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Shen X, Yang T, Du Y, Hao N, Cao J, Wu T, Wang C. Research on the function of CsMYB36 based on an effective hair root transformation system. PLANT SIGNALING & BEHAVIOR 2024; 19:2345983. [PMID: 38686613 PMCID: PMC11062371 DOI: 10.1080/15592324.2024.2345983] [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: 03/05/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
The hairy root induction system was used to efficiently investigate gene expression and function in plant root. Cucumber is a significant vegetable crop worldwide, with shallow roots, few lateral roots, and weak root systems, resulting in low nutrient absorption and utilization efficiency. Identifying essential genes related to root development and nutrient absorption is an effective way to improve the growth and development of cucumbers. However, genetic mechanisms underlying cucumber root development have not been explored. Here, we report a novel, rapid, effective hairy root transformation system. Compared to the in vitro cotyledon transformation method, this method shortened the time needed to obtain transgenic roots by 13 days. Furthermore, we combined this root transformation method with CRISPR/Cas9 technology and validated our system by exploring the expression and function of CsMYB36, a pivotal gene associated with root development and nutrient uptake. The hairy root transformation system established in this study provides a powerful method for rapidly identifying essential genes related to root development in cucumber and other horticultural crop species. This advancement holds promise for expediting research on root biology and molecular breeding strategies, contributing to the broader understanding and improvements crop growth and development.
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Affiliation(s)
- Xi Shen
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Ting Yang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, China
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Gasca-Pineda J, Monterrubio B, Sánchez-de la Vega G, Aguirre-Planter E, Lira-Saade R, Eguiarte LE. Conservation genomics of the wild pumpkin Cucurbita radicans in Central Mexico: The influence of a changing environment on the genetic diversity and differentiation of a rare species. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01552-1. [PMID: 38977618 DOI: 10.1007/s10265-024-01552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 06/02/2024] [Indexed: 07/10/2024]
Abstract
The genetic diversity found in natural populations is the result of the evolutionary forces in response to historical and contemporary factors. The environmental characteristics and geological history of Mexico promoted the evolution and diversification of plant species, including wild relatives of crops such as the wild pumpkins (Cucurbita). Wild pumpkin species are found in a variety of habitats, evidencing their capability to adapt to different environments. Despite the potential value of wild Cucurbita as a genetic reservoir for crops, there is a lack of studies on their genetic diversity. Cucurbita radicans is an endangered species threatened by habitat destruction leading to low densities in small and isolated populations. Here, we analyze Genotype by Sequencing genomic data of the wild pumpkin C. radicans to evaluate the influence of factors like isolation, demographic history, and the environment shaping the amount and distribution of its genetic variation. We analyzed 91 individuals from 14 localities along its reported distribution. We obtained 5,107 SNPs and found medium-high levels of genetic diversity and genetic structure distributed in four main geographic areas with different environmental conditions. Moreover, we found signals of demographic growth related to historical climatic shifts. Outlier loci analysis showed significant association with the environment, principally with precipitation variables. Also, the outlier loci displayed differential changes in their frequencies in response to future global climate change scenarios. Using the results of genetic structure, outlier loci and multivariate analyses of the environmental conditions, we propose priority localities for conservation that encompass most of the genetic diversity of C. radicans.
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Affiliation(s)
- Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, Ciudad de México, 04510, México.
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, 54090, México.
| | - Brenda Monterrubio
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, 54090, México
| | - Guillermo Sánchez-de la Vega
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, 54090, México
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, Ciudad de México, 04510, México
| | - Rafael Lira-Saade
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, 54090, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, Ciudad de México, 04510, México.
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3
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Ahmad S, Khan K, Saleh IA, Okla MK, Alaraidh IA, AbdElgawad H, Naeem M, Ahmad N, Fahad S. TALE gene family: identification, evolutionary and expression analysis under various exogenous hormones and waterlogging stress in Cucumis sativus L. BMC PLANT BIOLOGY 2024; 24:564. [PMID: 38879470 PMCID: PMC11179211 DOI: 10.1186/s12870-024-05274-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Three Amino acid Loop Extension (TALE) belongs to the homeobox group of genes that are important constituents of plant systems. The TALE gene family is instrumental not only in growth and development but also plays an essential role in regulating plant response to environmental adversaries. RESULTS In the present study, we isolated 21 CsTALE genes from the cucumber (Cucumis sativus L.) genome database. Bioinformatics tools were put in place to understand the structural and functional components of the CsTALE gene family. The evolutionary analysis dissected them into seven subclades (KNOX-I, KNOX-II, and BELL-I to BELL-V). The cis-acting elements in the promoter region of CsTALE genes disclosed that they are key regulators of hormonal and stress-related processes. Additionally, the STRING database advocated the concerting role of CsTALE proteins with other key transcription factors potent in plant developmental biology. The CsmiR319 and CsmiR167a-3p targeting the CsTALE15 and CsTALE16, respectively, further assert the importance of the CsTALE gene family posttranscriptional-related processes. Tissue-specific gene expression unfolded the fundamental involvement of CsTALE genes as they were expressed throughout the developmental stages. Under waterlogging stress, the CsTALE17 expressed significantly higher values in WL, WL-NAA, and WL-ETH but not in WL-MeJA-treated samples. CONCLUSIONS The present study reveals the evolution and functions of the CsTALE gene family in cucumber. Our work will provide a platform that will help future researchers address the issue of waterlogging stress in the Yangtze River Delta.
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Affiliation(s)
- Sheraz Ahmad
- College of Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, PR China.
| | - Khushboo Khan
- Faculty of Crop Production Sciences, The University of Agriculture Peshawar, Peshawar, Khyber Pakhtunkhwa, 25120, Pakistan
| | | | - Mohammad K Okla
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ibrahim A Alaraidh
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Shah Fahad
- Department of Agronomy, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, 23200, Pakistan.
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Peng H, Yi Y, Li J, Qing Y, Zhai X, Deng Y, Tian J, Zhang J, Hu Y, Qin X, Lu Y, Yao Y, Wang S, Zheng Y. A haplotype-resolved genome assembly of Malus domestica 'Red Fuji'. Sci Data 2024; 11:592. [PMID: 38844753 PMCID: PMC11156929 DOI: 10.1038/s41597-024-03401-1] [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: 12/13/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
The 'Red Fuji' apple (Malus domestica), is one of the most important and popular economic crops worldwide in the fruit industry. Using PacBio HiFi long reads and Hi-C reads, we assembled a high-quality haplotype-resolved genome of 'Red Fuji', with sizes of 668.7 and 668.8 Mb, and N50 sizes of 34.1 and 31.4 Mb. About 97.2% of sequences were anchored in 34 chromosomes. We annotated both haploid genomes, identifying a total of 95,439 protein-coding genes in the two haplotype genomes, with 98% functional annotation. The haplotype-resolved genome of 'Red Fuji' apple stands as a precise benchmark for an array of analyses, such as comparative genomics, transcriptomics, and allelic expression studies. This comprehensive resource is paramount in unraveling variations in allelic expression, advancing quality improvements, and refining breeding efforts.
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Affiliation(s)
- Haixu Peng
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - You Qing
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - Yulin Deng
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China
| | - Ji Tian
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Jie Zhang
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Yujing Hu
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Xiaoxiao Qin
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Yanfen Lu
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China
| | - Sen Wang
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China.
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China.
| | - Yi Zheng
- Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture, Bejing, 102206, China.
- Bioinformatics Center, Bejing University of Agriculture, Bejing, 102206, China.
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5
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Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y, Fei Z, Zheng Y. HortGenome Search Engine, a universal genomic search engine for horticultural crops. HORTICULTURE RESEARCH 2024; 11:uhae100. [PMID: 38863996 PMCID: PMC11165154 DOI: 10.1093/hr/uhae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Abstract
Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.
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Affiliation(s)
- Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shangxiao Wei
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yuling Deng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shaoyuan Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hua Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yijian Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hui Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yiding Wang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Renlong Zhang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Lu Ning
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
- Library, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
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6
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Wang W, Wei Y, Xu Z, Shen C, Li A, Guan D, Zhang X, Liu B. Evidence Supporting a Role of Alternative Splicing Participates in Melon ( Cucumis melo L.) Fruit Ripening. Int J Mol Sci 2024; 25:5886. [PMID: 38892093 PMCID: PMC11172951 DOI: 10.3390/ijms25115886] [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: 04/21/2024] [Revised: 05/19/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation.
