1
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Cao S, Sawettalake N, Li P, Fan S, Shen L. DNA methylation variations underlie lettuce domestication and divergence. Genome Biol 2024; 25:158. [PMID: 38886807 PMCID: PMC11184767 DOI: 10.1186/s13059-024-03310-x] [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: 06/30/2023] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown. RESULTS To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop. CONCLUSION Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Nunchanoke Sawettalake
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Ping Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Sheng Fan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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2
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Byrne ME, Imlay E, Ridza NNB. Shaping leaves through TALE homeodomain transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3220-3232. [PMID: 38527334 PMCID: PMC11156807 DOI: 10.1093/jxb/erae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/24/2024] [Indexed: 03/27/2024]
Abstract
The first TALE homeodomain transcription factor gene to be described in plants was maize knotted1 (kn1). Dominant mutations in kn1 disrupt leaf development, with abnormal knots of tissue forming in the leaf blade. kn1 was found to be expressed in the shoot meristem but not in a peripheral region that gives rise to leaves. Furthermore, KN1 and closely related proteins were excluded from initiating and developing leaves. These findings were a prelude to a large body of work wherein TALE homeodomain proteins have been identified as vital regulators of meristem homeostasis and organ development in plants. KN1 homologues are widely represented across land plant taxa. Thus, studying the regulation and mechanistic action of this gene class has allowed investigations into the evolution of diverse plant morphologies. This review will focus on the function of TALE homeodomain transcription factors in leaf development in eudicots. Here, we discuss how TALE homeodomain proteins contribute to a spectrum of leaf forms, from the simple leaves of Arabidopsis thaliana to the compound leaves of Cardamine hirsuta and species beyond the Brassicaceae.
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Affiliation(s)
- Mary E Byrne
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Eleanor Imlay
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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3
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Fang X, Zhu Z, Li J, Wang X, Wei C, Zhang X, Dai Z, Liu S, Luan F. Identification of Chromosomal Regions and Candidate Genes for Round leaf Locus in Cucumis melo L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1134. [PMID: 38674543 PMCID: PMC11054961 DOI: 10.3390/plants13081134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl (Round leaf), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537.07 kb region on chromosome 8 of the melon genome. Subsequent genetic fine-mapping efforts, leveraging a larger F2 population encompassing 1322 plants and incorporating F2:3 phenotypic data, further refined the locus to an 80.27 kb interval housing five candidate genes. Promoter analysis and coding sequence cloning confirmed that one of these candidates, MELO3C019152.2 (Cmppr encoding a pentatricopeptide repeat-containing family protein, Cmppr), stands out as a strong candidate gene for the Cmrl locus. Notably, comparisons of Cmrl expressions across various stages of leaf development and different leaf regions suggest a pivotal role of Cmrl in the morphogenesis of melon leaves.
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Affiliation(s)
- Xufeng Fang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Junyan Li
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Chunhua Wei
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Xian Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Zuyun Dai
- Anhui Jianghuai Horticulture Technology Co., Ltd., Hefei 230031, China;
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
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4
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Zhou W, Yang T, Zeng L, Chen J, Wang Y, Guo X, You L, Liu Y, Du W, Yang F, Hua C, Cai J, van Hintum T, Liu H, Gu Y, Wei X, Wei T. LettuceDB: an integrated multi-omics database for cultivated lettuce. Database (Oxford) 2024; 2024:baae018. [PMID: 38557635 PMCID: PMC10984620 DOI: 10.1093/database/baae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/01/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
Crop genomics has advanced rapidly during the past decade, which generated a great abundance of omics data from multi-omics studies. How to utilize the accumulating data becomes a critical and urgent demand in crop science. As an attempt to integrate multi-omics data, we developed a database, LettuceDB (https://db.cngb.org/lettuce/), aiming to assemble multidimensional data for cultivated and wild lettuce germplasm. The database includes genome, variome, phenome, microbiome and spatial transcriptome. By integrating user-friendly bioinformatics tools, LettuceDB will serve as a one-stop platform for lettuce research and breeding in the future. Database URL: https://db.cngb.org/lettuce/.
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Affiliation(s)
- Wenhui Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Wuhan 430074, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen 518120, China
- Guangdong Genomics Data Center, BGl research, Shenzhen 518120, China
| | - Liucui Zeng
- BGI Research, Wuhan 430074, China
- South China Agricultural University, Guangzhou 510642, China
| | - Jing Chen
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Xing Guo
- BGI Research, Wuhan 430074, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Lijin You
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yiqun Liu
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Fan Yang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Cong Hua
- BGI Research, Wuhan 430074, China
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Jia Cai
- BGI Research, Wuhan 430074, China
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Theo van Hintum
- Centre for Genetic Resources, the Netherlands, P.O. Box 16, Wageningen 6700 AA, The Netherlands
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Ying Gu
- BGI Research, Wuhan 430074, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen 518120, China
- Guangdong Genomics Data Center, BGl research, Shenzhen 518120, China
| | - Tong Wei
- BGI Research, Wuhan 430074, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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5
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Xie S, Luo G, An G, Wang B, Kuang H, Wang X. Lskipk Lsatpase double mutants are necessary and sufficient for the compact plant architecture of butterhead lettuce. HORTICULTURE RESEARCH 2024; 11:uhad280. [PMID: 38371637 PMCID: PMC10873588 DOI: 10.1093/hr/uhad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/11/2023] [Indexed: 02/20/2024]
Abstract
Lettuce, an important leafy vegetable crop worldwide, has rich variations in plant architecture. Butterhead lettuce, a popular horticultural type, has a unique plant architecture with loose leafy heads. The genetic and molecular mechanisms for such a compact plant architecture remain unclear. In this study we constructed a segregating population through crossing a butterhead cultivar and a stem lettuce cultivar. Genetic analysis identified the LsKIPK gene, which encodes a kinase, as the candidate gene controlling butterhead plant architecture. The Lskipk gene in the butterhead parent had a nonsense mutation, leading to a partial predicted protein. CRISPR/Cas9 and complementation tests verified its functions in plant architecture. We showed that the loss of function of LsKIPK is necessary but not sufficient for the butterhead plant architecture. To identify additional genes required for butterhead lettuce, we crossed a butterhead cultivar and a crisphead cultivar, both with the mutated Lskipk gene. Genetic mapping identified a new gene encoding an ATPase contributing to butterhead plant architecture. Knockout and complementation tests showed that loss of function of LsATPase is also required for the development of butterhead plant architecture. The Lskipk Lsatpase double mutation could reduce leaf size and leaf angle, leading to butterhead plant architecture. Expression and cytology analysis indicated that the loss of function of LsKIPK and LsATPase contributed to butterhead plant architecture by regulating cell wall development, a regulatory mechanism different from that for crisphead. This study provides new gene resources and theory for the breeding of the crop ideotype.
