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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [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: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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Wu JW, Zhao ZY, Hu RC, Huang YF. Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs. PLANT MOLECULAR BIOLOGY 2024; 114:20. [PMID: 38363403 PMCID: PMC10873456 DOI: 10.1007/s11103-023-01410-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: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024]
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.
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Affiliation(s)
- Jia-Wen Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150000, China
| | - Zi-Yi Zhao
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Ren-Chuan Hu
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Yun-Feng Huang
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China.
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Shaheen T, Rehman A, Abeed AHA, Waqas M, Aslam A, Azeem F, Qasim M, Afzal M, Azhar MF, Attia KA, Abushady AM, Ercisli S, Nahid N. Identification and expression analysis of SBP-Box-like ( SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea ( Cajanus cajan). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23237. [PMID: 38354689 DOI: 10.1071/fp23237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/25/2023] [Indexed: 02/16/2024]
Abstract
The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan ). In the present study, 11 members of the CcSPL gene family were identified in C. cajan . The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan , Arabidopsis thaliana , Cicer arietinum , Glycine max , Phaseolus vulgaris , Vigna unguiculata and Arachis hypogaea . Further, the identification of gene structure, motif analysis, domain analysis and presence of cis -regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14 ) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits.
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Affiliation(s)
- Tayyaba Shaheen
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Abdul Rehman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Amany H A Abeed
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Muhammad Waqas
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Asad Aslam
- Key Laboratory for Sustainable Forest Ecosystem Management - Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Afzal
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Farooq Azhar
- Department of Forestry and Range Management, Faculty of Agricultural Sciences and Technology, Bahauddin Zakaria University, Multan 60800, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Riyadh 11451, Saudi Arabia
| | - Asmaa M Abushady
- Biotechnology School, Nile University, 26th July Corridor, Sheikh Zayed City, Giza 12588, Egypt; and Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
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Xue G, Wu W, Fan Y, Ma C, Xiong R, Bai Q, Yao X, Weng W, Cheng J, Ruan J. Genome-wide identification, evolution, and role of SPL gene family in beet (Beta vulgaris L.) under cold stress. BMC Genomics 2024; 25:101. [PMID: 38262939 PMCID: PMC10804631 DOI: 10.1186/s12864-024-09995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world's main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available. RESULTS Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy. CONCLUSION Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.
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Affiliation(s)
- Guoxing Xue
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Weijiao Wu
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, 843199, Aksu, People's Republic of China
| | - Chao Ma
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Ruiqi Xiong
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Qing Bai
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Xin Yao
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China.
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Alisha A, Szweykowska-Kulinska Z, Sierocka I. Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes. Sci Rep 2024; 14:1611. [PMID: 38238367 PMCID: PMC10796333 DOI: 10.1038/s41598-024-51626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.
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Affiliation(s)
- Alisha Alisha
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Wu L, Meng F, Su X, Chen N, Peng D, Xing S. Transcriptomic responses to cold stress in Dendrobium huoshanense C.Z. Tang et S.J. Cheng. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1633-1646. [PMID: 38162923 PMCID: PMC10754796 DOI: 10.1007/s12298-023-01385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 01/03/2024]
Abstract
Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a perennial epiphytic herb of the family Orchidaceae. The main metabolites of D. huoshanense include polysaccharides and flavonoids. Low temperature is the main environmental factor that limits the growth and development of plants. However, changes that occur at the molecular level in response to low temperatures in D. huoshanense are poorly understood. We performed a transcriptome analysis at two time points of 0 d (control group) and 7 d (cold stress group) under culture of D. huoshanense at 4 °C. A total of 37.63 Gb transcriptomic data were generated using the MGI 2000 platform. These reads were assembled into 170,754 transcripts and 23,724 differentially expressed genes (DEGs) were obtained. Pathway analysis indicated that "flavonoid biosynthesis," "anthocyanin biosynthesis," "flavone and flavonol biosynthesis," and "plant hormone signal transduction" might play a vital role in the response of D. huoshanense to cold stress. Several important pathway genes were identified to be altered under cold stress, such as genes encoding polysaccharides, flavonoids, and plant hormone-signaling transduction kinase. In addition, the content of mannose and total flavonoids increased under cold stress. Twelve DEGs related to polysaccharides, flavonoid, and hormone pathways were selected from the transcriptome data for validation with real-time quantitative PCR (RT-qPCR). Our results provide a transcriptome database and candidate genes for further study of the response of D. huoshanense to cold stress. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01385-7.
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Affiliation(s)
- Liping Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012 China
- Department of Pharmacy, Tongling Municipal Hospital, Tongling, 244000 China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012 China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012 China
| | - Xinglong Su
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012 China
| | - Na Chen
- Institute of Health and Medicine, Joint Research Center for Chinese Herbal Medicine of Anhui, Hefei Comprehensive National Science Center, Bozhou, 236800 China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012 China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012 China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, 230038 China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012 China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012 China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012 China
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Lukanda MM, Dramadri IO, Adjei EA, Badji A, Arusei P, Gitonga HW, Wasswa P, Edema R, Ochwo-Ssemakula M, Tukamuhabwa P, Muthuri HM, Tusiime G. Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Genes (Basel) 2023; 14:1271. [PMID: 37372451 DOI: 10.3390/genes14061271] [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: 03/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.