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Affiliation(s)
- Wenjiao Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
| | - Yuping Wei
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Zhaoying Xu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Chengcheng Shen
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Ang Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Dailu Guan
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA;
| | - Xuejun Zhang
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Bin Liu
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
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7
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Zhou Y, Shen Q, Cai L, Zhao H, Zhang K, Ma Y, Bo Y, Lyu X, Yang J, Hu Z, Zhang M. Promoter variations of ClERF1 gene determines flesh firmness in watermelon. BMC PLANT BIOLOGY 2024; 24:290. [PMID: 38627629 PMCID: PMC11020897 DOI: 10.1186/s12870-024-05000-z] [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: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer's preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon. RESULTS In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis. CONCLUSIONS Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.
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Affiliation(s)
- Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lingmin Cai
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
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8
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Zhao L, Zhou W, He J, Li DZ, Li HT. Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant. eLife 2024; 12:RP89941. [PMID: 38353667 PMCID: PMC10942601 DOI: 10.7554/elife.89941] [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] [Indexed: 02/16/2024] Open
Abstract
Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Wei Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Jun He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
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9
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Kiryushkin AS, Ilina EL, Kiikova TY, Pawlowski K, Demchenko KN. Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber ( Cucumis sativus)? Int J Mol Sci 2024; 25:1975. [PMID: 38396652 PMCID: PMC10888659 DOI: 10.3390/ijms25041975] [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: 12/12/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
The architecture of the root system is fundamental to plant productivity. The rate of root growth, the density of lateral roots, and the spatial structure of lateral and adventitious roots determine the developmental plasticity of the root system in response to changes in environmental conditions. One of the genes involved in the regulation of the slope angle of lateral roots is DEEPER ROOTING 1 (DRO1). Its orthologs and paralogs have been identified in rice, Arabidopsis, and several other species. However, nothing is known about the formation of the slope angle of lateral roots in species with the initiation of lateral root primordia within the parental root meristem. To address this knowledge gap, we identified orthologs and paralogs of the DRO1 gene in cucumber (Cucumis sativus) using a phylogenetic analysis of IGT protein family members. Differences in the transcriptional response of CsDRO1, CsDRO1-LIKE1 (CsDRO1L1), and CsDRO1-LIKE2 (CsDRO1L2) to exogenous auxin were analyzed. The results showed that only CsDRO1L1 is auxin-responsive. An analysis of promoter-reporter fusions demonstrated that the CsDRO1, CsDRO1L1, and CsDRO1L2 genes were expressed in the meristem in cell files of the central cylinder, endodermis, and cortex; the three genes displayed different expression patterns in cucumber roots with only partial overlap. A knockout of individual CsDRO1, CsDRO1L1, and CsDRO1L2 genes was performed via CRISPR/Cas9 gene editing. Our study suggests that the knockout of individual genes does not affect the slope angle formation during lateral root primordia development in the cucumber parental root.
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Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Tatyana Y. Kiikova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
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10
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Ceylan Y, Altunoglu YC, Horuz E. HSF and Hsp Gene Families in sunflower: a comprehensive genome-wide determination survey and expression patterns under abiotic stress conditions. PROTOPLASMA 2023; 260:1473-1491. [PMID: 37154904 DOI: 10.1007/s00709-023-01862-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Sunflowers belong to the Asteraceae family, which comprises nutrimental and economic oilseed plants. Heat shock proteins (Hsps) are protein families vital for all organisms' growth and survival. Besides the ordinary conditions, the expression of these proteins ascends during abiotic stress factors such as high temperature, salinity, and drought. Using bioinformatics approaches, the current study identified and analyzed HSF and Hsp gene family members in the sunflower (Helianthus annuus L.) plant. HSF, sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100 domains were analyzed in the sunflower genome, and 88, 72, 192, 52, 85, 49, and 148 genes were identified, respectively. The motif structures of the proteins in the same phylogenetic tree were similar, and the α-helical form was dominant in all the protein families except for sHsp. The estimated three-dimensional structure of 28 sHsp proteins was determined as β-sheets. Considering protein-protein interactions, the Hsp60-09 protein (38 interactions) was found to be the most interacting protein. The most orthologous gene pairs (58 genes) were identified between Hsp70 genes and Arabidopsis genes. The expression analysis of selected genes was performed under high temperature, drought, and high temperature-drought combined stress conditions in two sunflower cultivars. In stress conditions, gene expressions were upregulated for almost all genes in the first half and first hours at large. The expressions of HanHSF-45 and HanHsp70-29 genes were raised in two cultivars under high temperature and high temperature-drought combined stress conditions. This study presents a blueprint for subsequent research and delivers comprehensive knowledge of this vital protein domain.
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Affiliation(s)
- Yusuf Ceylan
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Bartın University, Bartin, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
| | - Erdoğan Horuz
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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11
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Waldo BD, Branham SE, Levi A, Wechter WP, Rutter WB. Distinct Genomic Loci Underlie Quantitative Resistance to Meloidogyne enterolobii Galling and Reproduction in Citrullus amarus. PLANT DISEASE 2023; 107:2126-2132. [PMID: 36548923 DOI: 10.1094/pdis-09-22-2228-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Meloidogyne enterolobii is a virulent species of root-knot nematode that threatens watermelon (Citrullus lanatus) production in the southeastern United States. There are no known sources of root-knot nematode resistance in cultivated C. lanatus. Specific genotypes of a wild watermelon relative, C. amarus, are resistant against M. incognita but the genetics that underly this resistance are still unknown and it is not clear that this same resistance will be effective against M. enterolobii. To identify and characterize new sources of resistance to M. enterolobii, we screened 108 diverse C. amarus lines alongside a susceptible C. lanatus cultivar (Charleston Gray) for resistance against M. enterolobii. Different C. amarus genotypes ranged from resistant to susceptible for the three resistance phenotypes measured; mean percent root system galled ranged from 10 to 73%, mean egg mass counts ranged from 0.3 to 64.5, and mean eggs per gram of root ranged from 326 to 146,160. We used each of these three resistance phenotypes combined with whole-genome resequencing data to conduct a genome-wide association scan that identified significant associations between M. enterolobii resistance and 11 single-nucleotide polymorphisms (SNPs) within the C. amarus genome. Interestingly, SNPs associated with reduced galling and egg masses were located within a single quantitative trait locus (QTL) on chromosome Ca03, while reductions in nematode eggs per gram of root were associated with separate QTL on chromosomes Ca04 and Ca08. The results of this study suggest that multiple genes are involved with M. enterolobii resistance in C. amarus and the SNPs identified will assist with efforts to breed for M. enterolobii resistance in watermelon.
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Affiliation(s)
- Benjamin D Waldo
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
| | - Sandra E Branham
- Coastal Research and Education Center, Clemson University, Charleston, SC 29414
| | - Amnon Levi
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC 29414
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12
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Márquez-Molins J, Villalba-Bermell P, Corell-Sierra J, Pallás V, Gomez G. Integrative time-scale and multi-omics analysis of host responses to viroid infection. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37378473 DOI: 10.1111/pce.14647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.
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Affiliation(s)
- Joan Márquez-Molins
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Pascual Villalba-Bermell
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Julia Corell-Sierra
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Vicente Pallás
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Gustavo Gomez
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
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13
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Singh A, Mahato AK, Maurya A, Rajkumar S, Singh AK, Bhardwaj R, Kaushik SK, Kumar S, Gupta V, Singh K, Singh R. Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1203855. [PMID: 37448872 PMCID: PMC10337998 DOI: 10.3389/fpls.2023.1203855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023]
Abstract
Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3' and 5' flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user's query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.
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Affiliation(s)
- Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. Rajkumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - A. K. Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. K. Kaushik
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sandeep Kumar
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Veena Gupta
- Division of Germplasm Conservation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Singh
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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14
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in Cucumber ( Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 ( RALF34) Tell Us? Int J Mol Sci 2023; 24:ijms24098440. [PMID: 37176146 PMCID: PMC10179419 DOI: 10.3390/ijms24098440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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Affiliation(s)
- Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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15
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Shumilina J, Kiryushkin AS, Frolova N, Mashkina V, Ilina EL, Puchkova VA, Danko K, Silinskaya S, Serebryakov EB, Soboleva A, Bilova T, Orlova A, Guseva ED, Repkin E, Pawlowski K, Frolov A, Demchenko KN. Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots. Int J Mol Sci 2023; 24:ijms24087654. [PMID: 37108821 PMCID: PMC10140933 DOI: 10.3390/ijms24087654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators.