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Affiliation(s)
- Sai Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guangbao Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guanghui An
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- College of Horticulture, Henan Agricultural University, 450002 Zhengzhou, China
| | - Bincai Wang
- North Park, Wuhan Academy of Agricultural Sciences, Wuhu Eco-park, Huangpi District, Wuhan, China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
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6
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Zong X, Liu Y, Lin X, He D, Dong Z, Guo T, Li J, Li H, Wang F. Foliar spraying of lanthanum activates endocytosis in lettuce (Lactuca sativa L.) root cells, increasing Cd and Pb accumulation and their bioaccessibility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168374. [PMID: 37956851 DOI: 10.1016/j.scitotenv.2023.168374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
Cadmium (Cd) and lead (Pb) accumulate easily in leafy vegetables and can harm human health. Lanthanum (La) have been used to improve agricultural yield and quality, but the effect of La application on Cd/Pb enrichment in leafy vegetables remains incomplete currently. A previous study reported that the endocytosis in lettuce leaf cells can be activated by La, leading to an increase in Pb accumulation in lettuce leaves. However, it has not been investigated whether foliar application of La enhances root cellular endocytosis and promotes its uptake of Cd and Pb. In this study, the influence of La on the uptake of Cd and Pb, Cd bioaccessibility, and the safety risks of cultivating lettuce under Cd and Pb stress were explored. It was found that La increased Cd (16-30 % in shoot, 16-34 % in root) and Pb (25-29 % in shoot, 17-23 % in root) accumulation in lettuce. The increased accumulation of Cd and Pb could be attributed to La-enhanced endocytosis. Meanwhile, La enhanced the toxicity of both Cd and Pb, inhibited lettuce growth, and aggravated the damage to the photosynthetic and antioxidant systems. Finally, gastrointestinal simulation experiments showed that La increased the Cd bioaccessibility in both gastric and intestinal phase by 7-108 % and 9-87 %, respectively. These results offer valuable insights into the safety of REEs for agricultural applications.
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Affiliation(s)
- Xinyan Zong
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China
| | - Yongqiang Liu
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China
| | - Xinying Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ding He
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China
| | - Zhongtian Dong
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Ting Guo
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China
| | - Jining Li
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China
| | - Hongbo Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Fenghe Wang
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing, Jiangsu 210023, China.
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7
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Jia P, Wang Y, Sharif R, Dong QL, Liu Y, Luan HA, Zhang XM, Guo SP, Qi GH. KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review. Int J Biol Macromol 2023; 253:126878. [PMID: 37703987 DOI: 10.1016/j.ijbiomac.2023.126878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
| | - Yuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Qing-Long Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Hao-An Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue-Mei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Sup-Ping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Guo-Hui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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8
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Tabusam J, Liu M, Luo L, Zulfiqar S, Shen S, Ma W, Zhao J. Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L. J Adv Res 2023; 53:49-59. [PMID: 36581197 PMCID: PMC10658314 DOI: 10.1016/j.jare.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies. AIM OF REVIEW Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development. KEY SCIENTIFIC CONCEPTS OF REVIEW Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.
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Affiliation(s)
- Javaria Tabusam
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Lei Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Sumer Zulfiqar
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Wei Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
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9
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Simko I. Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types. AOB PLANTS 2023; 15:plad060. [PMID: 37680204 PMCID: PMC10482144 DOI: 10.1093/aobpla/plad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce (Lactuca sativa), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies.
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Affiliation(s)
- Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
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10
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Shen F, Qin Y, Wang R, Huang X, Wang Y, Gao T, He J, Zhou Y, Jiao Y, Wei J, Li L, Yang X. Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae. Nat Commun 2023; 14:4334. [PMID: 37474573 PMCID: PMC10359422 DOI: 10.1038/s41467-023-40002-9] [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: 10/12/2022] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
The Asteraceae (daisy family) is one of the largest families of plants. The genetic basis for its high biodiversity and excellent adaptability has not been elucidated. Here, we compare the genomes of 29 terrestrial plant species, including two de novo chromosome-scale genome assemblies for stem lettuce, a member of Asteraceae, and Scaevola taccada, a member of Goodeniaceae that is one of the closest outgroups of Asteraceae. We show that Asteraceae originated ~80 million years ago and experienced repeated paleopolyploidization. PII, the universal regulator of nitrogen-carbon (N-C) assimilation present in almost all domains of life, has conspicuously lost across Asteraceae. Meanwhile, Asteraceae has stepwise upgraded the N-C balance system via paleopolyploidization and tandem duplications of key metabolic genes, resulting in enhanced nitrogen uptake and fatty acid biosynthesis. In addition to suggesting a molecular basis for their ecological success, the unique N-C balance system reported for Asteraceae offers a potential crop improvement strategy.
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Affiliation(s)
- Fei Shen
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Yajuan Qin
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Rui Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Xin Huang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Ying Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, China
| | - Junna He
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, China
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China.
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China.
| | - Xiaozeng Yang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China.