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Affiliation(s)
- Musondolya Mathe Lukanda
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Faculté des Sciences Agronomiques, Université Catholique du Graben, Butembo P.O. Box 29, Democratic Republic of the Congo
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Emmanuel Amponsah Adjei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Council for Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Arfang Badji
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Perpetua Arusei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Department of Biological Sciences, Moi University, Eldoret P.O. Box 3900-30100, Kenya
| | - Hellen Wairimu Gitonga
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Mildred Ochwo-Ssemakula
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Harun Murithi Muthuri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- International Institute of Tropical Agriculture (IITA), ILRI, Nairobi P.O. Box 30709-00100, Kenya
| | - Geoffrey Tusiime
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Zhou M, Jiang Y, Liu X, Kong W, Zhang C, Yang J, Ke S, Li Y. Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice ( Oryza sativa). Int J Mol Sci 2023; 24:ijms24108522. [PMID: 37239869 DOI: 10.3390/ijms24108522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.
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Affiliation(s)
- Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yifei Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Shenzhen Branch, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China
| | - Jian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Simin Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Niazi A, Iranbakhsh A, Esmaeel Zadeh M, Ebadi M, Oraghi Ardebili Z. Zinc oxide nanoparticles (ZnONPs) influenced seed development, grain quality, and remobilization by affecting the transcription of microRNA 171 (miR171), miR156, NAM, and SUT genes in wheat (Triticum aestivum): a biological advantage and risk assessment study. PROTOPLASMA 2023; 260:839-851. [PMID: 36318315 DOI: 10.1007/s00709-022-01817-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Limited studies have been conducted on the role of microRNAs (miRs) and transcription factors in regulating plant cell responses to nanoparticles. This study attempted to address whether the foliar application of zinc oxide nanoparticles (ZnONPs; 0, 10, 25, and 50 mgL-1) can affect miRs, gene expression, and wheat grain quality. The seedlings were sprayed with ZnONPs (0, 10, 25, and 50 mgL-1) or bulk counterpart (BZnO) five times at 72 h intervals. The application of ZnONPs at 10 mgL-1 increased the number of spikelets and seed weight, while the nano-supplement at 50 mgL-1 was accompanied by severe restriction on developing spikes and grains. ZnONPs, in a dose-dependent manner, transcriptionally influenced miR156 and miR171. The expression of miR171 showed a similar trend to that of miR156. The ZnONPs at optimum concentration upregulated the NAM transcription factor and sucrose transporter (SUT) at transcriptional levels. However, the transcription of both NAM and SUT genes displayed a downward trend in response to the toxic dose of ZnONPs (50 mgL-1). Utilization of ZnONPs increased proline and total soluble phenolic content. Monitoring the accumulation of carbohydrates, including fructan, glucose, fructose, and sucrose, revealed that ZnONPs at 10 mgL-1 modified the source/sink communication and nutrient remobilization. The molecular and physiological data revealed that the expression of miR156 and miR171 is tightly linked to seed grain development, remobilization of carbohydrates, and genes involved in nutrient transportation. This study establishes a novel strategy for obtaining higher yields in crops. This biological risk assessment investigation also displays the potential hazard of applying ZnONPs at the flowering developmental phase.
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Affiliation(s)
- Atefe Niazi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Mohsen Esmaeel Zadeh
- Seed and Plant Improvement Institute, Agricultural Research Education & Extension Organization, Karaj, Iran
| | - Mostafa Ebadi
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under Drought and Salt Stresses in Sweet Potato [ Ipomoea batatas (L.) Lam]. Genes (Basel) 2023; 14:genes14010217. [PMID: 36672958 PMCID: PMC9858669 DOI: 10.3390/genes14010217] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The domain of unknown function 668 (DUF668) is a gene family that plays a vital role in responses to adversity coercion stresses in plant. However, the function of the DUF668 gene family is not fully understood in sweet potato. In this study, bioinformatics methods were used to analyze the number, physicochemical properties, evolution, structure, and promoter cis-acting elements of the IbDUF668 family genes, and RNA-seq and qRT-PCR were performed to detect gene expression and their regulation under hormonal and abiotic stress. A total of 14 IbDUF668 proteins were identified in sweet potato, distributed on nine chromosomes. By phylogenetic analysis, IbDUF668 proteins can be divided into two subfamilies. Transcriptome expression profiling revealed that many genes from DUF668 in sweet potato showed specificity and differential expression under cold, heat, drought, salt and hormones (ABA, GA3 and IAA). Four genes (IbDUF668-6, 7, 11 and 13) of sweet potato were significantly upregulated by qRT-PCR under ABA, drought and NaCl stress. Results suggest that the DUF668 gene family is involved in drought and salt tolerance in sweet potato, and it will further provide the basic information of DUF668 gene mechanisms in plants.