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Affiliation(s)
- Julia Shumilina
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Nadezhda Frolova
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Valeria Mashkina
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Vera A Puchkova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katerina Danko
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | | | | | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Tatiana Bilova
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Egor Repkin
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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16
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Ling J, Liu R, Hao Y, Li Y, Ping X, Yang Q, Yang Y, Lu X, Xie B, Zhao J, Mao Z. Comprehensive analysis of the WRKY gene family in Cucumis metuliferus and their expression profile in response to an early stage of root knot nematode infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1143171. [PMID: 37021316 PMCID: PMC10067755 DOI: 10.3389/fpls.2023.1143171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Root-knot nematode (RKN) is a major factor that limits the growth and productivity of important Cucumis crops, such as cucumber and melon, which lack RKN-resistance genes in their genome. Cucumis metuliferus is a wild Cucumis species that displays a high degree of RKN-resistance. WRKY transcription factors were involved in plant response to biotic stresses. However, little is known on the function of WRKY genes in response to RKN infection in Cucumis crops. In this study, Cucumis metuliferus 60 WRKY genes (CmWRKY) were identified in the C. metuliferus genome, and their conserved domains were classified into three main groups based on multiple sequence alignment and phylogenetic analysis. Synteny analysis indicated that the WRKY genes were highly conserved in Cucumis crops. Transcriptome data from of C. metuliferus roots inoculated with RKN revealed that 16 CmWRKY genes showed differential expression, of which 13 genes were upregulated and three genes were downregulated, indicating that these CmWRKY genes are important to C. metuliferus response to RKN infection. Two differentially expression CmWRKY genes (CmWRKY10 and CmWRKY28) were selected for further functional analysis. Both CmWRKY genes were localized in nucleus, indicating they may play roles in transcriptional regulation. This study provides a foundation for further research on the function of CmWRKY genes in RKN stress resistance and elucidation of the regulatory mechanism.
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Affiliation(s)
- Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yali Hao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingxing Ping
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qihong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofei Lu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Nie H, Kim M, Lee S, Lim S, Lee MS, Kim JH, Noh SJ, Park SW, Kim ST, Shin AY, Lee Y, Kwon SY. High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2023; 14:1142856. [PMID: 36938051 PMCID: PMC10014564 DOI: 10.3389/fpls.2023.1142856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The unique color and type characteristics of watermelon fruits are regulated by many molecular mechanisms. However, it still needs to be combined with more abundant genetic data to fine-tune the positioning. We assembled genomes of two Korean inbred watermelon lines (cv. 242-1 and 159-1) with unique color and fruit-type characteristics and identified 23,921 and 24,451 protein-coding genes in the two genomes, respectively. To obtain more precise results for further study, we resequenced one individual of each parental line and an F2 population composed of 87 individuals. This identified 1,539 single-nucleotide polymorphisms (SNPs) and 80 InDel markers that provided a high-density genetic linkage map with a total length of 3,036.9 cM. Quantitative trait locus mapping identified 15 QTLs for watermelon fruit quality-related traits, including β-carotene and lycopene content in fruit flesh, fruit shape index, skin thickness, flesh color, and rind color. By investigating the mapping intervals, we identified 33 candidate genes containing variants in the coding sequence. Among them, Cla97C01G008760 was annotated as a phytoene synthase with a single-nucleotide variant (A → G) in the first exon at 9,539,129 bp of chromosome 1 that resulted in the conversion of a lysine to glutamic acid, indicating that this gene might regulate flesh color changes at the protein level. These findings not only prove the importance of a phytoene synthase gene in pigmentation but also explain an important reason for the color change of watermelon flesh.
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Affiliation(s)
- Hualin Nie
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Moonkyo Kim
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
- Division of Life Science, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Sohee Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Mi Sun Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Ju Hyeok Kim
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Sol Ji Noh
- Watermelon and Strawberry Research Institute, Chungcheongbuk-do Agricultural Research and Extension Services, Cheongju, Republic of Korea
| | - Seong Won Park
- Watermelon and Strawberry Research Institute, Chungcheongbuk-do Agricultural Research and Extension Services, Cheongju, Republic of Korea
| | - Sang-Tae Kim
- Department of Medical and Biological Sciences, Catholic University of Korea, Bucheon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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18
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Li X, Lin S, Xiang C, Liu W, Zhang X, Wang C, Lu X, Liu M, Wang T, Liu Z, Wang N, Gao L, Han X, Zhang W. CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae. Comput Struct Biotechnol J 2023; 21:837-846. [PMID: 36698975 PMCID: PMC9842799 DOI: 10.1016/j.csbj.2023.01.012] [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: 10/16/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
As an internal modification of transcripts, RNA methylation determines RNA fate by changing RNA-protein binding affinity. In plants, RNA methylation is ubiquitous and is involved in all aspects of RNA post-transcriptional regulation. For instance, long-distance mobile RNAs, strongly influenced by their methylation status, play important roles in plant growth, development and environmental adaptation. Cucumber/pumpkin heterografts are widely used to improve stress tolerance of cucumber and to study mobile RNA signals due to their strong developed vasculature system. Here, we developed the Cucume (Cucurbit RNA methylation, http://cucume.cn/) database for these two important vegetables, cucumber (Cucumis sativus L.) and pumpkin (Cucurbita moschata) with high productivity worldwide. We identified mRNAs harboring 5-methylcytosine (m5C) and N6-methyladenosine (m6A) sites in pumpkin and cucumber at the whole genome level via Methylated RNA Immunoprecipitation sequencing (MeRIP-seq) of different tissues and the vascular exudates. In addition to RNA methylation sites, the Cucume database includes graft-transmissible systemic mRNAs identified in previous studies using cucumber/pumpkin heterografts. The further integration of cucumber genome-wide association analysis (GWAS) and quantitative trait loci (QTL) allows the study of RNA methylation-related genetic and epigenetic regulation in cucurbits. Therefore, the here developed Cucume database will promote understanding the role of cucurbit RNA methylation in RNA mobility and QTL, ultimately benefitting future breeding of agronomic crop germplasms.
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Affiliation(s)
- Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Shujin Lin
- College of Biology Science and Engineering, Fuzhou University, Fuzhou, China
| | - Chenggang Xiang
- College of Life Science and Technology, HongHe University, Mengzi, Yunnan, 661100, China
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojing Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Cuicui Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Mengshuang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Naonao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiao Han
- College of Biology Science and Engineering, Fuzhou University, Fuzhou, China,Corresponding authors.
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China,Corresponding authors.
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19
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Yang S, Sun Z, Zhang G, Wang L, Zhong Q. Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars. Food Res Int 2023; 163:112287. [PMID: 36596193 DOI: 10.1016/j.foodres.2022.112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.
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Affiliation(s)
- Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100, China
| | - Zhu Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Guangnan Zhang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China.
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20
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Genome-Wide Identification of the SUN Gene Family in Melon ( Cucumis melo) and Functional Characterization of Two CmSUN Genes in Regulating Fruit Shape Variation. Int J Mol Sci 2022; 23:ijms232416047. [PMID: 36555689 PMCID: PMC9785357 DOI: 10.3390/ijms232416047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Melon (Cucumis melo) is an important economic crop cultivated worldwide. A unique SUN gene family plays a crucial role in regulating plant growth and fruit development, but many SUN family genes and their function have not been well-characterized in melon. In the present study, we performed genome-wide identification and bioinformatics analysis and identified 24 CmSUN family genes that contain integrated and conserved IQ67 domain in the melon genome. Transcriptome data analysis and qRT-PCR results showed that most CmSUNs are specifically enriched in melon reproductive organs, such as young flowers and ovaries. Through genetic transformation in melons, we found that overexpression of CmSUN23-24 and CmSUN25-26-27c led to an increased fruit shape index, suggesting that they act as essential regulators in melon fruit shape variation. Subcellular localization revealed that the CmSUN23-24 protein is located in the cytoplasmic membrane. A direct interaction between CmSUN23-24 and a Calmodulin protein CmCaM5 was found by yeast two-hybrid assay, which indicated their participation in the calcium signal transduction pathway in regulating plant growth. These findings revealed the molecular characteristics, expression profile, and functional pattern of the CmSUN genes, and may provide the theoretical basis for the genetic improvement of melon fruit breeding.