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11
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Shen F, He H, Huang X, Deng Y, Yang X. Insights into the convergent evolution of fructan biosynthesis in angiosperms from the highly characteristic chicory genome. THE NEW PHYTOLOGIST 2023; 238:1245-1262. [PMID: 36751914 DOI: 10.1111/nph.18796] [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: 09/22/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Fructans in angiosperms play essential roles in physiological functions and environmental adaptations. As a major source of industrial fructans (especially inulin-type), chicory (Cichorium intybus L.) is a model species for studying fructan biosynthesis. However, the genes underlying this process and their evolutionary history in angiosperms remain elusive. We combined multiple sequencing technologies to assemble and annotate the chicory genome and scan its (epi)genomic features, such as genomic components, DNA methylation, and three-dimensional (3D) structure. We also performed a comparative genomics analysis to uncover the associations between key traits and gene families. We achieved a nearly complete chicory genome assembly and found that continuous bursts of a few highly active retrotransposon families largely shaped the (epi)genomic characteristics. The highly methylated genome with its unique 3D structure potentially influences critical biological processes. Our comprehensive comparative genomics analysis deciphered the genetic basis for the rich sesquiterpene content in chicory and indicated that the fructan-accumulating trait resulted from convergent evolution in angiosperms due to shifts in critical sites of fructan-active enzymes. The highly characterized chicory genome provides insight into Asteraceae evolution and fructan biosynthesis in angiosperms.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hao He
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Huang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yang Deng
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaozeng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
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12
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Ritonga FN, Zhou D, Zhang Y, Song R, Li C, Li J, Gao J. The Roles of Gibberellins in Regulating Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:1243. [PMID: 36986931 PMCID: PMC10051486 DOI: 10.3390/plants12061243] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/11/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Plant growth and development are correlated with many aspects, including phytohormones, which have specific functions. However, the mechanism underlying the process has not been well elucidated. Gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development, including cell elongation, leaf expansion, leaf senescence, seed germination, and leafy head formation. The central genes involved in GA biosynthesis include GA20 oxidase genes (GA20oxs), GA3oxs, and GA2oxs, which correlate with bioactive GAs. The GA content and GA biosynthesis genes are affected by light, carbon availability, stresses, phytohormone crosstalk, and transcription factors (TFs) as well. However, GA is the main hormone associated with BR, ABA, SA, JA, cytokinin, and auxin, regulating a wide range of growth and developmental processes. DELLA proteins act as plant growth suppressors by inhibiting the elongation and proliferation of cells. GAs induce DELLA repressor protein degradation during the GA biosynthesis process to control several critical developmental processes by interacting with F-box, PIFS, ROS, SCLl3, and other proteins. Bioactive GA levels are inversely related to DELLA proteins, and a lack of DELLA function consequently activates GA responses. In this review, we summarized the diverse roles of GAs in plant development stages, with a focus on GA biosynthesis and signal transduction, to develop new insight and an understanding of the mechanisms underlying plant development.
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Affiliation(s)
- Faujiah Nurhasanah Ritonga
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
- Graduate School, Padjadjaran University, Bandung 40132, West Java, Indonesia
| | - Dandan Zhou
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Yihui Zhang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Runxian Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Cheng Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Jingjuan Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Jianwei Gao
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
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13
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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14
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Soran ML, Sîrb AN, Lung I, Opriş O, Culicov O, Stegarescu A, Nekhoroshkov P, Gligor DM. A Multi-Method Approach for Impact Assessment of Some Heavy Metals on Lactuca sativa L. Molecules 2023; 28:759. [PMID: 36677817 PMCID: PMC9863620 DOI: 10.3390/molecules28020759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Heavy metals represent a large category of pollutants. Heavy metals are the focus of researchers around the world, mainly due to their harmful effects on plants. In this paper, the influence of copper, cadmium, manganese, nickel, zinc and lead, present in soil in different concentrations (below the permissible limit, the maximum permissible concentration and a concentration higher than the maximum permissible limit) on lettuce (Lactuca sativa L.) was evaluated. For this purpose, the authors analyzed the variation of photosynthetic pigments, total polyphenols, antioxidant activity and the elemental content in the studied plants. The experimental results showed that the variation of the content of biologically active compounds, elemental content and the antioxidant activity in the plants grown in contaminated soil, compared to the control plants, depends on the type and concentration of the metal added to the soil. The biggest decrease was recorded for plants grown in soil treated with Ni I (-42.38%) for chlorophyll a, Zn II (-32.92%) for chlorophyll b, Ni I (-40.46%) for carotenoids, Pb I (-40.95%) for polyphenols and Cu III (-29.42%) for DPPH. On the other hand, the largest increase regarding the amount of biologically active compounds was registered for Mn I (88.24%) in the case of the chlorophyll a, Mn I (65.56%) for chlorophyll b, Pb I (116.03%) for carotenoids, Ni III (1351.23%) for polyphenols and Ni III (1149.35%) for DPPH.
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Affiliation(s)
- Maria-Loredana Soran
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Aura Nicoleta Sîrb
- Faculty of Environmental Science and Engineering, Babeș-Bolyai University, 30 Fântânele, 400294 Cluj-Napoca, Romania
| | - Ildiko Lung
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Ocsana Opriş
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Otilia Culicov
- Joint Institute for Nuclear Research, 6 Joliot-Curie, 1419890 Dubna, Russia
- National Institute for Research and Development in Electrical Engineering ICPE-CA, 313 Splaiul Unirii, 030138 Bucharest, Romania
| | - Adina Stegarescu
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Pavel Nekhoroshkov
- Joint Institute for Nuclear Research, 6 Joliot-Curie, 1419890 Dubna, Russia
| | - Delia-Maria Gligor
- Faculty of Environmental Science and Engineering, Babeș-Bolyai University, 30 Fântânele, 400294 Cluj-Napoca, Romania
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15
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Guo Z, Li B, Du J, Shen F, Zhao Y, Deng Y, Kuang Z, Tao Y, Wan M, Lu X, Wang D, Wang Y, Han Y, Wei J, Li L, Guo X, Zhao C, Yang X. LettuceGDB: The community database for lettuce genetics and omics. PLANT COMMUNICATIONS 2023; 4:100425. [PMID: 35964156 PMCID: PMC9860171 DOI: 10.1016/j.xplc.2022.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.
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Affiliation(s)
- Zhonglong Guo
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China; College of Biology and the Environment, Nanjing Forestry University, Nanjing 510275, P.R. China
| | - Bo Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Jianjun Du
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing 100097, P.R. China
| | - Fei Shen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Yongxin Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Yang Deng
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Zheng Kuang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Yihan Tao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Miaomiao Wan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Xianju Lu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing 100097, P.R. China
| | - Dong Wang
- WeiRan Biotech, Beijing 100085, P.R. China
| | - Ying Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing 102206, P.R. China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Xinyu Guo
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing 100097, P.R. China.
| | - Chunjiang Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing 100097, P.R. China.
| | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing 100097, P.R. China.
