RR-TZF genes showed transcriptional activation activity in yeast. The results in this study will be beneficial in improving the stress resistance of P. massoniana and facilitating further studies on the biological and molecular functions of CCCH zinc finger proteins.
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16
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Liu C, Leng J, Li Y, Ge T, Li J, Chen Y, Guo C, Qi J. A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Res 2022; 50:9724-9737. [PMID: 36095130 PMCID: PMC9508851 DOI: 10.1093/nar/gkac773] [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: 05/03/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Leng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yonglong Li
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Tingting Ge
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Jinglong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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17
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Sasi JM, Gupta S, Singh A, Kujur A, Agarwal M, Katiyar-Agarwal S. Know when and how to die: gaining insights into the molecular regulation of leaf senescence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1515-1534. [PMID: 36389097 PMCID: PMC9530073 DOI: 10.1007/s12298-022-01224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.
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Affiliation(s)
- Jyothish Madambikattil Sasi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Apurva Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Alice Kujur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- USDA-ARS Plant Genetics Research Unit, The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Centre of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324 India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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18
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Wang M, Zhang H, Dai S, Feng S, Gong S, Wang J, Zhou A. AaZFP3, a Novel CCCH-Type Zinc Finger Protein from Adonis amurensis, Promotes Early Flowering in Arabidopsis by Regulating the Expression of Flowering-Related Genes. Int J Mol Sci 2022; 23:ijms23158166. [PMID: 35897742 PMCID: PMC9332444 DOI: 10.3390/ijms23158166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 02/05/2023] Open
Abstract
CCCH-type zinc finger proteins (ZFP) are a large family of proteins that play various important roles in plant growth and development; however, the functions of most proteins in this family are uncharacterized. In this study, a CCCH-type ZFP, AaZFP3, was identified in the floral organ of Adonis amurensis. Quantitative real-time PCR (qPCR) analysis revealed that AaZFP3 was widely expressed in the flowers of A.amurensis. Subcellular localization analysis showed that the AaZFP3 protein was mainly localized to the cytoplasm in tobacco and Arabidopsis. Furthermore, the overexpression of AaZFP3 promoted early flowering in Arabidopsis under both normal and relatively low-temperature conditions. RNA-sequencing and qPCR analyses revealed that the expression of multiple key flowering-time genes was altered in transgenic Arabidopsis overexpressing AaZFP3 compared to wild-type. Of these genes, FLOWERING LOCUS T (AtFT) expression was most significantly up-regulated, whereas FLOWERING LOCUS C (AtFLC) was significantly down-regulated. These results suggest that the overexpression of AaZFP3 promotes early flowering in Arabidopsis by affecting the expression of flowering-time genes. Overall, our study indicates that AaZFP3 may be involved in flowering regulation in A.amurensis and may represent an important genetic resource for improving flowering-time control in other ornamental plants or crops.
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19
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Ji X, Li J, Niu J, Mao R, Cao F, Li M. DiZF-C3H1, a zinc finger transcription factor from the dove tree (Davidia involucrata Baill.), plays a negative role in seed development and plant growth in Arabidopsis and tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111248. [PMID: 35487657 DOI: 10.1016/j.plantsci.2022.111248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 05/15/2023]
Abstract
Low seed fertility seriously limits the survival and adaption of rare plant species. Here, we identified a seed-specific gene, DiZF-C3H1, from the dove tree and verified its function. Overexpression of DiZF-C3H1 caused retarded root development, delayed anthesis, abnormal floral organs, and deformed siliques in transgenic Arabidopsis lines. No offspring were obtained in transgenic Arabidopsis lines due to serious seed abortion. Therefore, we performed further verification in tobacco. Similarly, overexpression of DiZF-C3H1 retarded root development and reduced berry size and seed yield in transgenic tobacco lines. Moreover, although transgenic tobacco offspring were obtained, the viability of transgenic seeds was reduced and their germination was delayed. In addition, faded flowers were observed in transgenic tobacco lines. Taken together, DiZF-C3H1 was verified to play a negative role in root growth, floral organ development, and especially seed development in Arabidopsis and tobacco. This appears to be a deleterious gene for these model plants with high seed fertility. However, this function might be of special significance for Davidia, whose seed dormancy period is extremely long; DiZF-C3H1 might play a critical role in the distinctive reproduction strategy adopted by this rare and endangered species.