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21
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Yeo SM, Hong J, Hossain MR, Jung HJ, Choe P, Nou IS. Genotyping by Sequencing (GBS)-Based QTL Mapping for Bacterial Fruit Blotch (BFB) in Watermelon. Genes (Basel) 2022; 13:genes13122250. [PMID: 36553516 PMCID: PMC9777634 DOI: 10.3390/genes13122250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Watermelon (Citrullus lanatus), an economically important and nutritionally rich Cucurbitaceous crop grown worldwide, is severely affected by bacterial fruit blotch (BFB). Development of resistant cultivar is the most eco-friendly, cost-effective, and sustainable way to tackle this disease. This requires wider understanding of the genetics of resistance to BFB. In this study, we identified quantitative trait loci (QTLs) associated with BFB resistance in an F2 mapping population developed from BFB-resistant 'PI 189225' (Citrullus amarus) and -susceptible 'SW 26' (C. lanatus) genotypes based on the polymorphic markers identified by genotyping by sequencing (GSB). A linkage map covering a total genetic distance of 3377.1 cM was constructed. Two QTLs for BFB resistance, namely, ClBFB10.1 and ClBFB10.2, both located on chromosome 10 explaining 18.84 and 15.41% of the phenotypic variations, respectively, were identified. Two SNP-based high-resolution melting (HRM) markers WmBFB10.1 and WmBFB10.2 having high positive correlation with resistance vs. susceptible alleles were developed. The efficacy of the markers was validated in another F2 population derived from SW34 × PI 189225. The highest phenotypic variation was found in the locus ClBFB10.2, which also contains three putative candidate genes for resistance to BFB. These findings will accelerate the development of BFB-resistant watermelon varieties via molecular breeding.
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Affiliation(s)
- Sang-Min Yeo
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Jeongeui Hong
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Mohammad Rashed Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Phillip Choe
- PPS Farming Corporation, Yongin 17096, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea
- Correspondence:
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22
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QTL associated with resistance to Stagonosporopsis citrulli in Citrullus amarus. Sci Rep 2022; 12:19628. [PMID: 36380003 PMCID: PMC9666438 DOI: 10.1038/s41598-022-23704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Gummy stem blight (GSB) is a fungal disease affecting cucurbit crops, including watermelon (Citrullus lanatus), leading to significant yield losses. The disease is caused by three Stagonosporopsis species, of which Stagonosporopsis citrulli is the most common in the southeastern United States. Currently no gummy stem blight-resistant watermelon cultivars are available to growers. In this study, QTL-seq in an interspecific population developed from Sugar Baby × PI 189225 (Citrullus amarus) identified QTL on chromosomes 2, 5, 9 and 11. A novel QTL on chromosome 5 (Qgsb5.2) associated with resistance to S. citrulli (PVE = 13.3%) was confirmed by genetic mapping. KASP marker assays were developed for selection of Qgsb5.2 to allow breeders to track the allele contributing resistance to GSB, reducing the need for laborious phenotyping. Pyramiding different GSB resistance QTL could be a useful strategy to develop GSB resistant watermelon cultivars.
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23
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Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2022; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
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Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany,Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China,Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- To whom correspondence should be addressed. Tel: +1 607 2543234; Fax: +1 607 2541242;
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24
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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25
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Hong JE, Hossain MR, Jung HJ, Nou IS. QTL associated with Gummy Stem Blight (GSB) resistance in watermelon. BMC Genomics 2022; 23:632. [PMID: 36057546 PMCID: PMC9441027 DOI: 10.1186/s12864-022-08849-2] [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: 02/09/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Background Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), produces devastating symptoms on whole plants of watermelon (Citrullus lanatus) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties. Results In this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F2 population developed from C. lanatus lines, ‘PI 279461’ (resistant) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1, ClGSB10.1, and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs (ClC01G014900 and ClC01G015010), two WRKY transcription factors (ClC01G014910 and ClC01G014990), and one AvrRpt-cleavage domain protein (ClC01G015130). Conclusion Two high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08849-2.
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Affiliation(s)
- Jeong-Eui Hong
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea
| | - Mohammad Rashed Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea.
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26
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LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071095. [PMID: 35888183 PMCID: PMC9316258 DOI: 10.3390/life12071095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/16/2022]
Abstract
Plant leaves, which convert light energy into chemical energy, serve as a major food source on Earth. The decrease in crop yield and quality is caused by plant leaf premature senescence. It is important to detect senescence-associated genes. In this study, we collected 5853 genes from a leaf senescence database and developed a leaf-senescence-associated genes (SAGs) prediction model using the support vector machine (SVM) and XGBoost algorithms. This is the first computational approach for predicting SAGs with the sequence dataset. The SVM-PCA-Kmer-PC-PseAAC model achieved the best performance (F1score = 0.866, accuracy = 0.862 and receiver operating characteristic = 0.922), and based on this model, we developed a SAGs prediction tool called “SAGs_Anno”. We identified a total of 1,398,277 SAGs from 3,165,746 gene sequences from 83 species, including 12 lower plants and 71 higher plants. Interestingly, leafy species showed a higher percentage of SAGs, while leafless species showed a lower percentage of SAGs. Finally, we constructed the Leaf SAGs Annotation Platform using these available datasets and the SAGs_Anno tool, which helps users to easily predict, download, and search for plant leaf SAGs of all species. Our study will provide rich resources for plant leaf-senescence-associated genes research.
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Lin X, Zhang N, Song H, Lin K, Pang E. Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber). G3 GENES|GENOMES|GENETICS 2022; 12:6585339. [PMID: 35554526 PMCID: PMC9258548 DOI: 10.1093/g3journal/jkac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022]
Abstract
Population-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher’s combination method by combining 4 haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found that these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in the Eurasian population and the gene controlling flesh thickness in the Xishuangbanna population. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.
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Affiliation(s)
- Xinrui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Ning Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
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Han D, Ma X, Zhang L, Zhang S, Sun Q, Li P, Shu J, Zhao Y. Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement. PLANTS 2022; 11:plants11121609. [PMID: 35736760 PMCID: PMC9228134 DOI: 10.3390/plants11121609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Cucumbers are rich in vitamins and minerals. The cucumber has recently become one of China’s main vegetable crops. More specifically, the adjustment of the Chinese agricultural industry’s structure and rapid economic development have resulted in increases in the planting area allocated to Chinese cucumber varieties and in the number of Chinese cucumber varieties. After complete sequencing of the “Chinese long” genome, the transcriptome, proteome, and metabolome were obtained. Cucumber has a small genome and short growing cycle, and these traits are conducive to the application of molecular breeding techniques for improving fruit quality. Here, we review the developments and applications of molecular markers and genetic maps for cucumber breeding and introduce the functions of gene families from the perspective of genomics, including fruit development and quality, hormone response, resistance to abiotic stress, epitomizing the development of other omics, and relationships among functions.
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Affiliation(s)
- Danni Han
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Xiaojun Ma
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Lei Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Pan Li
- School of Pharmacy, Liaocheng University, Liaocheng 252000, China;
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
- Correspondence: (J.S.); (Y.Z.)
| | - Yanting Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Correspondence: (J.S.); (Y.Z.)
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Lv S, Qiao X, Zhang W, Li Q, Wang P, Zhang S, Wu J. The origin and evolution of RNase T2 family and gametophytic self-incompatibility system in plants. Genome Biol Evol 2022; 14:6609977. [PMID: 35714207 PMCID: PMC9250077 DOI: 10.1093/gbe/evac093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Ribonuclease (RNase) T2 genes are found widely in both eukaryotes and prokaryotes, and genes from this family have been revealed to have various functions in plants. In particular, S-RNase is known to be the female determinant in the S-RNase-based gametophytic self-incompatibility (GSI) system. However, the origin and evolution of the RNase T2 gene family and GSI system are not well understood. In this study, 785 RNase T2 genes were identified in 81 sequenced plant genomes representing broad-scale diversity and divided into three subgroups (Class I, II, and III) based on phylogenetic and synteny network analysis. Class I was found to be of ancient origin and to emerge in green algae, Class II was shown to originate with the appearance of angiosperms, while Class III was discovered to be eudicot-specific. Each of the three major classes could be further classified into several subclasses of which some subclasses were found to be lineage-specific. Furthermore, duplication, deletion, or inactivation of the S/S-like-locus was revealed to be linked to repeated loss and gain of self-incompatibility in different species from distantly related plant families with GSI. Finally, the origin and evolutionary history of S-locus in Rosaceae species was unraveled with independent loss and gain of S-RNase occurred in different subfamilies of Rosaceae. Our findings provide insights into the origin and evolution of the RNase T2 family and the GSI system in plants.