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16
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Hao N, Cao J, Wang C, Zhu Y, Du Y, Wu T. Understanding the molecular mechanism of leaf morphogenesis in vegetable crops conduces to breeding process. FRONTIERS IN PLANT SCIENCE 2022; 13:971453. [PMID: 36570936 PMCID: PMC9773389 DOI: 10.3389/fpls.2022.971453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Leaf morphology can affect the development and yield of plants by regulating plant architecture and photosynthesis. Several factors can determine the final leaf morphology, including the leaf complexity, size, shape, and margin type, which suggests that leaf morphogenesis is a complex regulation network. The formation of diverse leaf morphology is precisely controlled by gene regulation on translation and transcription levels. To further reveal this, more and more genome data has been published for different kinds of vegetable crops and advanced genotyping approaches have also been applied to identify the causal genes for the target traits. Therefore, the studies on the molecular regulation of leaf morphogenesis in vegetable crops have also been largely improved. This review will summarize the progress on identified genes or regulatory mechanisms of leaf morphogenesis and development in vegetable crops. These identified markers can be applied for further molecular-assisted selection (MAS) in vegetable crops. Overall, the review will contribute to understanding the leaf morphology of different crops from the perspective of molecular regulation and shortening the breeding cycle for vegetable crops.
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Affiliation(s)
- Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Yipeng Zhu
- Guiyang Productivity Promotion Center, Guiyang Science and Technology Bureau, Guiyang, China
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
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17
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Guo X, Liang J, Lin R, Zhang L, Zhang Z, Wu J, Wang X. Single-cell transcriptome reveals differentiation between adaxial and abaxial mesophyll cells in Brassica rapa. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2233-2235. [PMID: 36039389 PMCID: PMC9674316 DOI: 10.1111/pbi.13919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 05/27/2023]
Affiliation(s)
- Xinlei Guo
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Jianli Liang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Runmao Lin
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Lupeng Zhang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Zhicheng Zhang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Jian Wu
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
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18
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Jia Y, Yu P, Shao W, An G, Chen J, Yu C, Kuang H. Up-regulation of LsKN1 promotes cytokinin and suppresses gibberellin biosynthesis to generate wavy leaves in lettuce. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6615-6629. [PMID: 35816166 DOI: 10.1093/jxb/erac311] [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: 03/14/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Lettuce (Lactuca sativa) is one of the most popular vegetables worldwide, and diverse leaf shapes, including wavy leaves, are important commercial traits. In this study, we examined the genetics of wavy leaves using an F2 segregating population, and identified a major QTL controlling wavy leaves. The candidate region contained LsKN1, which has previously been shown to be indispensable for leafy heads in lettuce. Complementation tests and knockout experiments verified the function of LsKN1 in producing wavy leaves. The LsKN1∇ allele, which has the insertion of a transposon and has previously been shown to control leafy heads, promoted wavy leaves in our population. Transposition of the CACTA transposon from LsKN1 compromised its function for wavy leaves. High expression of LsKN1 up-regulated several key genes associated with cytokinin (CK) to increase the content in the leaves, whereas it down-regulated the expression of genes in the gibberellin (GA) biosynthesis pathway to decrease the content. Application of CK to leaves enhanced the wavy phenotype, while application of GA dramatically flattened the leaves. We conclude that the changes in CK and GA contents that result from high expression of LsKN1 switch determinate cells to indeterminate, and consequently leads to the development of wavy leaves.
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Affiliation(s)
- Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Pei Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wei Shao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Guanghui An
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People's Republic of China
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19
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An G, Yu C, Yan C, Wang M, Zhang W, Jia Y, Shi C, Larkin RM, Chen J, Lavelle D, Michelmore RW, Kuang H. Loss-of-function of SAWTOOTH 1 affects leaf dorsiventrality genes to promote leafy heads in lettuce. THE PLANT CELL 2022; 34:4329-4347. [PMID: 35916734 PMCID: PMC9614500 DOI: 10.1093/plcell/koac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The mechanisms underlying leafy heads in vegetables are poorly understood. Here, we cloned a quantitative trait locus (QTL) controlling leafy heads in lettuce (Lactuca sativa). The QTL encodes a transcription factor, SAWTOOTH 1 (LsSAW1), which has a BEL1-like homeodomain and is a homolog of Arabidopsis thaliana. A 1-bp deletion in Lssaw1 contributes to the development of leafy heads. Laser-capture microdissection and RNA-sequencing showed that LsSAW1 regulates leaf dorsiventrality and loss-of-function of Lssaw1 downregulates the expression of many adaxial genes but upregulates abaxial genes. LsSAW1 binds to the promoter region of the adaxial gene ASYMMETRIC LEAVES 1 (LsAS1) to upregulate its expression. Overexpression of LsAS1 compromised the effects of Lssaw1 on heading. LsSAW1 also binds to the promoter region of the abaxial gene YABBY 1 (LsYAB1), but downregulates its expression. Overexpression of LsYAB1 led to bending leaves in LsSAW1 genotypes. LsSAW1 directly interacts with KNOTTED 1 (LsKN1), which is necessary for leafy heads in lettuce. RNA-seq data showed that LsSAW1 and LsKN1 exert antagonistic effects on the expression of thousands of genes. LsSAW1 compromises the ability of LsKN1 to repress LsAS1. Our results suggest that downregulation or loss-of-function of adaxial genes and upregulation of abaxial genes allow for the development of leafy heads.
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Affiliation(s)
- Guanghui An
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenghuan Yan
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Menglu Wang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dean Lavelle
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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20
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Chen X, Zhang X, Chen H, Xu X. Physiology and proteomics reveal Fulvic acid mitigates Cadmium adverse effects on growth and photosynthetic properties of lettuce. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111418. [PMID: 35985414 DOI: 10.1016/j.plantsci.2022.111418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Understanding the molecular mechanisms of plants in response to Cd stress is crucial for improving plants adaptation to Cd stress. Fulvic acid (FA) is an active humic substance that is often used as a soil conditioner. However, there are few reports on the role of FA against Cd stress. The aim of this study was to determine the effects of Fulvic acid on alleviation of Cd toxicity in lettuce (Lactuca sativa L) under hydroponic conditions. Our results showed that 20 μmol/L Cd stress significantly reduced photosynthetic pigment metabolism and the expression of photosynthetic apparatus-related proteins, thereby inhibiting photosynthetic electron transport, net photosynthetic rate and negatively affecting photosynthetic carbon assimilation and growth of lettuce. However, proteomic findings suggest that the application of FA can reduce the adverse effects of Cd contamination. Compared to Cd stress alone, FA significantly increased the expression of Light-harvesting proteins, reaction center and electron transport-related proteins. Further results showed that FA at 0.5 g/L reduced the uptake of Cd by the roots, resulting in a 23.5% reduction in total Cd content in lettuce. Moreover, FA enhanced S metabolism and rebuilt redox homeostasis in cells. Overall, these findings provide new insights into the mechanism of cadmium toxicity mitigation in lettuce by FA. Which is recommended as an eco-friendly tool for improving the photosynthesis performance and biomass of lettuce under Cd stress.