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Affiliation(s)
- Xiaomin Ji
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jian Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jie Niu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Rongjie Mao
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Fuxiang Cao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410004, China
| | - Meng Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China.
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Khan SU, Zheng Y, Chachar Z, Zhang X, Zhou G, Zong N, Leng P, Zhao J. Dissection of Maize Drought Tolerance at the Flowering Stage Using Genome-Wide Association Studies. Genes (Basel) 2022; 13:genes13040564. [PMID: 35456369 PMCID: PMC9031386 DOI: 10.3390/genes13040564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Drought is one of the most critical environmental factors constraining maize production. When it occurs at the flowering stage, serious yield losses are caused, and often, the damage is irretrievable. In this study, anthesis to silk interval (ASI), plant height (PH), and ear biomass at the silking date (EBM) of 279 inbred lines were studied under both water-stress (WS) and well-water (WW) field conditions, for three consecutive years. Averagely, ASI was extended by 25.96%, EBM was decreased by 17.54%, and the PH was reduced by 12.47% under drought stress. Genome-wide association studies were carried out using phenotypic values under WS, WW, and drought-tolerance index (WS-WW or WS/WW) and applying a mixed linear model that controls both population structure and relative kinship. In total, 71, 159, and 21 SNPs, located in 32, 59, and 12 genes, were significantly (P < 10−5) associated with ASI, EBM, and PH, respectively. Only a few overlapped candidate genes were found to be associated with the same drought-related traits under different environments, for example, ARABIDILLO 1, glycoprotein, Tic22-like, and zinc-finger family protein for ASI; 26S proteasome non-ATPase and pyridoxal phosphate transferase for EBM; 11-ß-hydroxysteroid dehydrogenase, uncharacterised, Leu-rich repeat protein kinase, and SF16 protein for PH. Furthermore, most candidate genes were revealed to be drought-responsive in an association panel. Meanwhile, the favourable alleles/key variations were identified with a haplotype analysis. These candidate genes and their key variations provide insight into the genetic basis of drought tolerance, especially for the female inflorescence, and will facilitate drought-tolerant maize breeding.
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Affiliation(s)
- Siffat Ullah Khan
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Yanxiao Zheng
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Zaid Chachar
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Xuhuan Zhang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Guyi Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Na Zong
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Pengfei Leng
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
- Correspondence: (P.L.); (J.Z.)
| | - Jun Zhao
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
- Correspondence: (P.L.); (J.Z.)
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21
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Ai Q, Pan W, Zeng Y, Li Y, Cui L. CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis. BMC PLANT BIOLOGY 2022; 22:117. [PMID: 35291942 PMCID: PMC8922935 DOI: 10.1186/s12870-022-03500-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. RESULTS In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.
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Affiliation(s)
- Qi Ai
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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22
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Seok HY, Kim T, Lee SY, Moon YH. Non-TZF Transcriptional Activator AtC3H12 Negatively Affects Seed Germination and Seedling Development in Arabidopsis. Int J Mol Sci 2022; 23:1572. [PMID: 35163496 PMCID: PMC8835867 DOI: 10.3390/ijms23031572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/09/2022] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
CCCH zinc finger proteins are a large protein family and are classified as either tandem CCCH zinc finger (TZF) or non-TZF proteins. The roles of TZF genes in several plants have been well determined, whereas the functions of many non-TZF genes in plants remain uncharacterized. Herein, we describe biological and molecular functions of AtC3H12, an Arabidopsis non-TZF protein containing three CCCH zinc finger motifs. AtC3H12 has orthologs in several plant species but has no paralog in Arabidopsis. AtC3H12-overexpressing transgenic plants (OXs) germinated slower than wild-type (WT) plants, whereas atc3h12 mutants germinated faster than WT plants. The fresh weight (FW) and primary root lengths of AtC3H12 OX seedlings were lighter and shorter than those of WT seedlings, respectively. In contrast, FW and primary root lengths of atc3h12 seedlings were heavier and longer than those of WT seedlings, respectively. AtC3H12 was localized in the nucleus and displayed transactivation activity in both yeast and Arabidopsis. We found that the 97-197 aa region of AtC3H12 is an important part for its transactivation activity. Detection of expression levels and analysis of Arabidopsis transgenic plants harboring a PAtC3H12::GUS construct showed that AtC3H12 expression increases as the Arabidopsis seedlings develop. Taken together, our results demonstrate that AtC3H12 negatively affects seed germination and seedling development as a nuclear transcriptional activator in Arabidopsis. To our knowledge, this is the first report to show that non-TZF proteins negatively affect plant development as nuclear transcriptional activators.
