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Liu Z, Duan N, Yang Z, Yue L, Fei Z, Kong S. Identification of male-fertility gene AsaNRF1 and molecular marker development in cultivated garlic ( Allium sativum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1419260. [PMID: 38863545 PMCID: PMC11165202 DOI: 10.3389/fpls.2024.1419260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Garlic cultivars are predominantly characterized by their sterility and reliance on asexual reproduction, which have traditionally prevented the use of hybrid breeding for cultivar improvement in garlic. Our investigation has revealed a notable exception in the garlic line G398, which demonstrates the ability to produce fertile pollen. Notably, at the seventh stage of anther development, callose degradation in the sterile line G390 was impeded, while G398 exhibited normal callose degradation. Transcriptome profiling revealed an enhanced expression of the callose-degrading gene, AsaNRF1, in the mature flower buds of the fertile line G398 compared to the sterile line G390. An insertion in the promoter of AsaNRF1 in G390 was identified, which led to its reduced expression at the tetrad stage and consequently delayed callose degradation, potentially resulting in the male sterility of G390. A discriminatory marker was developed to distinguish between fertile G398 and sterile G390, facilitating the assessment of male fertility in garlic germplasm resources. This study introduces a practical approach to harnessing garlic hybridization, which can further facilitate the breeding of new cultivars and the creation of novel male-fertile garlic germplasm using modern molecular biology methods.
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Affiliation(s)
- Zezhou Liu
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Key Laboratory for Biology of Greenhouse Vegetables of Shandong Province/National Center for Vegetable Improvement, Jinan, China
| | - Naibin Duan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zonghui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Key Laboratory for Biology of Greenhouse Vegetables of Shandong Province/National Center for Vegetable Improvement, Jinan, China
| | - Lixin Yue
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Key Laboratory for Biology of Greenhouse Vegetables of Shandong Province/National Center for Vegetable Improvement, Jinan, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Suping Kong
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Key Laboratory for Biology of Greenhouse Vegetables of Shandong Province/National Center for Vegetable Improvement, Jinan, China
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2
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Shemesh-Mayer E, Faigenboim A, Sherman A, Gao S, Zeng Z, Liu T, Kamenetsky-Goldstein R. Deprivation of Sexual Reproduction during Garlic Domestication and Crop Evolution. Int J Mol Sci 2023; 24:16777. [PMID: 38069099 PMCID: PMC10706073 DOI: 10.3390/ijms242316777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Garlic, originating in the mountains of Central Asia, has undergone domestication and subsequent widespread introduction to diverse regions. Human selection for adaptation to various climates has resulted in the development of numerous garlic varieties, each characterized by specific morphological and physiological traits. However, this process has led to a loss of fertility and seed production in garlic crops. In this study, we conducted morpho-physiological and transcriptome analyses, along with whole-genome resequencing of 41 garlic accessions from different regions, in order to assess the variations in reproductive traits among garlic populations. Our findings indicate that the evolution of garlic crops was associated with mutations in genes related to vernalization and the circadian clock. The decline in sexual reproduction is not solely attributed to a few mutations in specific genes, but is correlated with extensive alterations in the genetic regulation of the annual cycle, stress adaptations, and environmental requirements. The regulation of flowering ability, stress response, and metabolism occurs at both the genetic and transcriptional levels. We conclude that the migration and evolution of garlic crops involve substantial and diverse changes across the entire genome landscape. The construction of a garlic pan-genome, encompassing genetic diversity from various garlic populations, will provide further insights for research into and the improvement of garlic crops.
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Affiliation(s)
- Einat Shemesh-Mayer
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Adi Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Song Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Zheng Zeng
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Touming Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Rina Kamenetsky-Goldstein
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
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3
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Wang H, Shemesh-Mayer E, Zhang J, Gao S, Zeng Z, Yang Z, Zhang X, Jia H, Wang Y, Song J, Zhang X, Yang W, He Q, Sherman A, Li L, Kamenetsky R, Liu T. Genome resequencing reveals the evolutionary history of garlic reproduction traits. HORTICULTURE RESEARCH 2023; 10:uhad208. [PMID: 38046855 PMCID: PMC10689055 DOI: 10.1093/hr/uhad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/11/2023] [Indexed: 12/05/2023]
Abstract
The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.