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Affiliation(s)
- Xiaojing Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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21
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Wang M, Lavelle D, Yu C, Zhang W, Chen J, Wang X, Michelmore RW, Kuang H. The upregulated LsKN1 gene transforms pinnately to palmately lobed leaves through auxin, gibberellin, and leaf dorsiventrality pathways in lettuce. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1756-1769. [PMID: 35634731 PMCID: PMC9398307 DOI: 10.1111/pbi.13861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Leaf shape represents a vital agronomic trait for leafy vegetables such as lettuce. Some lettuce cultivars produce lobed leaves, varying from pinnately to palmately lobed, but the genetic mechanisms remain unclear. In this study, we cloned one major quantitative trait locus (QTL) controlling palmately lobed leaves. The candidate gene, LsKN1, encodes a homeobox transcription factor, and has been shown previously to be critical for the development of leafy heads in lettuce. The LsKN1 allele that is upregulated by the insertion of a transposon promotes the development of palmately lobed leaves. We demonstrated that LsKN1 upregulated LsCUC2 and LsCUC3 through different mechanisms, and their upregulation was critical for the development of palmately lobed leaves. LsKN1 binds the promoter of LsPID to promote auxin biosynthesis, which positively contributes to the development of palmately lobed leaves. In contrast, LsKN1 suppresses GA biosynthesis to promote palmately lobed leaves. LsKN1 also binds to the promoter of LsAS1, a dorsiventrality gene, to downregulate its expression. Overexpression of the LsAS1 gene compromised the effects of the LsKN1 gene changing palmately to pinnately lobed leaves. Our study illustrated that the upregulated LsKN1 gene led to palmately lobed leaves in lettuce by integrating several downstream pathways, including auxin, gibberellin, and leaf dorsiventrality pathways.
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Affiliation(s)
- Menglu Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Dean Lavelle
- Genome Center and Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Xin Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Richard W Michelmore
- Genome Center and Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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Zhang T, Xiang Y, Geng L, Jiang W, Cheng S, Zhao Y. A Non-Canonical MITE in the WOX11 Promoter Is Associated with Robust Crown Root development in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1052-1062. [PMID: 35727725 DOI: 10.1093/pcp/pcac075] [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: 10/27/2021] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The formation of tissues and organs in multicellular organisms is tightly controlled by transcriptional programs determined by temporal and spatial patterns of gene expression. As an important regulator of rice crown root development, WOX11 is essential for crown root formation and its transcript level is positively correlated with crown root biomass. However, how WOX11 is regulated during crown root primordium emergence and outgrowth still remains unknown. In this study, variations of the WOX11 genomic sequence were analyzed, and the highest genetic diversity was found within its promoter, which contained a non-canonical miniature inverted-repeat transposable element (ncMITE) sequence. Analysis of the WOX11 promoter-driven reporter gene GUS (β-glucuronidase) transgenic plants pWOX11(ncMITE+):GUS and pWOX11(ncMITE-):GUS uncovered higher GUS expression levels in crown roots of pWOX11(ncMITE+):GUS plants. Furthermore, pWOX11(ncMITE+):WOX11-FLAG in wox11 background could complement the crown root number and length compared to those of the wild type, while pWOX11(ncMITE-):WOX11-FLAG could not. These results suggested that the ncMITE was positively associated with WOX11 transcripts in rice crown roots. In addition, DNA methylation nearby the ncMITE region attenuated the activation effect of the ncMITE on WOX11 expression, which might also be the cause conferred to the root-specific expression of WOX11. This work provides novel insight into WOX11 expression regulation and reveals a promising target for genetic improvement of root architecture in rice.
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Affiliation(s)
- Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
- College of Bioengineering, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Saifeng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
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23
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Yang X, Wang J, Mao X, Li C, Li L, Xue Y, He L, Jing R. A Locus Controlling Leaf Rolling Degree in Wheat under Drought Stress Identified by Bulked Segregant Analysis. PLANTS 2022; 11:plants11162076. [PMID: 36015380 PMCID: PMC9414355 DOI: 10.3390/plants11162076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
Drought stress frequently occurs, which seriously restricts the production of wheat (Triticum aestivum L.). Leaf rolling is a typical physiological phenomenon of plants during drought stress. To understand the genetic mechanism of wheat leaf rolling, we constructed an F2 segregating population by crossing the slight-rolling wheat cultivar “Aikang 58” (AK58) with the serious-rolling wheat cultivar ″Zhongmai 36″ (ZM36). A combination of bulked segregant analysis (BSA) with Wheat 660K SNP Array was used to identify molecular markers linked to leaf rolling degree. A major locus for leaf rolling degree under drought stress was detected on chromosome 7A. We named this locus LEAF ROLLING DEGREE 1 (LERD1), which was ultimately mapped to a region between 717.82 and 720.18 Mb. Twenty-one genes were predicted in this region, among which the basic helix-loop-helix (bHLH) transcription factor TraesCS7A01G543300 was considered to be the most likely candidate gene for LERD1. The TraesCS7A01G543300 is highly homologous to the Arabidopsis ICE1 family proteins ICE/SCREAM, SCREAM2 and bHLH093, which control stomatal initiation and development. Two nucleotide variation sites were detected in the promoter region of TraesCS7A01G543300 between the two wheat cultivars. Gene expression assays indicated that TraesCS7A01G543300 was higher expressed in AK58 seedlings than that of ZM36. This research discovered a candidate gene related to wheat leaf rolling under drought stress, which may be helpful for understanding the leaf rolling mechanism and molecular breeding in wheat.
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Affiliation(s)
- Xi Yang
- College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghong Xue
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liheng He
- College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence: (L.H.); (R.J.)
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (L.H.); (R.J.)