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Affiliation(s)
- Hye-Yeon Seok
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Taehyoung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
| | - Sun-Young Lee
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Yong-Hwan Moon
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
- Department of Molecular Biology, Pusan National University, Busan 46241, Korea
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23
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Overexpression of CpWRKY75 from Chimonanthus praecox Promotes Flowering Time in Transgenic Arabidopsis. Genes (Basel) 2021; 13:genes13010068. [PMID: 35052409 PMCID: PMC8774968 DOI: 10.3390/genes13010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors play critical roles in the physiological processes of plants. Although the roles of WRKYs have been characterized in some model plants, their roles in woody plants, especially wintersweet (Chimonanthus praecox), are largely unclear. In this study, a wintersweet WRKY gene named CpWRKY75 belonging to group IIc was isolated and its characteristics were identified. CpWRKY75 is a nucleus-localized protein, and exhibited no transcriptional activation activity in yeast. CpWRKY75 was highly expressed in flowers at different bloom stages. Ectopic expression of CpWRKY75 significantly promoted the flowering time of transgenic Arabidopsis (Arabidopsis thaliana), as determined by the rosette leaf number and first flower open time. The expression levels of flowering-related genes were quantified by qRT-PCR, and the results suggested that CpWRKY75 had obvious influence on the expression level of MICRORNA156C (MIR156C), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), FLOWERING LOCUS T (FT), LEAFY (LFY), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), APETALA1 (AP1), CAULIFLOWER (CAL), and FRUITFULL (FUL). These results suggest that CpWRKY75 might have a flowering time regulation function, and additionally provide a new gene resource for the genetic engineering of woody flowering plants.
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24
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Lo S, Parker T, Muñoz-Amatriaín M, Berny-Mier Y Teran JC, Jernstedt J, Close TJ, Gepts P. Genetic, anatomical, and environmental patterns related to pod shattering resistance in domesticated cowpea [Vigna unguiculata (L.) Walp]. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6219-6229. [PMID: 34106233 DOI: 10.1093/jxb/erab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/06/2021] [Indexed: 05/27/2023]
Abstract
Pod shattering, which causes the explosive release of seeds from the pod, is one of the main sources of yield losses in cowpea in arid and semi-arid areas. Reduction of shattering has therefore been a primary target for selection during domestication and improvement of cowpea, among other species. Using a mini-core diversity panel of 368 cowpea accessions, four regions with a statistically significant association with pod shattering were identified. Two genes (Vigun03g321100 and Vigun11g100600), involved in cell wall biosynthesis, were identified as strong candidates for pod shattering. Microscopic analysis was conducted on a subset of accessions representing the full spectrum of shattering phenotypes. This analysis indicated that the extent of wall fiber deposition was highly correlated with shattering. The results from this study also demonstrate that pod shattering in cowpea is exacerbated by arid environmental conditions. Finally, using a subset of West African landraces, patterns of historical selection for shattering resistance related to precipitation in the environment of origin were identified. Together, these results shed light on sources of resistance to pod shattering, which will, in turn, improve climate resilience of a major global nutritional staple.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Travis Parker
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523,USA
| | | | - Judy Jernstedt
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
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25
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Han G, Qiao Z, Li Y, Wang C, Wang B. The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms22158327. [PMID: 34361093 PMCID: PMC8347928 DOI: 10.3390/ijms22158327] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 01/07/2023] Open
Abstract
Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.