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Yao W, Li C, Fu H, Yang M, Wu H, Ding Y, Li L, Lin S. Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus. Int J Mol Sci 2022; 23:ijms232214035. [PMID: 36430513 PMCID: PMC9695801 DOI: 10.3390/ijms232214035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants.
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Affiliation(s)
- Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Chuanzhe Li
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Huaian 223001, China
| | - Huajun Fu
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Meng Yang
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (L.L.); (S.L.)
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (L.L.); (S.L.)
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Analysis of Homologous Regions of Small RNAs MIR397 and MIR408 Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives. Cells 2022; 11:cells11213461. [DOI: 10.3390/cells11213461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
MIRNAs are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. MIR397 (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and MIR408 (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved MIRNA families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of MIR397 and MIR408 in Oryza sativa and its six wild progenitors, three non-Oryza species, and one dicot species. We analyzed the 100 kb segments harboring MIRNA homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature MIR397 and MIR408 were highly conserved among all Oryza species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding MIRNAs was only conserved in Oryza spp.; disrupted in Sorghum, maize, and wheat; and completely lost in Arabidopsis. There were deletions, rearrangements, and translocations within the 100 kb segments in Oryza spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all MIRNAs under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future Oryza research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.
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Wang Y, Zhao J, Deng X, Wang P, Geng S, Gao W, Guo P, Chen Q, Li C, Qu Y. Genome-wide analysis of serine carboxypeptidase-like protein (SCPL) family and functional validation of Gh_SCPL42 unchromosome conferring cotton Verticillium der Verticillium wilt stress in Gossypium hirsutum. BMC PLANT BIOLOGY 2022; 22:421. [PMID: 36045341 PMCID: PMC9434971 DOI: 10.1186/s12870-022-03804-5] [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: 02/20/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Serine carboxypeptidase-like protein (SCPL) plays an important role in response to stress in plant. However, our knowledge of the function of the SCPL gene family is limited. RESULTS In this study, a comprehensive and systematic analysis of SCPL gene family was conducted to explore the phylogeny and evolution of the SCPL gene in Gossypium hirsutum. The phenotype and molecular mechanism of silencing of the Gh_SCPL42 under Verticillium wilt stress was also studied. Our results showed that 96 SCPL genes were observed in genome of G. hirsutum, which distributed on 25 chromosomes and most of them were located in the nucleus. The phylogenetic tree analysis showed that members of SCPL gene family can be divided into three subgroups in G. hirsutum, which are relatively conservative in evolution. SCPL gene has a wide range of tissue expression types in G. hirsutum. Promoter analysis showed that the most cis-acting elements related to MeJA and ABA were contained. Through RNA-seq combined with genotyping, it was found that 11 GhSCPL genes not only had significant expression changes during Verticillium wilt stress but also had differential SNPs in the upstream, downstream, exonic or intronic regions. The expression of these 11 genes in the resistant (Zhongzhimian 2) and susceptible (Junmian 1) materials was further analyzed by qRT-PCR, it was found that 6 genes showed significant expression differences in the two materials. Among them, Gh_SCPL42 has the most obvious expression change. Furthermore, virus-induced gene silencing (VIGS) showed necrosis and yellowing of leaves and significantly higher disease severity index (DSI) and disease severity rate (DSR) values in VIGS plants than in control silenced Gh_SCPL42 plants. Moreover, the expression levels of genes related to the SA and JA pathways were significantly downregulated. These results show that Gh_SCPL42 might improve resistance to Verticillium wilt through the SA and JA pathways in G. hirsutum. CONCLUSION In conclusion, our findings indicated that Gh_SCPL42 gene plays an important role in resistance to Verticillium wilt in cotton. It was provided an important theoretical basis for further research on the function of SCPL gene family and the molecular mechanism of resistance to Verticillium wilt in cotton.
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Affiliation(s)
- Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peng Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peipei Guo
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Chunping Li
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830052, China.
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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14
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Lai D, Fan Y, Xue G, He A, Yang H, He C, Li Y, Ruan J, Yan J, Cheng J. Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica). BMC Genomics 2022; 23:389. [PMID: 35596144 PMCID: PMC9122484 DOI: 10.1186/s12864-022-08633-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. Results In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. Conclusions In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08633-2.
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Affiliation(s)
- Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.,School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524000, People's Republic of China
| | - Yijing Li
- Henan Cancer Hospital, Zhengzhou, 450001, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Jun Yan
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.