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24
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Liu M, Huang L, Zhang Y, Yan Z, Wang N. Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins. TREE PHYSIOLOGY 2022; 42:tpac086. [PMID: 35980326 DOI: 10.1093/treephys/tpac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.
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Affiliation(s)
- Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China
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25
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Zhao Y, Zhang Y, Zhang W, Shi Y, Jiang C, Song X, Tuskan GA, Zeng W, Zhang J, Lu M. The PagKNAT2/6b-PagBOP1/2a Regulatory Module Controls Leaf Morphogenesis in Populus. Int J Mol Sci 2022; 23:ijms23105581. [PMID: 35628391 PMCID: PMC9145908 DOI: 10.3390/ijms23105581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 12/04/2022] Open
Abstract
Leaf morphogenesis requires precise regulation of gene expression to achieve organ separation and flat-leaf form. The poplar KNOTTED-like homeobox gene PagKNAT2/6b could change plant architecture, especially leaf shape, in response to drought stress. However, its regulatory mechanism in leaf development remains unclear. In this work, gene expression analyses of PagKNAT2/6b suggested that PagKNAT2/6b was highly expressed during leaf development. Moreover, the leaf shape changes along the adaxial-abaxial, medial-lateral, and proximal-distal axes caused by the mis-expression of PagKNAT2/6b demonstrated that its overexpression (PagKNAT2/6b OE) and SRDX dominant repression (PagKNAT2/6b SRDX) poplars had an impact on the leaf axial development. The crinkle leaf of PagKNAT2/6b OE was consistent with the differential expression gene PagBOP1/2a (BLADE-ON-PETIOLE), which was the critical gene for regulating leaf development. Further study showed that PagBOP1/2a was directly activated by PagKNAT2/6b through a novel cis-acting element "CTCTT". Together, the PagKNAT2/6b-PagBOP1/2a module regulates poplar leaf morphology by affecting axial development, which provides insights aimed at leaf shape modification for further improving the drought tolerance of woody plants.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Yifan Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Weilin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Yangxin Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Gerald A. Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA;
| | - Wei Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
- Correspondence: (J.Z.); (M.L.)
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (J.Z.); (M.L.)
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26
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Cui Y, Fan B, Xu X, Sheng S, Xu Y, Wang X. A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. Front Genet 2022; 12:802738. [PMID: 35132310 PMCID: PMC8817757 DOI: 10.3389/fgene.2021.802738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.
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Affiliation(s)
- Yang Cui
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Baolian Fan
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Xu Xu
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Shasha Sheng
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Xiaoyun Wang
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
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27
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Tang Q, Kuang H, Yu C, An G, Tao R, Zhang W, Jia Y. Non-vernalization requirement in Chinese kale caused by loss of BoFLC and low expressions of its paralogs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:473-483. [PMID: 34716468 PMCID: PMC8866342 DOI: 10.1007/s00122-021-03977-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
We identified the loss of BoFLC gene as the cause of non-vernalization requirement in B. oleracea. Our developed codominant marker of BoFLC gene can be used for breeding program of B. oleracea crops. Many species of the Brassicaceae family, including some Brassica crops, require vernalization to avoid pre-winter flowering. Vernalization is an unfavorable trait for Chinese kale (Brassica oleracea var. chinensis Lei), a stem vegetable, and therefore it has been lost during its domestication/breeding process. To reveal the genetics of vernalization variation, we constructed an F2 population through crossing a Chinese kale (a non-vernalization crop) with a kale (a vernalization crop). Using bulked segregant analysis (BSA) and RNA-seq, we identified one major quantitative trait locus (QTL) controlling vernalization and fine-mapped it to a region spanning 80 kb. Synteny analysis and PCR-based sequencing results revealed that compared to that of the kale parent, the candidate region of the Chinese kale parent lost a 9,325-bp fragment containing FLC homolog (BoFLC). In addition to the BoFLC gene, there are four other FLC homologs in the genome of B. oleracea, including Bo3g005470, Bo3g024250, Bo9g173370, and Bo9g173400. The qPCR analysis showed that the BoFLC had the highest expression among the five members of the FLC family. Considering the low expression levels of the four paralogs of BoFLC, we speculate that its paralogs cannot compensate the function of the lost BoFLC, therefore the presence/absence (PA) polymorphism of BoFLC determines the vernalization variation. Based on the PA polymorphism of BoFLC, we designed a codominant marker for the vernalization trait, which can be used for breeding programs of B. oleracea crops.
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Affiliation(s)
- Qiwei Tang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanghui An
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rong Tao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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Guo X, Liang J, Lin R, Zhang L, Wu J, Wang X. Series-Spatial Transcriptome Profiling of Leafy Head Reveals the Key Transition Leaves for Head Formation in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 12:787826. [PMID: 35069646 PMCID: PMC8770947 DOI: 10.3389/fpls.2021.787826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 05/12/2023]
Abstract
Chinese cabbage is an important leaf heading vegetable crop. At the heading stage, its leaves across inner to outer show significant morphological differentiation. However, the genetic control of this complex leaf morphological differentiation remains unclear. Here, we reported the transcriptome profiling of Chinese cabbage plant at the heading stage using 24 spatially dissected tissues representing different regions of the inner to outer leaves. Genome-wide transcriptome analysis clearly separated the inner leaf tissues from the outer leaf tissues. In particular, we identified the key transition leaf by the spatial expression analysis of key genes for leaf development and sugar metabolism. We observed that the key transition leaves were the first inwardly curved ones. Surprisingly, most of the heading candidate genes identified by domestication selection analysis obviously showed a corresponding expression transition, supporting that key transition leaves are related to leafy head formation. The key transition leaves were controlled by a complex signal network, including not only internal hormones and protein kinases but also external light and other stimuli. Our findings provide new insights and the rich resource to unravel the genetic control of heading traits.
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Jiang X, Zhang W, Fernie AR, Wen W. Combining novel technologies with interdisciplinary basic research to enhance horticultural crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:35-46. [PMID: 34699639 DOI: 10.1111/tpj.15553] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.