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Affiliation(s)
- Shouzheng Lv
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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Zhou C, Lin C, Xing P, Li X, Song Z. SmGDB: genome database of Salvia miltiorrhiza, an important TCM Plant. Genes Genomics 2022; 44:699-707. [PMID: 35460467 DOI: 10.1007/s13258-022-01251-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Salvia miltiorrhiza is an important traditional Chinese medicinal (TCM) plant and a model plant in the genetic study of TCM. A series of omics related to Danshen have been published. Integrating, managing, storing, and sharing data has become an urgent problem to be solved in S. miltiorrhiza genetic studies. OBJECTIVES The genome database is the link for the exchange, acquisition, and use of different omics data between data producers and users, maximizing value and utilization of data. METHODS The genome database included DSS3 genome and five RNA-Seq data. The back-end performs data search and retrieval through the LAMP (Linux, Apache, MySQL, PHP) framework. RESULTS Here, we present SmGDB (S. miltiorrhiza genome database; http://8.140.162.85/ ), which houses the latest version of genome sequence and annotation data for S. miltiorrhiza, combining three unpublished RNA-Seq data from our group and two released RNA-Seq data. We also identified a novel gene cluster including seven CYP71D genes involved in the tanshinone synthesis pathway based on genome sequences and expression data. Besides, SmGDB provides user-friendly web interfaces for querying and browsing gene annotation, structure, location, and expression profiles for concerned genes. Popular bioinformatics tools such as 'BLAST', 'Search', 'Heatmap', 'JBrowse', etc., were also provided in SmGDB. CONCLUSIONS SmGDB will provide utility for characterizing the structure of the S. miltiorrhiza genome and better understanding gene functions and biological processes underlying complex secondary metabolism in Danshen.
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Affiliation(s)
- Changhao Zhou
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Caicai Lin
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Piyi Xing
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Xingfeng Li
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China. .,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China.
| | - Zhenqiao Song
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China.
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Parvathi MS, Antony PD, Kutty MS. Multiple Stressors in Vegetable Production: Insights for Trait-Based Crop Improvement in Cucurbits. FRONTIERS IN PLANT SCIENCE 2022; 13:861637. [PMID: 35592574 PMCID: PMC9111534 DOI: 10.3389/fpls.2022.861637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Vegetable production is a key determinant of contribution from the agricultural sector toward national Gross Domestic Product in a country like India, the second largest producer of fresh vegetables in the world. This calls for a careful scrutiny of the threats to vegetable farming in the event of climate extremes, environmental degradation and incidence of plant pests/diseases. Cucurbits are a vast group of vegetables grown almost throughout the world, which contribute to the daily diet on a global scale. Increasing food supply to cater to the ever-increasing world population, calls for intensive, off-season and year-round cultivation of cucurbits. Current situation predisposes these crops to a multitude of stressors, often simultaneously, under field conditions. This scenario warrants a systematic understanding of the different stress specific traits/mechanisms/pathways and their crosstalk that have been examined in cucurbits and identification of gaps and formulation of perspectives on prospective research directions. The careful dissection of plant responses under specific production environments will help in trait identification for genotype selection, germplasm screens to identify superior donors or for direct genetic manipulation by modern tools for crop improvement. Cucurbits exhibit a wide range of acclimatory responses to both biotic and abiotic stresses, among which a few like morphological characters like waxiness of cuticle; primary and secondary metabolic adjustments; membrane thermostability, osmoregulation and, protein and reactive oxygen species homeostasis and turnover contributing to cellular tolerance, appear to be common and involved in cross talk under combinatorial stress exposures. This is assumed to have profound influence in triggering system level acclimation responses that safeguard growth and metabolism. The possible strategies attempted such as grafting initiatives, molecular breeding, novel genetic manipulation avenues like gene editing and ameliorative stress mitigation approaches, have paved way to unravel the prospects for combined stress tolerance. The advent of next generation sequencing technologies and big data management of the omics output generated have added to the mettle of such emanated concepts and ideas. In this review, we attempt to compile the progress made in deciphering the biotic and abiotic stress responses of cucurbits and their associated traits, both individually and in combination.
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Affiliation(s)
- M. S. Parvathi
- Department of Plant Physiology, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - P. Deepthy Antony
- Centre for Intellectual Property Rights, Technology Management and Trade, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - M. Sangeeta Kutty
- Department of Vegetable Science, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
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Yang J, Zhang J, Du H, Zhao H, Li H, Xu Y, Mao A, Zhang X, Fu Y, Xia Y, Wen C. The vegetable SNP database: An integrated resource for plant breeders and scientists. Genomics 2022; 114:110348. [PMID: 35339630 DOI: 10.1016/j.ygeno.2022.110348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/24/2022] [Accepted: 03/20/2022] [Indexed: 01/14/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are widely used in genetic research and molecular breeding. To date, the genomes of many vegetable crops have been assembled, and hundreds of core germplasms for each vegetable have been sequenced. However, these data are not currently easily accessible because they are stored on different public databases. Therefore, a vegetable crop SNP database should be developed that hosts SNPs demonstrated to have a high success rate in genotyping for genetic research (herein, "alpha SNPs"). We constructed a database (VegSNPDB, http://www.vegsnpdb.cn/) containing the sequence data of 2032 germplasms from 16 vegetable crop species. VegSNPDB hosts 118,725,944 SNPs of which 4,877,305 were alpha SNPs. SNPs can be searched by chromosome number, position, SNP type, genetic population, or specific individuals, as well as the values of MAF, PIC, and heterozygosity. We hope that VegSNPDB will become an important SNP database for the vegetable research community.
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Affiliation(s)
- Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Heshan Du
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Yong Xu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Xiaofei Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Yiqian Fu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Yang Xia
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China; State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300380, China.
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Bhowmick BK, Jha S. A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa. COMPARATIVE CYTOGENETICS 2022; 16:93-125. [PMID: 36761811 PMCID: PMC9849056 DOI: 10.3897/compcytogen.v16.i2.79033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/13/2023]
Abstract
The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata-700006, West Bengal, IndiaScottish Church CollegeKolkataIndia
| | - Sumita Jha
- Plant Cytogenetics and Biotechnology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
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Krishnamurthy P, Pothiraj R, Suthanthiram B, Somasundaram SM, Subbaraya U. Phylogenomic classification and synteny network analyses deciphered the evolutionary landscape of aldo-keto reductase (AKR) gene superfamily in the plant kingdom. Gene 2022; 816:146169. [PMID: 35026291 DOI: 10.1016/j.gene.2021.146169] [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: 07/29/2021] [Revised: 10/29/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022]
Abstract
Aldo-keto reductase-domain (PF00248) containing proteins (AKRs) are NAD(P)(H)-dependent oxidoreductases of a multigene superfamily that mediate versatile functions in plants ranging from detoxification, metal chelation, potassium ion efflux to specialized metabolism. To uncover the complete repertoire of AKR gene superfamily in plants, a systematic kingdom-wide identification, phylogeny reconstruction, classification and synteny network clustering analyses were performed in this study using 74 diverse plant genomes. Plant AKRs were omnipresent, legitimately classified into 4 groups (based on phylogeny) and 14 subgroups (based on the ≥ 60% of protein sequence identity). Species composition of AKR subgroups highlights their distinct emergence during plant evolution. Loss of AKR subgroups among plants was apparent and that various lineage-, order/family- and species-specific losses were observed. The subgroups IA, IVB and IVF were flourished and diversified well during plant evolution, likely related to the complexity of plant's specialized metabolism and environmental adaptation. About 65% of AKRs were in genomic synteny regions across the plant kingdom and the AKRs relevant to important functions (e.g. vitamin B6 metabolism) were in profoundly conserved angiosperm-wide synteny communities. This study underscores the evolutionary landscape of plant AKRs and provides a comprehensive resource to facilitate the functional characterization of them.
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Affiliation(s)
| | - Ramanujam Pothiraj
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620 102, India
| | - Backiyarani Suthanthiram
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620 102, India
| | | | - Uma Subbaraya
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620 102, India
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35
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Liu Y, Zhang Y, Zheng Y, Nie X, Wang Y, Yu W, Su S, Cao Q, Qin L, Xing Y. Beta-Amylase and Phosphatidic Acid Involved in Recalcitrant Seed Germination of Chinese Chestnut. FRONTIERS IN PLANT SCIENCE 2022; 13:828270. [PMID: 35401618 PMCID: PMC8990265 DOI: 10.3389/fpls.2022.828270] [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: 12/03/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Chinese chestnut (Castanea mollissima), a species with recalcitrant seeds, is an important source of nuts and forest ecosystem services. The germination rate of recalcitrant seeds is low in natural habitats and decreases under conditions of desiccation and low temperature. The germination rate of cultivated Chinese chestnut seeds is significantly higher than that of wild seeds. To explore the reasons for the higher germination rate of cultivated seeds in Chinese chestnut, 113,524 structural variants (SVs) between the wild and cultivated Chinese chestnut genomes were detected through genome comparison. Genotyping these SVs in 60 Chinese chestnut accessions identified allele frequency changes during Chinese chestnut domestication, and some SVs are overlapping genes for controlling seed germination. Transcriptome analysis revealed downregulation of the abscisic acid synthesis genes and upregulation of the beta-amylase synthesis genes in strongly selected genes of cultivated seeds. On the other hand, hormone and enzyme activity assays indicated a decrease in endogenous ABA level and an increase in beta-amylase activity in cultivated seeds. These results shed light on the higher germination rate of cultivated seeds. Moreover, phosphatidic acid synthesis genes are highly expressed in seed germination stages of wild Chinese chestnut and may play a role in recalcitrant seed germination. These findings provide new insight into the regulation of wild seed germination and promote natural regeneration and succession in forest ecosystems.