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Affiliation(s)
- Haiping Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Einat Shemesh-Mayer
- Institute of Plant Sciences, Agricultural Research Organization—The Volcani Institute, Rishon LeZion, Israel
| | - Jiangjiang Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Song Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xueyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huixia Jia
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, China
| | - Jiangping Song
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization—The Volcani Institute, Rishon LeZion, Israel
| | - Lin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rina Kamenetsky
- Institute of Plant Sciences, Agricultural Research Organization—The Volcani Institute, Rishon LeZion, Israel
| | - Touming Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
- Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, China
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4
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Mo Z, Ke Y, Huang Y, Duan L, Wang P, Luo W, Que Y, Pi K, Zeng S, Liu R. Integrated transcriptome and proteome analysis provides insights into the mechanism of cytoplasmic male sterility (CMS) in tobacco (Nicotiana tabacum L.). J Proteomics 2023; 275:104825. [PMID: 36754348 DOI: 10.1016/j.jprot.2023.104825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/06/2023] [Accepted: 01/15/2023] [Indexed: 02/08/2023]
Abstract
Cytoplasmic male sterility (CMS) is critical in maximizing crop yield and quality by utilizing tobacco heterosis. However, the mechanism of tobacco CMS formation remains unknown. Using paraffin section observation, transcriptome sequencing, and TMT proteomic analysis, this study describes the differences in expression profiles in morphology, transcription, and translation between the sua-CMS tobacco line (MSYY87) and its corresponding maintainer line (YY87). According to the microspore morphology, MSYY87 began to exhibit abnormal microspore development during the early stages of germination and differentiation (androgynous primordium differentiation stage). According to transcriptomic and proteomic analyses, 17 genes/proteins involved in lipid transport/binding and phenylpropane metabolism were significantly down-regulated at both the mRNA and protein levels. Through further analysis, we identified some key genes that may be involved in tobacco male sterility, including β-GLU related to energy metabolism, 4CL and bHLHs related to anther wall formation, nsLTPs related to pollen germination and anther cuticle, and bHLHs related to pollen tapetum degradation. We speculate that the down-regulation of these genes affects the normal physiological metabolism, making tobacco plants show male sterility. SIGNIFICANCE: Cytoplasmic male sterility (CMS) plays a vital role in utilizing tobacco heterosis and enhancing crop yield and quality. We observed paraffin sections and conducted transcriptome sequencing and mitochondrial proteomics to examine the tobacco CMS line Yunyan 87 (MSYY87) and its maintainer line Yunyan 87 (YY87). The down-regulation expression of β-GLU resulted in insufficient ATP supply, which resulted in disordered energy metabolism. The down-regulation expression of 4CL, nsLTPs and bHLHs may affect the formation of anther wall and anther cuticle, pollen germination, as well as the degradation of pollen tapetum. These various abnormal physiological processes, the male sterility of tobacco is finally caused. The findings shed light on the molecular mechanisms of tobacco CMS and serve as a model for fertility research in other flowering plants.
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Affiliation(s)
- Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Yuzhou Ke
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Ying Huang
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Pingsong Wang
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Wen Luo
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Yuanhui Que
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Kai Pi
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Shuaibo Zeng
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China.
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5
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Parreño R, Rodríguez-Alcocer E, Martínez-Guardiola C, Carrasco L, Castillo P, Arbona V, Jover-Gil S, Candela H. Turning Garlic into a Modern Crop: State of the Art and Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:1212. [PMID: 36986902 PMCID: PMC10057115 DOI: 10.3390/plants12061212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.