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Affiliation(s)
- Xiaohui Jiang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Tea Research Institute, Guangdong Provincial Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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30
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Zhang L, Qian J, Han Y, Jia Y, Kuang H, Chen J. Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale-green leaves in lettuce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:182-195. [PMID: 34724596 DOI: 10.1111/tpj.15563] [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: 06/10/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023]
Abstract
Lettuce (Lactuca sativa) is one of the most important vegetable crops in the world. As a leafy vegetable, the polymorphism of lettuce leaves from dark to pale green is an important trait. However, the genetic and molecular mechanisms underlying such variations remain poorly understood. In this study, one major locus controlling the polymorphism of dark- and pale-green leaves in lettuce was identified using genome-wide association studies (GWAS). This locus was then fine mapped to an interval of 5375 bp on chromosome 4 using a segregating population containing 2480 progeny. Only one gene, homologous to the GLK genes in Arabidopsis and other plants, is present in the candidate region. A complementation test confirmed that the candidate gene, LsGLK, contributes to the variation of dark- and pale-green leaves. Sequence analysis showed that a CACTA transposon of 7434 bp was inserted 10 bp downstream of the stop codon of LsGLK, followed by a duplication of a 1826-bp fragment covering exons 3-6 of the LsGLK gene. The transposon insertion did not change the expression level of the LsGLK gene. However, because of alternative splicing, only 6% of the transcripts produced from the transposon insertion were wild-type transcripts, which led to the production of pale-green leaves. An evolutionary analysis revealed that the insertion of the CACTA transposon occurred in cultivated lettuce and might have been selected in particular cultivars to satisfy the diverse demands of consumers. In this study, we demonstrated that a transposon insertion near a gene may affect its splicing and consequently generate phenotypic variations.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Jinlong Qian
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yuting Han
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
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Deng Y, Qin Y, Yang P, Du J, Kuang Z, Zhao Y, Wang Y, Li D, Wei J, Guo X, Li L, Yang X. Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce. FRONTIERS IN PLANT SCIENCE 2021; 12:781836. [PMID: 35003165 PMCID: PMC8739914 DOI: 10.3389/fpls.2021.781836] [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: 09/23/2021] [Accepted: 10/28/2021] [Indexed: 05/28/2023]
Abstract
MicroRNA (miRNA) is an important endogenous post-transcriptional regulator, while lettuce (Lactuca sativa) is a leafy vegetable of global economic significance. However, there are few studies on miRNAs in lettuce, and research on miRNA regulatory network in lettuce is absent. In this study, through deep sequencing of small RNAs in different tissues, together with a reference genome, 157 high-confidence miRNA loci in lettuce were comprehensively identified, and their expression patterns were determined. Using a combination of computational prediction and high-throughput experimental verification, a set of reliable lettuce miRNA targets were obtained. Furthermore, through RNA-Seq, the expression profiles of these targets and a comprehensive view of the negative regulatory relationship between miRNAs and their targets was acquired based on a correlation analysis. To further understand miRNA functions, a miRNA regulatory network was constructed, with miRNAs at the core and combining transcription factors and miRNA target genes. This regulatory network, mainly composed of feed forward loop motifs, greatly increases understanding of the potential functions of miRNAs, and many unknown potential regulatory links were discovered. Finally, considering its specific expression pattern, Lsa-MIR408 as a hub gene was employed to illustrate the function of the regulatory network, and genetic experiments revealed its ability to increase the fresh weight and achene size of lettuce. In short, this work lays a solid foundation for the study of miRNA functions and regulatory networks in lettuce.
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Affiliation(s)
- Yang Deng
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Yajuan Qin
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Pan Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianjun Du
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing, China
| | - Zheng Kuang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yongxin Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Ying Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Dayong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing Vegetable Research Center, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Xinyu Guo
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
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Molecular Analysis Uncovers the Mechanism of Fertility Restoration in Temperature-Sensitive Polima Cytoplasmic Male-Sterile Brassica napus. Int J Mol Sci 2021; 22:ijms222212450. [PMID: 34830333 PMCID: PMC8617660 DOI: 10.3390/ijms222212450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Temperature-sensitive male sterility is a heritable agronomic trait affected by genotype-environment interactions. In rapeseed (Brassica napus), Polima (pol) temperature-sensitive cytoplasmic male sterility (TCMS) is commonly used for two-line breeding, as the fertility of pol TCMS lines can be partially restored at certain temperatures. However, little is known about the underlying molecular mechanism that controls fertility restoration. Therefore, we aimed to investigate the fertility conversion mechanism of the pol TCMS line at two different ambient temperatures (16 °C and 25 °C). Our results showed that the anthers developed and produced vigorous pollen at 16 °C but not at 25 °C. In addition, we identified a novel co-transcript of orf224-atp6 in the mitochondria that might lead to fertility conversion of the pol TCMS line. RNA-seq analysis showed that 1637 genes were significantly differentially expressed in the fertile flowers of 596-L when compared to the sterile flower of 1318 and 596-H. Detailed analysis revealed that differentially expressed genes were involved in temperature response, ROS accumulation, anther development, and mitochondrial function. Single-molecule long-read isoform sequencing combined with RNA sequencing revealed numerous genes produce alternative splicing transcripts at high temperatures. Here, we also found that alternative oxidase, type II NAD(P)H dehydrogenases, and transcription factor Hsfs might play a crucial role in male fertility under the low-temperature condition. RNA sequencing and bulked segregant analysis coupled with whole-genome sequencing identified the candidate genes involved in the post-transcriptional modification of orf224. Overall, our study described a putative mechanism of fertility restoration in a pol TCMS line controlled by ambient temperature that might help utilise TCMS in the two-line breeding of Brassica crops.
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Zhang B, Tong Y, Luo K, Zhai Z, Liu X, Shi Z, Zhang D, Li D. Identification of GROWTH-REGULATING FACTOR transcription factors in lettuce (Lactuca sativa) genome and functional analysis of LsaGRF5 in leaf size regulation. BMC PLANT BIOLOGY 2021; 21:485. [PMID: 34688264 PMCID: PMC8539887 DOI: 10.1186/s12870-021-03261-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/06/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND GROWTH-REGULATING FACTORs (GRFs), a type of plant-specific transcription factors, play important roles in regulating plant growth and development. Although GRF gene family has been identified in various plant species, a genome-wide analysis of this family in lettuce (Lactuca sativa L.) has not been reported yet. RESULTS Here we identified 15 GRF genes in lettuce and performed comprehensive analysis of them, including chromosomal locations, gene structures, and conserved motifs. Through phylogenic analysis, we divided LsaGRFs into six groups. Transactivation assays and subcellular localization of LsaGRF5 showed that this protein is likely to act as a transcriptional factor in the cell nucleus. Furthermore, transgenic lettuce lines overexpressing LsaGRF5 exhibited larger leaves, while smaller leaves were observed in LsaMIR396a overexpression lines, in which LsaGRF5 was down-regulated. CONCLUSIONS These results in lettuce provide insight into the molecular mechanism of GRF gene family in regulating leaf growth and development and foundational information for genetic improvement of the lettuce variations specialized in leaf character.