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15
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Genome-Wide Identification, Characterization, and Expression Profiling Analysis of SPL Gene Family during the Inflorescence Development in Trifolium repens. Genes (Basel) 2022; 13:genes13050900. [PMID: 35627286 PMCID: PMC9140761 DOI: 10.3390/genes13050900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 02/05/2023] Open
Abstract
Trifolium repens is the most widely cultivated perennial legume forage in temperate region around the world. It has rich nutritional value and good palatability, seasonal complementarity with grasses, and can improve the feed intake and digestibility of livestock. However, flowering time and inflorescence development directly affects the quality and yield of T. repens, as well as seed production. The Squa promoter binding protein-like (SPL) gene family is a plant specific transcription factor family, which has been proved to play a critical role in regulating plant formation time and development of flowers. In this study, a total of 37 TrSPL genes were identified from the whole genome of T. repens and were divided into nine clades based on phylogenetic tree. Seventeen TrSPL genes have potential target sites for miR156. The conserved motif of squamosa promoter binding protein (SBP) contains two zinc finger structures and one NLS structure. Gene structure analysis showed that all TrSPL genes contained SBP domain, while ankyrin repeat region was just distributed in part of genes. 37 TrSPL genes were relatively dispersedly distributed on 16 chromosomes, and 5 pairs of segmental repeat genes were found, which indicated that segmental duplication was the main way of gene expansion. Furthermore, the gene expression profiling showed that TrSPL11, TrSPL13, TrSPL22, and TrSPL26 were highly expressed only in the early stage of inflorescence development, while TrSPL1 and TrSPL6 are highly expressed only in the mature inflorescence. Significantly, the expression of TrSPL4 and TrSPL12 increased gradually with the development of inflorescences. The results of this study will provide valuable clues for candidate gene selection and elucidating the molecular mechanism of T. repens flowering regulation.
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Zhang C, Nie X, Kong W, Deng X, Sun T, Liu X, Li Y. Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops. Genes (Basel) 2022; 13:863. [PMID: 35627248 PMCID: PMC9141362 DOI: 10.3390/genes13050863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs' biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C19-GA2ox, C20-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C19-GA2ox, and C20-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes' evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress.
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Affiliation(s)
- Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
| | - Xin Nie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
- Shenzhen Branch, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (C.Z.); (W.K.); (X.D.); (T.S.); (X.L.)
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17
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Schulte LM, Koirtyohann KM, McGinnis KM. Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues. G3 GENES|GENOMES|GENETICS 2022; 12:6566301. [PMID: 35404453 PMCID: PMC9157096 DOI: 10.1093/g3journal/jkac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/30/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Plants regulate gene expression at the transcriptional and post-transcriptional levels to produce a variety of functionally diverse cells and tissues that ensure normal growth, development, and environmental response. Although distinct gene expression patterns have been characterized between different plant tissues, the specific role of transcriptional regulation of tissue-specific expression is not well-characterized in plants. RNA-seq, while widely used to assay for changes in transcript abundance, does not discriminate between differential expression caused by mRNA degradation and active transcription. Recently, the presence of intron sequences in RNA-seq analysis of libraries constructed with total RNA has been found to coincide with genes undergoing active transcription. We have adapted the intron RNA-sequencing analysis to determine genome-wide transcriptional activity in 2 different maize (Zea mays) tissues: husk and V2-inner stem tissue. A total of 5,341 genes were predicted to be transcriptionally differentially expressed between the 2 tissues, including many genes expected to have biological activity relevant to the functional and developmental identity of each tissue. Correlations with transcriptional enhancer and transcription factor activity support the validity of intron RNA-sequencing predictions of transcriptional regulation. A subset of transcription factors was further analyzed using gene regulatory network analysis to determine the possible impact of their activation. The predicted regulatory patterns between these genes were used to model a potential gene regulatory network of transcription factors and regulatory targets.
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Affiliation(s)
- Lauren M Schulte
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Kathryn M Koirtyohann
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Zhang L, Huang Y, Zheng Y, Liu X, Zhou S, Yang X, Liu S, Li Y, Li J, Zhao S, Wang H, Ji Y, Zhang J, Pu M, Zhao Z, Fan J, Wang W. Osa-miR535 targets SQUAMOSA promoter binding protein-like 4 to regulate blast disease resistance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:166-178. [PMID: 34997660 PMCID: PMC9305248 DOI: 10.1111/tpj.15663] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Many rice microRNAs have been identified as fine-tuning factors in the regulation of agronomic traits and immunity. Among them, Osa-miR535 targets SQUAMOSA promoter binding protein-like 14 (OsSPL14) to positively regulate tillers but negatively regulate yield and immunity. Here, we uncovered that Osa-miR535 targets another SPL gene, OsSPL4, to suppress rice immunity against Magnaporthe oryzae. Overexpression of Osa-miR535 significantly decreased the accumulation of the fusion protein SPL4TBS -YFP that contains the target site of Osa-miR535 in OsSPL4. Consistently, Osa-miR535 mediated the cleavage of OsSPL4 mRNA between the 10th and 11th base pair of the predicted binding site at the 3' untranslated region. Transgenic rice lines overexpressing OsSPL4 (OXSPL4) displayed enhanced blast disease resistance accompanied by enhanced immune responses, including increased expression of defense-relative genes and up-accumulated H2 O2 . By contrast, the knockout mutant osspl4 exhibited susceptibility. Moreover, OsSPL4 binds to the promoter of GH3.2, an indole-3-acetic acid-amido synthetase, and promotes its expression. Together, these data indicate that Os-miR535 targets OsSPL4 and OsSPL4-GH3.2, which may parallel the OsSPL14-WRKY45 module in rice blast disease resistance.