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Affiliation(s)
- Guoliang Han
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
| | | | | | | | - Baoshan Wang
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
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26
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Xie Z, Yu G, Lei S, Zhang C, Huang B. CCCH protein-PvCCCH69 acted as a repressor for leaf senescence through suppressing ABA-signaling pathway. HORTICULTURE RESEARCH 2021; 8:165. [PMID: 34234106 PMCID: PMC8263708 DOI: 10.1038/s41438-021-00604-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 05/19/2023]
Abstract
CCCH is a subfamily of zinc finger proteins involved in plant growth, development, and stresses response. The function of CCCH in regulating leaf senescence, especially its roles in abscisic acid (ABA)-mediated leaf senescence is largely unknown. The objective of this study was to determine functions and mechanisms of CCCH gene in regulating leaf senescence in switchgrass (Panicum virgatum). A CCCH gene, PvCCCH69 (PvC3H69), was cloned from switchgrass. Overexpressing PvC3H69 in rice suppressed both natural senescence with leaf aging and dark-induced leaf senescence. Endogenous ABA content, ABA biosynthesis genes (NCED3, NCED5, and AAO3), and ABA signaling-related genes (SnRKs, ABI5, and ABF2/3/4) exhibited significantly lower levels in senescencing leaves of PvC3H69-OE plants than those in WT plants. PvC3H69-suppression of leaf senescence was associated with transcriptional upregulation of genes mainly involved in the light-dependent process of photosynthesis, including light-harvesting complex proteins, PSI proteins, and PSII proteins and downregulation of ABA biosynthesis and signaling genes and senescence-associated genes. PvC3H69 could act as a repressor for leaf senescence via upregulating photosynthetic proteins and repressing ABA synthesis and ABA signaling pathways.
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Affiliation(s)
- Zheni Xie
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohui Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Shanshan Lei
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenchen Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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27
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Li CH, Fang QX, Zhang WJ, Li YH, Zhang JZ, Chen S, Yin ZG, Li WJ, Liu WD, Yi Z, Mu ZS, Du JD. Genome-wide identification of the CCCH gene family in rose (Rosa chinensis Jacq.) reveals its potential functions. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1901609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Cai-hua Li
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Qing-xi Fang
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Wen-Jing Zhang
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Yu-huan Li
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Jin-zhu Zhang
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Shuai Chen
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhen-Gong Yin
- Edible Bean Research Laboratory, Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, PR China
| | - Wei-Jia Li
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Wen-da Liu
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Zheng Yi
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Zhong-sheng Mu
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Ji-dao Du
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
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28
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Akhatar J, Goyal A, Kaur N, Atri C, Mittal M, Singh MP, Kaur R, Rialch I, Banga SS. Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss. Sci Rep 2021; 11:4278. [PMID: 33608616 PMCID: PMC7896068 DOI: 10.1038/s41598-021-83689-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
Timely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.
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Affiliation(s)
- Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mohini Prabha Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Indu Rialch
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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29
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Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
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Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
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Gu Q, Ke H, Liu Z, Lv X, Sun Z, Zhang M, Chen L, Yang J, Zhang Y, Wu L, Li Z, Wu J, Wang G, Meng C, Zhang G, Wang X, Ma Z. A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3395-3408. [PMID: 32894321 DOI: 10.1007/s00122-020-03676-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/21/2020] [Indexed: 05/18/2023]
Abstract
A high-density linkage map of an intraspecific RIL population was constructed using 6187 bins to identify QTLs for fibre quality- and yield-related traits in upland cotton by whole-genome resequencing. Good fibre quality and high yield are important production goals in cotton (Gossypium hirsutum L.), which is a leading natural fibre crop worldwide. However, a greater understanding of the genetic variants underlying fibre quality- and yield-related traits is still required. In this study, a large-scale population including 588 F7 recombinant inbred lines, derived from an intraspecific cross between the upland cotton cv. Nongdamian13, which exhibits high quality, and Nongda601, which exhibits a high yield, was genotyped by using 232,946 polymorphic single-nucleotide polymorphisms obtained via a whole-genome resequencing strategy with 4.3-fold genome coverage. We constructed a high-density bin linkage map containing 6187 bin markers spanning 4478.98 cM with an average distance of 0.72 cM. We identified 58 individual quantitative trait loci (QTLs) and 25 QTL clusters harbouring 94 QTLs, and 119 previously undescribed QTLs controlling 13 fibre quality and yield traits across eight environments. Importantly, the QTL counts for fibre quality in the Dt subgenome were more than two times that in the At subgenome, and chromosome D02 harboured the greatest number of QTLs and clusters. Furthermore, we discovered 24 stable QTLs for fibre quality and 12 stable QTLs for yield traits. Four novel major stable QTLs related to fibre length, fibre strength and lint percentage, and seven previously unreported candidate genes with significantly differential expression between the two parents were identified and validated by RNA-seq. Our research provides valuable information for improving the fibre quality and yield in cotton breeding.