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Affiliation(s)
- Bin Zhang
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, PR China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, 100097, PR China
| | - Yanan Tong
- Biotechnology Research Center, China Three Gorges University, Yichang, 443002, PR China
| | - Kangsheng Luo
- Biotechnology Research Center, China Three Gorges University, Yichang, 443002, PR China
| | - Zhaodong Zhai
- College of Life Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Xue Liu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, PR China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, 100097, PR China
| | - Zhenying Shi
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China
| | - Dechun Zhang
- Biotechnology Research Center, China Three Gorges University, Yichang, 443002, PR China.
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, PR China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, 100097, PR China.
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Luo C, Wang S, Ning K, Chen Z, Wang Y, Yang J, Wang Q. LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2 in lettuce. HORTICULTURE RESEARCH 2021; 8:184. [PMID: 34465756 PMCID: PMC8408249 DOI: 10.1038/s41438-021-00622-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/21/2021] [Accepted: 05/20/2021] [Indexed: 05/24/2023]
Abstract
Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
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Affiliation(s)
- Chen Luo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shenglin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kang Ning
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zijing Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qian Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Gurdon C, Kozik A, Tao R, Poulev A, Armas I, Michelmore RW, Raskin I. Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family. PLANT PHYSIOLOGY 2021; 186:929-944. [PMID: 33768232 PMCID: PMC8195511 DOI: 10.1093/plphys/kiab143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/02/2021] [Indexed: 06/01/2023]
Abstract
Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from red cultivar NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. GSL harbors CACTA 1 (LsC1), a 3.9-kb active nonautonomous CACTA superfamily transposon inserted in the 5' untranslated region of anthocyanidin synthase (ANS), a gene coding for a key enzyme in anthocyanin biosynthesis. Both terminal inverted repeats (TIRs) of this transposon were intact, enabling somatic excision of the mobile element, which led to the restoration of ANS expression and the accumulation of red anthocyanins in sectors on otherwise green leaves. GSL-DG harbors CACTA 2 (LsC2), a 1.1-kb truncated copy of LsC1 that lacks one of the TIRs, rendering the transposon inactive. RNA-sequencing and reverse transcription quantitative PCR of NAR, GSL, and GSL-DG indicated the relative expression level of ANS was strongly influenced by the transposon insertions. Analysis of flavonoid content indicated leaf cyanidin levels correlated positively with ANS expression. Bioinformatic analysis of the cv Salinas lettuce reference genome led to the discovery and characterization of an LsC1 transposon family with a putative transposon copy number greater than 1,700. Homologs of tnpA and tnpD, the genes encoding two proteins necessary for activation of transposition of CACTA elements, were also identified in the lettuce genome.
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Affiliation(s)
- Csanad Gurdon
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
| | | | - Rong Tao
- UC Davis Genome Center, Davis, California 95616, USA
| | - Alexander Poulev
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
| | - Isabel Armas
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
| | | | - Ilya Raskin
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
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Darqui FS, Radonic LM, Beracochea VC, Hopp HE, López Bilbao M. Peculiarities of the Transformation of Asteraceae Family Species: The Cases of Sunflower and Lettuce. FRONTIERS IN PLANT SCIENCE 2021; 12:767459. [PMID: 34899788 PMCID: PMC8662702 DOI: 10.3389/fpls.2021.767459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/02/2021] [Indexed: 05/17/2023]
Abstract
The Asteraceae family is the largest and most diversified family of the Angiosperms, characterized by the presence of numerous clustered inflorescences, which have the appearance of a single compound flower. It is estimated that this family represents around 10% of all flowered species, with a great biodiversity, covering all environments on the planet, except Antarctica. Also, it includes economically important crops, such as lettuce, sunflower, and chrysanthemum; wild flowers; herbs, and several species that produce molecules with pharmacological properties. Nevertheless, the biotechnological improvement of this family is limited to a few species and their genetic transformation was achieved later than in other plant families. Lettuce (Lactuca sativa L.) is a model species in molecular biology and plant biotechnology that has easily adapted to tissue culture, with efficient shoot regeneration from different tissues, organs, cells, and protoplasts. Due to this plasticity, it was possible to obtain transgenic plants tolerant to biotic or abiotic stresses as well as for the production of commercially interesting molecules (molecular farming). These advances, together with the complete sequencing of lettuce genome allowed the rapid adoption of gene editing using the CRISPR system. On the other hand, sunflower (Helianthus annuus L.) is a species that for years was considered recalcitrant to in vitro culture. Although this difficulty was overcome and some publications were made on sunflower genetic transformation, until now there is no transgenic variety commercialized or authorized for cultivation. In this article, we review similarities (such as avoiding the utilization of the CaMV35S promoter in transformation vectors) and differences (such as transformation efficiency) in the state of the art of genetic transformation techniques performed in these two species.
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Affiliation(s)
- Flavia Soledad Darqui
- IABIMO (Instituto de Agrobiotecnología y Biología Molecular), UEDD INTA-CONICET, CNIA, Buenos Aires, Argentina
| | - Laura Mabel Radonic
- IABIMO (Instituto de Agrobiotecnología y Biología Molecular), UEDD INTA-CONICET, CNIA, Buenos Aires, Argentina
| | - Valeria Cecilia Beracochea
- IABIMO (Instituto de Agrobiotecnología y Biología Molecular), UEDD INTA-CONICET, CNIA, Buenos Aires, Argentina
| | - H. Esteban Hopp
- IABIMO (Instituto de Agrobiotecnología y Biología Molecular), UEDD INTA-CONICET, CNIA, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Marisa López Bilbao
- IABIMO (Instituto de Agrobiotecnología y Biología Molecular), UEDD INTA-CONICET, CNIA, Buenos Aires, Argentina
- *Correspondence: Marisa López Bilbao,
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