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Affiliation(s)
- Ling‐Li Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- College of Environmental Science & EngineeringChina West Normal University1 Shida RoadNanchongSichuan637002China
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Ya‐Ping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Xin‐Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Shou‐Lan Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Jin‐Lu Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- Present address:
College of Plant ProtectionYunnan Agricultural University95 Jinhei RoadKunmingYunnan650201China
| | - Sheng‐Li Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- Institute of South Subtropical CropsChinese Academy of Tropical Agricultural SciencesZhanjiangGuangdong524013China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
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Sun Y, Fu M, Wang L, Bai Y, Fang X, Wang Q, He Y, Zeng H. OsSPLs Regulate Male Fertility in Response to Different Temperatures by Flavonoid Biosynthesis and Tapetum PCD in PTGMS Rice. Int J Mol Sci 2022; 23:ijms23073744. [PMID: 35409103 PMCID: PMC8998824 DOI: 10.3390/ijms23073744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/19/2023] Open
Abstract
Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about SPLs participating in male fertility regulation are limited. Here, we identified 19 OsSPL family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that OsSPL2, OsSPL4, OsSPL16 and OsSPL17 affect male fertility in response to temperature changes through the MiR156-SPL module. WGCNA (weighted gene co-expression network analysis) revealed that CHI and APX1 were co-expressed with OsSPL17. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that OsSPL17 regulates the expression of flavonoid biosynthesis genes CHI, and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, OsSPL17 negatively regulates APX1 to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of OsSPL for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice.
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Affiliation(s)
| | | | | | | | | | | | - Ying He
- Correspondence: (Y.H.); (H.Z.)
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20
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Kabir N, Lin H, Kong X, Liu L, Qanmber G, Wang Y, Zhang L, Sun Z, Yang Z, Yu Y, Zhao N. Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). PLANTA 2021; 255:14. [PMID: 34862931 DOI: 10.1007/s00425-021-03782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Genome wide analysis, expression pattern analysis, and functional characterization of RAV genes highlight their roles in roots, stem development and hormonal response. RAV (Related to ABI3 and VP1) gene family members have been involved in tissues/organs growth and hormone signaling in various plant species. Here, we identified 247 RAVs from 12 different species with 33 RAV genes from G. hirsutum. Phylogenetic analysis classified RAV genes into four distinct groups. Analysis of gene structure showed that most GhRAVs lack introns. Motif distribution pattern and protein sequence logos indicated that GhRAV genes were highly conserved during the process of evolution. Promotor cis-acting elements revealed that promotor regions of GhRAV genes encode numerous elements related to plant growth, abiotic stresses and phytohormones. Chromosomal location information showed uneven distribution of 33 GhRAV genes on different chromosomes. Collinearity analysis identified 628 and 52 orthologous/ paralogous gene pairs in G. hirsutum and G. barbadense, respectively. Ka/Ks values indicated that GhRAV and GbRAV genes underwent strong purifying selection pressure. Selecton model and codon model selection revealed that GhRAV amino acids were under purifying selection and adaptive evolution exists among GhRAV proteins. Three dimensional structure of GhRAVs indicated the presence of numerous alpha helix and beta-barrels. Expression level revealed that some GhRAV genes exhibited high expression in roots (GhRAV3, GhRAV4, GhRAV11, GhRAV18, GhRAV20 and GhRAV30) and stem (GhRAV3 and GhRAV18), indicating their potential role in roots and stem development. GhRAV genes can be regulated by phytohormonal stresses (BL, JA and IAA). Our study provides a reference for future studies related to the functional analysis of GhRAVs in cotton.
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Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hai Lin
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Xianhui Kong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - YuXuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Na Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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21
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Hu J, Huang L, Chen G, Liu H, Zhang Y, Zhang R, Zhang S, Liu J, Hu Q, Hu F, Wang W, Ding Y. The Elite Alleles of OsSPL4 Regulate Grain Size and Increase Grain Yield in Rice. RICE (NEW YORK, N.Y.) 2021; 14:90. [PMID: 34727228 PMCID: PMC8563897 DOI: 10.1186/s12284-021-00531-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/16/2021] [Indexed: 05/18/2023]
Abstract
Grain weight and grain number, the two important yield traits, are mainly determined by grain size and panicle architecture in rice. Herein, we report the identification and functional analysis of OsSPL4 in panicle and grain development of rice. Using CRISPR/Cas9 system, two elite alleles of OsSPL4 were obtained, which exhibited an increasing number of grains per panicle and grain size, resulting in increase of rice yield. Cytological analysis showed that OsSPL4 could regulate spikelet development by promoting cell division. The results of RNA-seq and qRT-PCR validations also demonstrated that several MADS-box and cell-cycle genes were up-regulated in the mutation lines. Co-expression network revealed that many yield-related genes were involved in the regulation network of OsSPL4. In addition, OsSPL4 could be cleaved by the osa-miR156 in vivo, and the OsmiR156-OsSPL4 module might regulate the grain size in rice. Further analysis indicated that the large-grain allele of OsSPL4 in indica rice might introgress from aus varieties under artificial selection. Taken together, our findings suggested that OsSPL4 could be as a key regulator of grain size by acting on cell division control and provided a strategy for panicle architecture and grain size modification for yield improvement in rice.