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Affiliation(s)
- Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xing Lv
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jinhua Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
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Amkul K, Somta P, Laosatit K, Wang L. Identification of QTLs for Domestication-Related Traits in Zombi Pea [ Vigna vexillata (L.) A. Rich], a Lost Crop of Africa. Front Genet 2020; 11:803. [PMID: 33193562 PMCID: PMC7530282 DOI: 10.3389/fgene.2020.00803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
Zombi pea [Vigna vexillata (L.) A. Rich] is a legume crop found in Africa. Wild zombi pea is widely distributed throughout the tropical and subtropical regions, whereas domesticated zombi pea is rarely cultivated. Plant domestication is an evolutionary process in which the phenotypes of wild species, including seed dormancy, pod shattering, organ size, and architectural and phenological characteristics, undergo changes. The molecular mechanism underlying the domestication of zombi pea is relatively unknown. In this study, the genetic basis of the following 13 domestication-related traits was investigated in an F2 population comprising 198 individuals derived from a cross between cultivated (var. macrosperma) and wild (var. vexillata) zombi pea accessions: seed dormancy, pod shattering, days-to-flowering, days-to-maturity, stem thickness, stem length, number of branches, leaf area, pod length, 100-seed weight, seed width, seed length, and seeds per pod. A genetic map containing 6,529 single nucleotide polymorphisms constructed for the F2 population was used to identify quantitative trait loci (QTLs) for these traits. A total of 62 QTLs were identified for the 13 traits, with 1-11 QTLs per trait. The major QTLs for days-to-flowering, stem length, number of branches, pod length, 100-seed weight, seed length, and seeds per pod were clustered in linkage group 5. In contrast, the major QTLs for seed dormancy and pod shattering belonged to linkage groups 3 and 11, respectively. A comparative genomic analysis with the cowpea [Vigna unguiculata (L.) Walp.] genome used as the reference sequence (i.e., the genome of the legume species most closely related to zombi pea) enabled the identification of candidate genes for the major QTLs. Thus, we revealed the genomic regions associated with domestication-related traits and the candidate genes controlling these traits in zombi pea. The data presented herein may be useful for breeding new varieties of zombi pea and other Vigna species.
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Affiliation(s)
- Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand.,Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Cheng X, Cao J, Gao C, Gao W, Yan S, Yao H, Xu K, Liu X, Xu D, Pan X, Lu J, Chang C, Zhang H, Ma C. Identification of the wheat C3H gene family and expression analysis of candidates associated with seed dormancy and germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:524-537. [PMID: 33053501 DOI: 10.1016/j.plaphy.2020.09.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 05/01/2023]
Abstract
C3H zinc finger transcription factors play important roles in managing various biotic/abiotic stresses in Aarabidopsis, rice, and maize. The functions of these factors in wheat, however, remain largely unclear. We identified 88 TaC3H genes that were divided into four subfamilies in this analysis. Gene structure and conserved domain analyses indicate that most members of the same subfamily have similar structures. A total of 76 paralogous and 48 orthologous pairs were identified and Ka/Ks values were used to analyze replication relationships amongst wheat, rice, and Arabidopsis. Gene ontology (GO) annotation analysis showed that most TaC3H genes possessed molecular functions, while transcriptome results showed that the 88 TaC3H genes responded to water imbibition. Microarray data for 53 TaC3H genes were obtained and heat maps were generated; these results indicate that these genes are expressed in 13 wheat tissues. Subcellular localization prediction analysis indicates that most TaC3H genes are located in the nucleus. Promoter analysis indicates that most TaC3H genes contained cis-elements including ABRE, GARE-motif, and MBS, indicating that these can respond to various biotic/abiotic stresses. Transcriptome data and quantitative real-time PCR analysis of wheat cultivars with contrasting seed dormancy phenotypes show that five genes TaC3H4/-18/-37/-51/-72 were very likely involved in seed dormancy and germination. Exogenous ABA treatment further indicated that these five genes were responsive to ABA, suggesting that there may be a crosstalk between these genes and ABA signaling pathway in controlling seed dormancy and germination. These results provide a theoretical basis for subsequent studies on TaC3H gene function and also contribute to studies on the C3H gene in other species.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Chang Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Wei Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Shengnan Yan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Hui Yao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Kangle Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xue Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Dongmei Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xu Pan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