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Affiliation(s)
- Ricardo Parreño
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Eva Rodríguez-Alcocer
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | | | - Lucía Carrasco
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Purificación Castillo
- Departamento I+D, Coopaman S.C.L., Carretera Peñas De San Pedro, km 1.6, 02006 Albacete, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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6
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Shemesh-Mayer E, Faigenboim A, Ben Michael TE, Kamenetsky-Goldstein R. Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic. Int J Mol Sci 2022; 23:ijms232213876. [PMID: 36430354 PMCID: PMC9698152 DOI: 10.3390/ijms232213876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not found at the transcriptome level. Functions of TFL-like genes were reduced and replaced by FT-like homologs, whereas homologs of MFT-like genes were not found. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their role in garlic florogenesis. It is not yet clear whether AsLFY1 acts alone as the "pioneer transcription factor" or AsLFY2 also provides these functions. The presence of several orthologs of flowering genes that differ in their expression and co-expression network advocates ongoing evolution in the garlic genome and diversification of gene functions. We propose that the process of fertility deprivation in garlic cultivars is based on the loss of transcriptional functions of the specific genes.
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7
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Wen Y, Liu H, Meng H, Qiao L, Zhang G, Cheng Z. In vitro Induction and Phenotypic Variations of Autotetraploid Garlic ( Allium sativum L.) With Dwarfism. FRONTIERS IN PLANT SCIENCE 2022; 13:917910. [PMID: 35812906 PMCID: PMC9258943 DOI: 10.3389/fpls.2022.917910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 05/16/2023]
Abstract
Garlic (Allium sativum L.) is a compelling horticultural crop with high culinary and therapeutic values. Commercial garlic varieties are male-sterile and propagated asexually from individual cloves or bulbils. Consequently, its main breeding strategy has been confined to the time-consuming and inefficient selection approach from the existing germplasm. Polyploidy, meanwhile, plays a prominent role in conferring plants various changes in morphological, physiological, and ecological properties. Artificial polyploidy induction has gained pivotal attention to generate new genotype for further crop improvement as a mutational breeding method. In our study, efficient and reliable in vitro induction protocols of autotetraploid garlic were established by applying different antimitotic agents based on high-frequency direct shoot organogenesis initiated from inflorescence explant. The explants were cultured on solid medium containing various concentrations of colchicine or oryzalin for different duration days. Afterward, the ploidy levels of regenerated plantlets with stable and distinguished characters were confirmed by flow cytometry and chromosome counting. The colchicine concentration at 0.2% (w/v) combined with culture duration for 20 days was most efficient (the autotetraploid induction rate was 21.8%) compared to the induction rate of 4.3% using oryzalin at 60 μmol L-1 for 20 days. No polymorphic bands were detected by simple sequence repeat analysis between tetraploid and diploid plantlets. The tetraploids exhibited a stable and remarkable dwarfness effect rarely reported in artificial polyploidization among wide range of phenotypic variations. There are both morphological and cytological changes including extremely reduced plant height, thickening and broadening of leaves, disappearance of pseudostem, density reduction, and augmented width of stomatal. Furthermore, the level of phytohormones, including, indole propionic acid, gibberellin, brassinolide, zeatin, dihydrozeatin, and methyl jasmonate, was significantly lower in tetraploids than those in diploid controls, except indole acetic acid and abscisic acid, which could partly explain the dwarfness in hormonal regulation aspect. Moreover, as the typical secondary metabolites of garlic, organosulfur compounds including allicin, diallyl disulfide, and diallyl trisulfide accumulated a higher content significantly in tetraploids. The obtained dwarf genotype of autotetraploid garlic could bring new perspectives for the artificial polyploids breeding and be implemented as a new germplasm to facilitate investigation into whole-genome doubling consequences.
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Affiliation(s)
- Yanbin Wen
- College of Horticulture, Northwest A&F University, Xianyang, China
- Development Center of Fruit Vegetable and Herbal Tea, Datong, China
| | - Hongjiu Liu
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Huanwen Meng
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Lijun Qiao
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Guoqing Zhang
- Business School, Shanxi Datong University, Datong, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Xianyang, China
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8
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Ma D, Lai Z, Ding Q, Zhang K, Chang K, Li S, Zhao Z, Zhong F. Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:872137. [PMID: 35599909 PMCID: PMC9114813 DOI: 10.3389/fpls.2022.872137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.