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Affiliation(s)
- Jihong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liyu Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Guanglong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yesheng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- BGI-Baoshan, Baoshan, 678004, Yunnan, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Shilai Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Jintao Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Qingyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Fengyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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22
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Chen J, Li G, Zhang H, Yuan Z, Li W, Peng Z, Shi M, Ding W, Zhang H, Cheng Y, Yao JL, Xu J. Primary Bitter Taste of Citrus is Linked to a Functional Allele of the 1,2-Rhamnosyltransferase Gene Originating from Citrus grandis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9869-9882. [PMID: 34410124 DOI: 10.1021/acs.jafc.1c01211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
1,2-Rhamnosyltransferase (1,2RhaT) catalyzes the final step of production of flavanone neohesperidoside (FNH) that is responsible for the primary bitter taste of citrus fruits. In this study, species-specific flavonoid profiles were determined in 87 Citrus accessions by identifying eight main flavanone glycosides (FGs). Accumulation of FNHs was completely correlated to the presence of the 1,2RhaT gene in 87 citrus accessions analyzed using a novel 1,2RhaT-specific DNA marker. Pummelo (Citrus grandis) was identified as the genetic origin for a function allele of 1,2RhaT that underpinned FNH-bitterness in modern citrus cultivars. In addition, genes encoding six MYB and five bHLH transcription factors were shown to coexpress with 1,2RhaT and other flavonoid pathway genes related to FNH accumulation, indicating that these transcription factors may affect the fruit taste of citrus. This study provides a better understanding of bitterness formation in Citrus varieties and a genetic marker for the early selection of nonbitterness lines in citrus breeding programs.
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Affiliation(s)
- Jiajing Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Gu Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Haipeng Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ziyu Yuan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wenyun Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zhaoxin Peng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Meiyan Shi
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wenyu Ding
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Huixian Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P. R. China
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23
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Zhong H, Liu S, Sun T, Kong W, Deng X, Peng Z, Li Y. Multi-locus genome-wide association studies for five yield-related traits in rice. BMC PLANT BIOLOGY 2021; 21:364. [PMID: 34376143 PMCID: PMC8353822 DOI: 10.1186/s12870-021-03146-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/27/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Improving the overall production of rice with high quality is a major target of breeders. Mining potential yield-related loci have been geared towards developing efficient rice breeding strategies. In this study, one single-locus genome-wide association studies (SL-GWAS) method (MLM) in conjunction with five multi-locus genome-wide association studies (ML-GWAS) approaches (mrMLM, FASTmrMLM, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were conducted in a panel consisting of 529 rice core varieties with 607,201 SNPs. RESULTS A total of 152, 106, 12, 111, and 64 SNPs were detected by the MLM model associated with the five yield-related traits, namely grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and yield per plant (YPP), respectively. Furthermore, 74 significant quantitative trait nucleotides (QTNs) were presented across at least two ML-GWAS methods to be associated with the above five traits successively. Finally, 20 common QTNs were simultaneously discovered by both SL-GWAS and ML-GWAS methods. Based on genome annotation, gene expression analysis, and previous studies, two candidate key genes (LOC_Os09g02830 and LOC_Os07g31450) were characterized to affect GW and TGW, separately. CONCLUSIONS These outcomes will provide an indication for breeding high-yielding rice varieties in the immediate future.
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Affiliation(s)
- Hua Zhong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China, 430072
| | - Shuai Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China, 430072
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China, 430072
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China, 430072
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China, 430072.
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24
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Li J, Tang B, Li Y, Li C, Guo M, Chen H, Han S, Li J, Lou Q, Sun W, Wang P, Guo H, Ye W, Zhang Z, Zhang H, Yu S, Zhang L, Li Z. Rice SPL10 positively regulates trichome development through expression of HL6 and auxin-related genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1521-1537. [PMID: 34038040 DOI: 10.1111/jipb.13140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Trichomes function in plant defenses against biotic and abiotic stresses; examination of glabrous lines, which lack trichomes, has revealed key aspects of trichome development and function. Tests of allelism in 51 glabrous rice (Oryza sativa) accessions collected worldwide identified OsSPL10 and OsWOX3B as regulators of trichome development in rice. Here, we report that OsSPL10 acts as a transcriptional regulator controlling trichome development. Haplotype and transient expression analyses revealed that variation in the approximately 700-bp OsSPL10 promoter region is the primary cause of the glabrous phenotype in the indica cultivar WD-17993. Disruption of OsSPL10 by genome editing decreased leaf trichome density and length in the NIL-HL6 background. Plants with genotype OsSPL10WD-17993 /HL6 generated by crossing WD-17993 with NIL-HL6 also had fewer trichomes in the glumes. HAIRY LEAF6 (HL6) encodes another transcription factor that regulates trichome initiation and elongation, and OsSPL10 directly binds to the HL6 promoter to regulate its expression. Moreover, the transcript levels of auxin-related genes, such as OsYUCCA5 and OsPIN-FORMED1b, were altered in OsSPL10 overexpression and RNAi transgenic lines. Feeding tests using locusts (Locusta migratoria) demonstrated that non-glandular trichomes affect feeding by this herbivore. Our findings provide a molecular framework for trichome development and an ecological perspective on trichome functions.