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Affiliation(s)
- Yang Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Yu Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yi Zheng
- Bioinformatics Center, Beijing University of Agriculture, Beijing, China
| | - Xinghua Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yafeng Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Wenjie Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Shuchai Su
- Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ling Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yu Xing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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Nimmy MS, Kumar V, Suthanthiram B, Subbaraya U, Nagar R, Bharadwaj C, Jain PK, Krishnamurthy P. A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:774885. [PMID: 35371145 PMCID: PMC8970042 DOI: 10.3389/fpls.2022.774885] [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: 09/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.
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Affiliation(s)
| | - Vinod Kumar
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, India
| | | | - Uma Subbaraya
- Crop Improvement Division, ICAR–National Research Centre for Banana, Tiruchirappalli, India
| | - Ramawatar Nagar
- ICAR–National Institute for Plant Biotechnology, New Delhi, India
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Rodriguez-Granados NY, Ramirez-Prado JS, Brik-Chaouche R, An J, Manza-Mianza D, Sircar S, Troadec C, Hanique M, Soulard C, Costa R, Dogimont C, Latrasse D, Raynaud C, Boualem A, Benhamed M, Bendahmane A. CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1213-1228. [PMID: 34897855 DOI: 10.1111/tpj.15627] [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: 05/04/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.
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Affiliation(s)
- Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Juan Sebastian Ramirez-Prado
- Centre of Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Jing An
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Sanchari Sircar
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Melissa Hanique
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Camille Soulard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Rafael Costa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, BP 94, F-84143, Montfavet, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
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Rehman S, Rashid A, Manzoor MA, Li L, Sun W, Riaz MW, Li D, Zhuge Q. Genome-Wide Evolution and Comparative Analysis of Superoxide Dismutase Gene Family in Cucurbitaceae and Expression Analysis of Lagenaria siceraria Under Multiple Abiotic Stresses. Front Genet 2022; 12:784878. [PMID: 35211150 PMCID: PMC8861505 DOI: 10.3389/fgene.2021.784878] [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: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Superoxide dismutase (SOD) is an important enzyme that serves as the first line of defense in the plant antioxidant system and removes reactive oxygen species (ROS) under adverse conditions. The SOD protein family is widely distributed in the plant kingdom and plays a significant role in plant growth and development. However, the comprehensive analysis of the SOD gene family has not been conducted in Cucurbitaceae. Subsequently, 43 SOD genes were identified from Cucurbitaceae species [Citrullus lanatus (watermelon), Cucurbita pepo (zucchini), Cucumis sativus (cucumber), Lagenaria siceraria (bottle gourd), Cucumis melo (melon)]. According to evolutionary analysis, SOD genes were divided into eight subfamilies (I, II, III, IV, V, VI, VII, VIII). The gene structure analysis exhibited that the SOD gene family had comparatively preserved exon/intron assembly and motif as well. Phylogenetic and structural analysis revealed the functional divergence of Cucurbitaceae SOD gene family. Furthermore, microRNAs 6 miRNAs were predicted targeting 3 LsiSOD genes. Gene ontology annotation outcomes confirm the role of LsiSODs under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Promoter regions of the SOD family revealed that most cis-elements were involved in plant development, stress response, and plant hormones. Evaluation of the gene expression showed that most SOD genes were expressed in different tissues (root, flower, fruit, stem, and leaf). Finally, the expression profiles of eight LsiSOD genes analyzed by qRT-PCR suggested that these genetic reserves responded to drought, saline, heat, and cold stress. These findings laid the foundation for further study of the role of the SOD gene family in Cucurbitaceae. Also, they provided the potential for its use in the genetic improvement of Cucurbitaceae.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Arif Rashid
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | | | - Lingling Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
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Li J, Yang S, Yang X, Wu H, Tang H, Yang L. PlantGF: an analysis and annotation platform for plant gene families. Database (Oxford) 2022; 2022:6520816. [PMID: 35134149 PMCID: PMC9278324 DOI: 10.1093/database/baab088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/26/2021] [Accepted: 01/01/2022] [Indexed: 12/22/2022]
Abstract
Gene families contain genes that come from the same ancestor and have similar sequences and structures. They perform certain specific functions within and among different species. Currently, there is no complete process or platform for the rapid analysis of plant gene families. In this study, a comprehensive query and analysis platform of plant gene families, the Plant Gene Family Platform (PlantGF), was constructed. The platform is composed of four main parts: Search, Tools, Statistics and Auxiliary. A total of 2 909 580 gene family members were identified from 138 plant species in PlantGF. The data can be queried in the Search section through a user-friendly interface. A general process for gene family analysis, having nine steps, is provided. The platform also includes four online tools (HMM-Search, BLAST, MAFFT and HMMER) in the Tools section for useful additional analyses. The statistical analysis of the relevant gene families is shown on the Statistics page. Auxiliary pages are provided for data downloading. The datasets for all 138 plant species' protein sequences and their gene families can be acquired on the Download page. A user's manual and some useful links are displayed on the Manual and Links pages, respectively. To the best of our knowledge, PlantGF is the first comprehensive platform for studying plant gene families, and it will make important contributions to plant gene family-related research. Database URL: http://biodb.sdau.edu.cn/PGF/index.html.
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Affiliation(s)
| | | | - Xiaojie Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Taian 271018, China
| | - Hui Wu
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Taian 271018, China
| | - Heng Tang
- *Corresponding author: Tel: (+86) 0538-8241575; Email Correspondence may also be addressed to Heng Tang. Tel: (+86) 0538-8241575; Email
| | - Long Yang
- *Corresponding author: Tel: (+86) 0538-8241575; Email Correspondence may also be addressed to Heng Tang. Tel: (+86) 0538-8241575; Email
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40
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Geng S, Sohail H, Cao H, Sun J, Chen Z, Zhou L, Wang W, Ye R, Yang L, Bie Z. An efficient root transformation system for CRISPR/Cas9-based analyses of shoot-root communication in cucurbit crops. HORTICULTURE RESEARCH 2022; 9:uhab082. [PMID: 35048110 PMCID: PMC9071382 DOI: 10.1093/hr/uhab082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 05/28/2023]
Abstract
Cucurbit crops are suitable models for studying long-distance signaling in horticultural plants. Although thousands of substances are graft transmissible in cucurbits, functional studies have been hampered by the lack of efficient genetic transformation systems. Here, we report a convenient and efficient root transformation method for several cucurbit crops that will facilitate studies of functional genes and shoot-root crosstalk. We obtained healthy plants with completely transformed roots and non-transgenic shoots within 6 weeks. Furthermore, we combined this root transformation method with grafting, which allowed for gene manipulation in the rootstock. We validated our system by exploring salt tolerance mechanisms using a cucumber (Cucumis sativus)/pumpkin (Cucurbita moschata Duch.) (scion/rootstock) graft in which the sodium transporter gene High-affinity K+ transporter1 (CmoHKT1;1) was edited in the pumpkin rootstock, and by overexpressing the pumpkin tonoplast Na+/H+ antiporter gene Sodium hydrogen exchanger4 (CmoNHX4) in cucumber roots.
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Affiliation(s)
- Shouyu Geng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hamza Sohail
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Haishun Cao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jingyu Sun
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijian Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenbo Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Runwen Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhilong Bie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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41
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Oren E, Tzuri G, Dafna A, Rees ER, Song B, Freilich S, Elkind Y, Isaacson T, Schaffer AA, Tadmor Y, Burger J, Buckler ES, Gur A. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes. HORTICULTURE RESEARCH 2022; 9:uhab081. [PMID: 35043206 PMCID: PMC8968493 DOI: 10.1093/hr/uhab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 05/27/2023]
Abstract
Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.