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Hinckley WE, Brusslan JA. Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis. PLANT DIRECT 2020; 4:e00279. [PMID: 33204935 PMCID: PMC7649007 DOI: 10.1002/pld3.279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/13/2020] [Accepted: 09/30/2020] [Indexed: 05/29/2023]
Abstract
In plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. The molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early-phase transition. We hypothesized that leaf gene expression changes occurring in synchrony with bolting were regulating LS. ARABIDOPSIS TRITHORAX (ATX) enzymes are general methyltransferases that regulate the adult vegetative to reproductive phase transition. We generated an atx1, atx3, and atx4 (atx1,3,4) triple T-DNA insertion mutant that displays both early bolting and early LS. This mutant was used in an RNA-seq time-series experiment to identify gene expression changes in rosette leaves that are likely associated with bolting. By comparing the early bolting mutant to vegetative WT plants of the same age, we were able to generate a list of differentially expressed genes (DEGs) that change expression with bolting as the plants age. We trimmed the list by intersection with publicly available WT datasets, which removed genes from our DEG list that were atx1,3,4 specific. The resulting 398 bolting-associated genes (BAGs) are differentially expressed in a mature rosette leaf at bolting. The BAG list contains many well-characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting-associated LS regulators may contribute to the temporal coupling of bolting time to LS.
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Affiliation(s)
| | - Judy A. Brusslan
- Department of Biological SciencesCalifornia State UniversityLong Beach, Long BeachCAUSA
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Xu L, Xiong X, Liu W, Liu T, Yu Y, Cao J. BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis. Int J Mol Sci 2020; 21:ijms21176428. [PMID: 32899329 PMCID: PMC7504113 DOI: 10.3390/ijms21176428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/19/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
Chinese cabbage (Brassica campestris) is an economically important leaf vegetable crop worldwide. Mounting studies have shown that cysteine-cysteine-cysteine-histidine (CCCH) zinc-finger protein genes are involved in various plant growth and development processes. However, research on the involvement of these genes in male reproductive development is still in its infancy. Here, we identified 11 male fertility-related CCCH genes in Chinese cabbage. Among them, a pair of paralogs encoding novel non-tandem CCCH zinc-finger proteins, Brassica campestris Male Fertility 30a (BcMF30a) and BcMF30c, were further characterized. They were highly expressed in pollen during microgametogenesis and continued to express in germinated pollen. Further analyses demonstrated that both BcMF30a and BcMF30c may play a dual role as transcription factors and RNA-binding proteins in plant cells. Functional analysis showed that partial bcmf30a bcmf30c pollen grains were aborted due to the degradation of pollen inclusion at the microgametogenesis phase, and the germination rate of viable pollen was also greatly reduced, indicating that BcMF30a and BcMF30c are required for both pollen development and pollen germination. This research provided insights into the function of CCCH proteins in regulating male reproductive development and laid a theoretical basis for hybrid breeding of Chinese cabbage.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Weimiao Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Youjian Yu
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin’an 311300, China;
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-131-8501-1958
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Yan Z, Shi H, Liu Y, Jing M, Han Y. KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1375-1386. [PMID: 31701139 PMCID: PMC7031081 DOI: 10.1093/jxb/erz499] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.