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Affiliation(s)
- Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Bo Tang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingxiu Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chenguang Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Minjie Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haiyang Chen
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shichen Han
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jin Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Ye
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Zhang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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25
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Zhao J, Wang P, Gao W, Long Y, Wang Y, Geng S, Su X, Jiao Y, Chen Q, Qu Y. Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. BMC Genomics 2021; 22:395. [PMID: 34044774 PMCID: PMC8162019 DOI: 10.1186/s12864-021-07716-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited. Results Our study was conducted based on the DUF668 gene family identified from cotton genome sequencing. Phylogenetic analysis showed that the DUF668 family genes can be classified into four subgroups in cotton. We identified 32 DUF668 genes, which are distributed on 17 chromosomes and most of them located in the nucleus of Gossypium hirsutum. Gene structure and motif analyses revealed that the members of the DUF668 gene family can be clustered in G. hirsutum into two broad groups, which are relatively evolutionarily conserved. Transcriptome data analysis showed that the GhDUF668 genes are differentially expressed in different tissues under various stresses (cold, heat, drought, salt, and Verticillium dahliae), and expression is generally increased in roots and stems. Promoter and expression analyses indicated that Gh_DUF668–05, Gh_DUF668–08, Gh_DUF668–11, Gh_DUF668–23 and Gh_DUF668–28 in G. hirsutum might have evolved resistance to adverse stress. Additionally, qRT-PCR revealed that these 5 genes in four cotton lines, KK1543 (drought resistant), Xinluzao 26 (drought sensitive), Zhongzhimian 2 (disease resistant) and Simian 3 (susceptible), under drought and Verticillium wilt stress were all significantly induced. Roots had the highest expression of these 5 genes before and after the treatment. Among them, the expression levels of Gh_DUF668–08 and Gh_DUF668–23 increased sharply at 6 h and reached a maximum at 12 h under biotic and abiotic stress, which showed that they might be involved in the process of adverse stress resistance in cotton. Conclusion The significant changes in GhDUF668 expression in the roots after adverse stress indicate that GhDUF668 is likely to increase plant resistance to stress. This study provides an important theoretical basis for further research on the function of the DUF668 gene family and the molecular mechanism of adverse stress resistance in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07716-w.
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Affiliation(s)
- Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peng Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yilei Long
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Xuening Su
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yang Jiao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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Jiang X, Chen P, Zhang X, Liu Q, Li H. Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia. Open Life Sci 2021; 16:160-171. [PMID: 33817308 PMCID: PMC7968543 DOI: 10.1515/biol-2021-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
SQUAMOSA promoter-binding protein-like (SPL) transcription factors are very important for the plant growth and development. Here 15 RoSPLs were identified in Rubus occidentalis. The conserved domains and motifs, phylogenetic relationships, posttranscriptional regulation, and physiological function of the 92 SPL family genes in Fragaria vesca, Malus domestica, Prunus persica, R. occidentalis, and Pyrus pyrifolia were analyzed. Sequence alignment and phylogenetic analysis showed the SPL proteins had sequence conservation, some FvSPLs could be lost or developed, and there was a closer relationship between M. domestica and P. pyrifolia, F. vesca and R. occidentalis, respectively. Genes with similar motifs clustering together in the same group had their functional redundancy. Based on the function of SPLs in Arabidopsis thaliana, these SPLs could be involved in vegetative transition from juvenile to adult, morphological change in the reproductive phase, anthocyanin biosynthesis, and defense stress. Forty-eight SPLs had complementary sequences of miR156, of which nine PrpSPLs in P. persica and eight RoSPLs in R. occidentalis as the potential targets of miR156 were reported for the first time, suggesting the conservative regulatory effects of miR156 and indicating the roles of miR156-SPL modules in plant growth, development, and defense response. It provides a basic understanding of SPLs in Rosaceae plants.
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Affiliation(s)
- Xuwen Jiang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Peng Chen
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.,Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Gongye North Road No. 202, Jinan, 250100, China
| | - Xiaowen Zhang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Qizhi Liu
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Heqin Li
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
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Zhong H, Liu S, Meng X, Sun T, Deng Y, Kong W, Peng Z, Li Y. Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS. BMC Genomics 2021; 22:86. [PMID: 33509071 PMCID: PMC7842007 DOI: 10.1186/s12864-021-07391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
Background The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. Results In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. Conclusions Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07391-x.
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Affiliation(s)
- Hua Zhong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuai Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yujuan Deng
- Department of Computer Science and Engineering, Experimental Teaching Center, Shijiazhuang University, Shijiazhuang, Hebei, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China.
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Sun H, Mei J, Zhao W, Hou W, Zhang Y, Xu T, Wu S, Zhang L. Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato ( Ipomoea batatas). FRONTIERS IN PLANT SCIENCE 2021; 12:801061. [PMID: 35126426 PMCID: PMC8815303 DOI: 10.3389/fpls.2021.801061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 05/11/2023]
Abstract
As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.