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Affiliation(s)
- Elad Oren
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Galil Tzuri
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Asaf Dafna
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Evan R Rees
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
| | - Baoxing Song
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
| | - Shiri Freilich
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Yonatan Elkind
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tal Isaacson
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, Rishon LeZiyyon 7507101, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Edward S Buckler
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Amit Gur
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
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Heterosis and Combining Ability for Fruit Yield, Sweetness, β-Carotene, Ascorbic Acid, Firmness and Fusarium Wilt Resistance in Muskmelon (Cucumis melo L.) Involving Genetic Male Sterile Lines. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ten genetically diverse inbred lines, including two genic male sterile lines, of muskmelon (Cucumis melo L.) were crossed in a half-diallel to generate 45 F1 hybrids. These hybrids, along with the parental lines and commercial check, were evaluated for their fruit yield, level of phytochemicals and Fusarium wilt resistance. Both additive and non-additive genetic variances were important in governing the expression of all of the traits; however, the additive gene action for the fruit weight (g), flesh thickness (cm), rind thickness (mm), firmness (lb inch−2), β-carotene content (mg/100 g), non-additive variance for fruit yield (t ha−1), fruit number, total soluble solids (TSS, °Brix), ascorbic acid (mg/100 g) and reaction to Fusarium wilt were comparatively more important. The parental line MM-625 was the best general combiner for fruit yield, rind thickness and β-carotene content (mg/100 g). The exotic line Riogold was the best combiner for flesh thickness and firmness. The netted inbred line MM-610 was the best general combiner for fruit weight, ascorbic acid and reaction to Fusarium wilt. The inbred lines KP4HM-15 and MM-916 were the best general combiners for the number of fruits per vine and TSS. The best cross-combinations for fruit yield ha−1 and TSS were MS-1×M-610 and Kajri×MM-904, respectively. The hybrids KP4HM-15×MM Sel-103 and KP4HM-15×MM-1831 recorded the highest standard heterosis for fruit yield and TSS. The landrace-derived inbred lines Kajri, MM Sel-103 and KP4HM-15 produced moderate-to-highly FW-resistant hybrids. Out of the 121 SSR markers applied, 70 exhibited parental polymorphism. The markers DM0561, CMAAAGN14, TJ147, CMMS35_3, CMAGN45 and DE1337 identified specific/unique alleles in certain parental genotypes. Thus, the findings of this study revealed that the novel inbred lines can effectively be combined to generate heterotic F1 hybrids for yield and other traits, such as rind and flesh thickness, TSS, β-carotene content and firmness. Furthermore, SSR markers can potentially be utilized to confirm the genetic diversity among the parental lines, and for the DNA fingerprinting of F1 hybrids.
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Yamagishi N, Yoshikawa N. Efficient virus-induced gene silencing system in pumpkin (Cucurbita maxima) using apple latent spherical virus vector. J Virol Methods 2022; 301:114456. [PMID: 34999150 DOI: 10.1016/j.jviromet.2022.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Crude-sap of apple latent spherical virus (ALSV)-infected Chenopodium quinoa leaves was rub-inoculated on the expanded cotyledons of various Cucurbitaceae plants. Most of the species were systemically infected with the virus without obvious symptoms, except pumpkin (Cucurbita maxima). In pumpkin, the ALSV infection was restricted to inoculated cotyledons; it did not spread to the upper true leaves. In situ hybridization showed that the ALSV was confined to part of the cotyledon tissues and it did not invade the phloem tissue, when inoculated at the expanded cotyledon stage. However, when total RNAs from ALSV-infected C. quinoa leaves were inoculated into the cotyledons immediately after germination (folded cotyledon stage) using particle bombardment, ALSV efficiently caused systemic infection. Systemic infection of pumpkin seedlings occurred only when the cotyledons were inoculated within a few days after germination. No systemic infection was observed in the seedlings 4 days after germination. In the grafting test, ALSV was not transmitted from the infected rootstocks to the healthy scions of pumpkins. An efficient virus-induced gene silencing system for pumpkins was established, in which infection with ALSV vectors harboring the phytoene desaturase or sulfur gene fragments resulted in a uniform phenotype in the true leaves of pumpkin seedlings.
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Affiliation(s)
- Noriko Yamagishi
- Agri-Innovation Center, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Nobuyuki Yoshikawa
- Agri-Innovation Center, Iwate University, Morioka, Iwate 020-8550, Japan.
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44
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Zheng Q, Majsec K, Katagiri F. Pathogen-driven coevolution across the CBP60 plant immune regulator subfamilies confers resilience on the regulator module. THE NEW PHYTOLOGIST 2022; 233:479-495. [PMID: 34610150 DOI: 10.1111/nph.17769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Components of the plant immune signaling network need mechanisms that confer resilience against fast-evolving pathogen effectors that target them. Among eight Arabidopsis CaM-Binding Protein (CBP) 60 family members, AtCBP60g and AtSARD1 are partially functionally redundant, major positive immune regulators, and AtCBP60a is a negative immune regulator. We investigated possible resilience-conferring evolutionary mechanisms among the CBP60a, CBP60g and SARD1 immune regulatory subfamilies. Phylogenetic analysis was used to investigate the times of CBP60 subfamily neofunctionalization. Then, using the pairwise distance rank based on the newly developed analytical platform Protein Evolution Analysis in a Euclidean Space (PEAES), hypotheses of specific coevolutionary mechanisms that could confer resilience on the regulator module were tested. The immune regulator subfamilies diversified around the time of angiosperm divergence and have been evolving very quickly. We detected significant coevolutionary interactions across the immune regulator subfamilies in all of 12 diverse core eudicot species lineages tested. The coevolutionary interactions were consistent with the hypothesized coevolution mechanisms. Despite their unusually fast evolution, members across the CBP60 immune regulator subfamilies have influenced the evolution of each other long after their diversification in a way that could confer resilience on the immune regulator module against fast-evolving pathogen effectors.
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Affiliation(s)
- Qi Zheng
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Kristina Majsec
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
| | - Fumiaki Katagiri
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
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Tan C, Qiao H, Ma M, Wang X, Tian Y, Bai S, Hasi A. Genome-Wide Identification and Characterization of Melon bHLH Transcription Factors in Regulation of Fruit Development. PLANTS 2021; 10:plants10122721. [PMID: 34961193 PMCID: PMC8709311 DOI: 10.3390/plants10122721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor families in plants and plays crucial roles in plant development. Melon is an important horticultural plant as well as an attractive model plant for studying fruit ripening. However, the bHLH gene family of melon has not yet been identified, and its functions in fruit growth and ripening are seldom researched. In this study, 118 bHLH genes were identified in the melon genome. These CmbHLH genes were unevenly distributed on chromosomes 1 to 12, and five CmbHLHs were tandem repeat on chromosomes 4 and 8. There were 13 intron distribution patterns among the CmbHLH genes. Phylogenetic analysis illustrated that these CmbHLHs could be classified into 16 subfamilies. Expression patterns of the CmbHLH genes were studied using transcriptome data. Tissue specific expression of the CmbHLH32 gene was analysed by quantitative RT-PCR. The results showed that the CmbHLH32 gene was highly expressed in female flower and early developmental stage fruit. Transgenic melon lines overexpressing CmbHLH32 were generated, and overexpression of CmbHLH32 resulted in early fruit ripening compared to wild type. The CmbHLH transcription factor family was identified and analysed for the first time in melon, and overexpression of CmbHLH32 affected the ripening time of melon fruit. These findings laid a foundation for further study on the role of bHLH family members in the growth and development of melon.
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Affiliation(s)
- Chao Tan
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (C.T.); (H.Q.); (M.M.); (Y.T.)
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China;
| | - Huilei Qiao
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (C.T.); (H.Q.); (M.M.); (Y.T.)
| | - Ming Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (C.T.); (H.Q.); (M.M.); (Y.T.)
| | - Xue Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China;
| | - Yunyun Tian
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (C.T.); (H.Q.); (M.M.); (Y.T.)
| | - Selinge Bai
- Medical College, Inner Mongolia MINZU University, Tongliao 028000, China
- Correspondence: (S.B.); (A.H.)
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (C.T.); (H.Q.); (M.M.); (Y.T.)
- Correspondence: (S.B.); (A.H.)