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Affiliation(s)
- Zongyun Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Correspondence:
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36
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Chen F, Liu HL, Wang K, Gao YM, Wu M, Xiang Y. Identification of CCCH Zinc Finger Proteins Family in Moso Bamboo ( Phyllostachys edulis), and PeC3H74 Confers Drought Tolerance to Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:579255. [PMID: 33240298 PMCID: PMC7680867 DOI: 10.3389/fpls.2020.579255] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/12/2020] [Indexed: 05/12/2023]
Abstract
CCCH zinc finger proteins are a class of important zinc-finger transcription factors and have functions in various plant growth and stress responses, but their functions in moso bamboo (Phyllostachys edulis) are unclear. In this current study, we main investigated the structures, phylogenetic relationships, promoter elements and microsynteny of PeC3Hs. In this research, 119 CCCH zinc finger proteins (PeC3H1-119) identified genes in moso bamboo were divided into 13 subfamilies (A-M) based on phylogenetic analysis. Meanwhile, moso bamboo were treated with abscisic acid (ABA), methyl jasmonate (Me-JA) and gibberellic acid (GA) and 12 CCCH genes expression levels were assayed using qRT-PCR. In the three hormone treatments, 12 genes were up-regulated or down-regulated, respectively. In addition, PeC3H74 was localized on the cytomembrane, and it had self-activation activities. Phenotypic and physiological analysis showed that PeC3H74 (PeC3H74-OE) conferred drought tolerance of transgenic Arabidopsis, including H2O2 content, survival rate, electrolyte leakage as well as malondialdehyde content. Additionally, compared with wild-type plants, transgenic Arabidopsis thaliana seedling roots growth developed better under 10 μM ABA; Moreover, the stomatal of over-expressing PeC3H74 in Arabidopsis changed significantly under ABA treatment. The above results suggest that PeC3H74 was quickly screened by bioinformatics, and it may enhanced drought tolerance in plants through the ABA-dependent signaling pathway.
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Affiliation(s)
- Feng Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Huan-Long Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Kang Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Ya-Meng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- *Correspondence: Yan Xiang,
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Zhang H, Gao X, Zhi Y, Li X, Zhang Q, Niu J, Wang J, Zhai H, Zhao N, Li J, Liu Q, He S. A non-tandem CCCH-type zinc-finger protein, IbC3H18, functions as a nuclear transcriptional activator and enhances abiotic stress tolerance in sweet potato. THE NEW PHYTOLOGIST 2019; 223:1918-1936. [PMID: 31091337 DOI: 10.1111/nph.15925] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/08/2019] [Indexed: 05/21/2023]
Abstract
CCCH-type zinc-finger proteins play essential roles in regulating plant development and stress responses. However, the molecular and functional properties of non-tandem CCCH-type zinc-finger (non-TZF) proteins have been rarely characterized in plants. Here, we report the biological and molecular characterization of a sweet potato non-TZF gene, IbC3H18. We show that IbC3H18 exhibits tissue- and abiotic stress-specific expression, and could be effectively induced by abiotic stresses, including NaCl, polyethylene glycol (PEG) 6000, H2 O2 and abscisic acid (ABA) in sweet potato. Accordingly, overexpression of IbC3H18 led to increased, whereas knock-down of IbC3H18 resulted in decreased tolerance of sweet potato to salt, drought and oxidation stresses. In addition, IbC3H18 functions as a nuclear transcriptional activator and regulates the expression of a range of abiotic stress-responsive genes involved in reactive oxygen species (ROS) scavenging, ABA signaling, photosynthesis and ion transport pathways. Moreover, our data demonstrate that IbC3H18 physically interacts with IbPR5, and that overexpression of IbPR5 enhances salt and drought tolerance in transgenic tobacco plants. Collectively, our data indicate that IbC3H18 functions in enhancing abiotic stress tolerance in sweet potato, which may serve as a candidate gene for use in improving abiotic stress resistance in crops.
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Affiliation(s)
- Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoru Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuhai Zhi
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qian Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinbiao Niu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
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Pi B, He X, Ruan Y, Jang JC, Huang Y. Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC PLANT BIOLOGY 2018; 18:373. [PMID: 30587139 PMCID: PMC6307296 DOI: 10.1186/s12870-018-1608-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. RESULTS In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. CONCLUSION This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Xinghui He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Molecular Genetics, and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
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