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Affiliation(s)
- Haoyun Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingzhao Mei
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tao Xu,
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Shaoyuan Wu,
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Lei Zhang,
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Ma L, Liu X, Liu W, Wen H, Zhang Y, Pang Y, Wang X. Characterization of Squamosa-Promoter Binding Protein-Box Family Genes Reveals the Critical Role of MsSPL20 in Alfalfa Flowering Time Regulation. FRONTIERS IN PLANT SCIENCE 2021; 12:775690. [PMID: 35069631 PMCID: PMC8766856 DOI: 10.3389/fpls.2021.775690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/14/2021] [Indexed: 05/22/2023]
Abstract
SQUAMOSA Promoter-binding protein-Like (SPL) genes affect a broad range of plant biological processes and show potential application in crop improvement by genetic modification. As the most widely planted forage crop in the world, biomass and abiotic stresses tolerance are important breeding targets for alfalfa (Medicago sativa L.). Nevertheless, the systematic analysis of SPL genes in alfalfa genome remains lacking. In the present study, we characterized 22 putative non-redundant SPL genes in alfalfa genome and uncovered the abundant structural variation among MsSPL genes. The phylogenetic analysis of plant SPL proteins separated them into 10 clades and clade J was an alfalfa-specific clade, suggesting SPL genes in alfalfa might have experienced gene duplication and functional differentiation within the genome. Meanwhile, 11 MsSPL genes with perfect matches to miRNA response elements (MREs) could be degraded by miR156, and the cleavage sites were gene specific. In addition, we investigated the temporal and spatial expression patterns of MsSPL genes and their expression patterns in response to multiple treatments, characterizing candidate SPL genes in alfalfa development and abiotic stress tolerant regulation. More importantly, overexpression of the alfalfa-specific SPL gene (MsSPL20) showed stable delayed flowering time, as well as increased biomass. Further studies indicated that MsSPL20 delayed flowering time by regulating the expression of genes involved in floret development, including HD3A, FTIP1, TEM1, and HST1. Together, our findings provide valuable information for future research and utilization of SPL genes in alfalfa and elucidate a possibly alfalfa-specific flowering time regulation, thereby supplying candidate genes for alfalfa molecular-assisted breeding.
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Affiliation(s)
- Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiqiang Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Hongyu Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongchao Zhang
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yongzhen Pang,
| | - Xuemin Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Xuemin Wang,
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30
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Agarwal PR, Lahiri A. Comparative study of the SBP-box gene family in rice siblings. J Biosci 2020. [DOI: 10.1007/s12038-020-00048-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhu T, Liu Y, Ma L, Wang X, Zhang D, Han Y, Ding Q, Ma L. Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat. BMC PLANT BIOLOGY 2020; 20:420. [PMID: 32912142 PMCID: PMC7488452 DOI: 10.1186/s12870-020-02576-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. RESULTS In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). CONCLUSIONS The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.
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Affiliation(s)
- Ting Zhu
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Liting Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoying Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Dazhong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yucui Han
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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32
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Zhong H, Zhang H, Guo R, Wang Q, Huang X, Liao J, Li Y, Huang Y, Wang Z. Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns. Genes (Basel) 2019; 10:genes10120980. [PMID: 31795257 PMCID: PMC6969926 DOI: 10.3390/genes10120980] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The domain of unknown function (DUF) superfamily encodes proteins of unknown functions in plants. Among them, DUF668 family members in plants possess a 29 amino-acid conserved domain, and this family has not been described previously. Here, we report this plant-specific novel DUF668 gene family containing 12 OsDUF668 genes in rice (Oryza sativa) and 91 DUF668s for the other seven plant species. In our study, DUF668 genes were present in both dicot and monocot plants, indicating that DUF668 is a conserved gene family that originated by predating the dicot–monocot divergence. Based on the gene structure and motif composition, the DUF668 family consists of two distinct clades, I and II in the phylogenetic tree. Remarkably, OsDUF668 genes clustered on the chromosomes merely show close phylogenetic relationships, suggesting that gene duplications or collinearity seldom happened. Cis-elements prediction display that over 80% of DUF668s contain phytohormone and light responsiveness factors. Further comprehensive experimental analyses of the OsDUF668 family are implemented in 22 different tissues, five hormone treatments, seven environmental factor stresses, and two pathogen-defense related stresses. The OsDUF668 genes express ubiquitously in analyzed rice tissues, and seven genes show tissue-specific high expression profiles. All OsDUF668s respond to drought, and some of Avr9/Cf-9 rapidly elicited genes resist to salt, wound, and rice blast with rapidly altered expression patterns. These findings imply that OsDUF668 is essential for drought-enduring and plant defense. Together, our results bring the important role of the DUF668 gene family in rice development and fitness to the fore.
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Affiliation(s)
- Hua Zhong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hongyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
| | - Rong Guo
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
| | - Qiang Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
| | - Xiaoping Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
| | - Jianglin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, China
| | - Yangsheng Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, China
- Correspondence:
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