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Branham SE, Kousik C, Mandal MK, Wechter WP. Quantitative Trait Loci Mapping of Resistance to Powdery Mildew Race 1 in a Recombinant Inbred Line Population of Melon. PLANT DISEASE 2021; 105:3809-3815. [PMID: 34253041 DOI: 10.1094/pdis-12-20-2643-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Powdery mildew, caused by the fungus Podosphaera xanthii, is one of the most important diseases of melon. Although there are several pathogenic races of P. xanthii, race 1 is the predominant race in South Carolina and in other parts of the United States. We used a densely genotyped recombinant inbred line melon population for traditional quantitative trait loci (QTL) mapping, to identify two major (qPx1-5 and qPx1-12) and two minor (qPx1-4 and qPx1-10) QTLs (named according to race - chromosome number) associated with resistance to P. xanthii race 1. QTL mapping of disease severity in multiple tissues (hypocotyl, cotyledons, true leaves, and stems) identified the same genetic basis of resistance in all tissue types. Whole-genome resequencing of the parents was used for marker development across the major QTLs and functional annotation of single nucleotide polymorphisms (SNPs) for candidate gene analysis. Kompetitive allele-specific PCR (KASP) markers were tightly linked to the QTL peaks of qPx1-5 (pm1-5_25329892, pm1-5_25461503 and pm1-5_25625375) and qPx1-12 (pm1-12_22848920 and pm1-12_22904659) in the population and will enable efficient marker-assisted introgression of powdery mildew resistance into improved germplasm. Candidate genes were identified in both major QTL intervals that encode putative R genes with missense mutations between the parents. The candidate genes provide targets for future breeding efforts and a fundamental examination of resistance to powdery mildew in melon.
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Affiliation(s)
- Sandra E Branham
- Coastal Research and Education Center, Clemson University, Charleston, SC
| | - Chandrasekar Kousik
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414
| | - Mihir K Mandal
- Department of Biology, Claflin University, Orangeburg, SC 29115
| | - W Patrick Wechter
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414
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Wang X, Zheng Y, Chen B, Zhi C, Qiao L, Liu C, Pan Y, Cheng Z. Genome-wide identification of small heat shock protein (HSP20) homologs in three cucurbit species and the expression profiles of CsHSP20s under several abiotic stresses. Int J Biol Macromol 2021; 190:827-836. [PMID: 34492251 DOI: 10.1016/j.ijbiomac.2021.08.222] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022]
Abstract
Small heat shock protein (HSP20) genes play important roles in biological processes of plants. In this study, a total of 47 CsHSP20 genes, 45 CmHSP20 genes, and 47 ClHSP20 genes were genome-wide identified by 'hmmsearch' and BLASTP using the latest versions of cucumber, melon, and watermelon genomes, respectively. According to the phylogenetic relationships and predicted subcellular localizations, HSP20s of these three cucurbit species were divided into 8 subfamilies (CI-CIV, CP, ER, M, and PX), in which some HSP20s were closely related with each other based on the collinearity analysis. Specific expression patterns of CsHSP20s were checked in 10 different tissues of cucumber plants. RNA-seq analysis of transcript levels, combined with cis-acting elements and GO enrichment analysis suggested that CsHSP20s were responsive to several different types of abiotic stresses, including chilling, temperature and photoperiod, high temperature and high humidity, and salinity. In conclusion, results of this work not only provided valuable information for exploring the regulating mechanisms of CsHSP20s in responding to abiotic stresses in cucumber, but also shed light on the potentially evolutional relations among cucumber, melon, and watermelon from a perspective of comparative genomics that specified on HSP20 gene families.
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Affiliation(s)
- Xi'ao Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yujie Zheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Birong Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Chengchen Zhi
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Lijun Qiao
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ce Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Yu J, Wang K, Beckles DM. Starch branching enzymes as putative determinants of postharvest quality in horticultural crops. BMC PLANT BIOLOGY 2021; 21:479. [PMID: 34674662 PMCID: PMC8529802 DOI: 10.1186/s12870-021-03253-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Starch branching enzymes (SBEs) are key determinants of the structure and amount of the starch in plant organs, and as such, they have the capacity to influence plant growth, developmental, and fitness processes, and in addition, the industrial end-use of starch. However, little is known about the role of SBEs in determining starch structure-function relations in economically important horticultural crops such as fruit and leafy greens, many of which accumulate starch transiently. Further, a full understanding of the biological function of these types of starches is lacking. Because of this gap in knowledge, this minireview aims to provide an overview of SBEs in horticultural crops, to investigate the potential role of starch in determining postharvest quality. A systematic examination of SBE sequences in 43 diverse horticultural species, identified SBE1, 2 and 3 isoforms in all species examined except apple, olive, and Brassicaceae, which lacked SBE1, but had a duplicated SBE2. Among our findings after a comprehensive and critical review of published data, was that as apple, banana, and tomato fruits ripens, the ratio of the highly digestible amylopectin component of starch increases relative to the more digestion-resistant amylose fraction, with parallel increases in SBE2 transcription, fruit sugar content, and decreases in starch. It is tempting to speculate that during the ripening of these fruit when starch degradation occurs, there are rearrangements made to the structure of starch possibly via branching enzymes to increase starch digestibility to sugars. We propose that based on the known action of SBEs, and these observations, SBEs may affect produce quality, and shelf-life directly through starch accumulation, and indirectly, by altering sugar availability. Further studies where SBE activity is fine-tuned in these crops, can enrich our understanding of the role of starch across species and may improve horticulture postharvest quality.
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Affiliation(s)
- Jingwei Yu
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA
- Present Address: Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Keyun Wang
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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New early phenotypic markers for cucumber green mottle mosaic virus disease in cucumbers exposed to fluctuating extreme temperatures. Sci Rep 2021; 11:19060. [PMID: 34561518 PMCID: PMC8463606 DOI: 10.1038/s41598-021-98595-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/13/2021] [Indexed: 11/11/2022] Open
Abstract
Studies of early stages of cucumber green mottle mosaic virus (CGMMV) disease have been recently focused on plant molecular responses. However, extreme diurnal environmental temperatures, characteristic of global climate changes, could affect plant susceptibility and disease phenotype progression. Our studies of CGMMV disease progression, under simulated extreme temperature waves, have revealed two new disease initiation phenotypes that developed gradually, preceding severe symptom manifestations of post-recovery CGMMV systemic infections. 'Early post-recovery stage' bright yellow islands (BYIs) with defined boundaries amid asymptomatic leaf blades were first emerging followed by 'late post-recovery stage' BYIs with diffused boundaries. A deduced CGMMV disease progression scheme, postulating BYI symptom occurrence time-windows, revealed BYIs in field grown cucumber plants exposed to extreme diurnal temperatures. Profiling ontology of cucumber differentially expressed genes in BYIs vs the associated dark-green surrounding tissues disclosed activation of jasmonic acid (JA) pathway in 'early post-recovery stage' BYIs. JA signaling was inactivated in 'late post-recovery stage' BYIs concomitant with increasing expressions of JA signaling inhibitors and downregulation of JA responsive phenylpropanoid pathway. Our results disclosed a new phenotypic description of CGMMV disease initiation, characteristic of cucumbers grown under extreme environmental temperature fluctuations. The BYI phenotypes could define a time-window for CGMMV disease management applications.
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Genetic Loci Associated with Resistance to Zucchini Yellow Mosaic Virus in Squash. PLANTS 2021; 10:plants10091935. [PMID: 34579467 PMCID: PMC8465829 DOI: 10.3390/plants10091935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
Zucchini Yellow Mosaic Virus (ZYMV) is an aphid-transmitted potyvirus that causes severe yield losses in squash (Cucurbita moschata) production worldwide. Development of resistant cultivars using traditional breeding approaches relies on rigorous and resource-intensive phenotypic assays. QTL-seq, a whole genome re-sequencing based bulked segregant analysis, is a powerful tool for mapping quantitative trait loci (QTL) in crop plants. In the current study, the QTL-seq approach was used to identify genetic loci associated with ZYMV resistance in an F2 population (n = 174) derived from a cross between Nigerian Local (resistant) and Butterbush (susceptible). Whole genome re-sequencing of the parents and bulks of resistant and susceptible F2 progeny revealed a mapping rate between 94.04% and 98.76%, and a final effective mapping depth ranging from 81.77 to 101.73 across samples. QTL-seq analysis identified four QTLs significantly (p < 0.05) associated with ZYMV resistance on chromosome 2 (QtlZYMV-C02), 4 (QtlZYMV-C04), 8 (QtlZYMV-C08) and 20 (QtlZYMV-C20). Seven markers within the QTL intervals were tested for association with ZYMV resistance in the entire F2 population. For QtlZYMV-C08, one single nucleotide polymorphism (SNP) marker (KASP-6) was found to be significantly (p < 0.05) associated with ZYMV resistance, while two SNPs (KASP-1 and KASP-3) and an indel (Indel-2) marker were linked to resistance within QtlZYMV-C20. KASP-3 and KASP-6 are non-synonymous SNPs leading to amino acid substitutions in candidate disease resistant gene homologs on chromosomes 20 (CmoCh20G003040.1) and 8 (CmoCh08G007140.1), respectively. Identification of QTL and SNP markers associated with ZYMV resistance will facilitate marker-assisted selection for ZYMV resistance in squash.
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