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Affiliation(s)
- Dongna Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Zhengfeng Lai
- Subtropical Agricultural Research Institute, Fujian Academy of Agriculture Sciences, Fujian, China
| | - Qiansu Ding
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Kaizhen Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Zhizhu Zhao
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
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9
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De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, Stenberg S, Amadi OC, Žun G, Doberšek K, Taccioli C, Schacherer J, Petrovič U, Warringer J, Liti G. Domestication reprogrammed the budding yeast life cycle. Nat Ecol Evol 2022; 6:448-460. [PMID: 35210580 DOI: 10.1038/s41559-022-01671-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.
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Affiliation(s)
| | - Benjamin P Barré
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Karl Persson
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | | | - Chiara Vischioni
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Sakshi Khaiwal
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | - Onyetugo Chioma Amadi
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden.,Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Gašper Žun
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | | | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden.
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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10
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Yao J, Li R, Cheng Y, Li Z. A combined transcriptomic and proteomic analysis of chrysanthemum provides new insights into petal senescence. PLANTA 2021; 255:22. [PMID: 34918180 DOI: 10.1007/s00425-021-03808-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Numerous transcription factor genes and methylation-related genes were differentially expressed in senescent petals compared with control petals. Studying petal senescence is crucial for extending the postharvest longevity of cut flowers, but petal senescence remains relatively unexplored compared to well-studied leaf senescence. In this study, a combined transcriptomic and proteomic analysis of senescent (22 days after cutting) and control (0 day after cutting) petals was performed to investigate the molecular processes underlying petal senescence of chrysanthemum (Chrysanthemum morifolium Ramat.), an important cut flower crop worldwide. A total of 11,324 differentially expressed genes (DEGs), including 4888 up-regulated and 6436 down-regulated genes, and 403 differentially expressed proteins (DEPs), including 210 up-regulated and 193 down-regulated proteins, were identified at transcript and protein levels, respectively. A cross-comparison of transcriptomic and proteomic data identified 257 consistent DEGs/DEPs, including 122 up-regulated and 135 down-regulated DEGs/DEPs. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that "cutin, suberine and wax biosynthesis" is a main pathway for both DEGs and DEPs, especially for down-regulated DEGs/DEPs. Functional analysis indicated that chrysanthemum genes mainly encoding putative cytochrome P450s, non-specific lipid-transfer proteins, subtilisin-like proteases, AAA-ATPases, proteins essential for cuticular wax biosynthesis, and proteins in hormone signal transduction or ubiquitination were differentially expressed at both transcript and protein levels. In addition, numerous transcription factor genes and methylation-related genes were also differentially expressed, inferring an involvement of transcriptional and epigenetic regulation in petal senescence. These results provide a valuable resource of studying chrysanthemum senescence and significant insights into petal senescence.
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Affiliation(s)
- Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
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Malik G, Dhatt AS, Malik AA. A Review of Genetic Understanding and Amelioration of Edible Allium Species. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2019.1709202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Geetika Malik
- Division of Vegetable Science and Floriculture, ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K, India
| | - Ajmer Singh Dhatt
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ajaz Ahmed Malik
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar, J&K, India
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Yang X, Su Y, Wu J, Wan W, Chen H, Cao X, Wang J, Zhang Z, Wang Y, Ma D, Loake GJ, Jiang J. Parallel analysis of global garlic gene expression and alliin content following leaf wounding. BMC PLANT BIOLOGY 2021; 21:174. [PMID: 33838642 PMCID: PMC8035738 DOI: 10.1186/s12870-021-02948-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Allium sativum (garlic) is an economically important food source and medicinal plant rich in sulfides and other protective substances such as alliin, the precursor of allicin biosynthesis. Cysteine, serine and sulfur is the precursor of alliin biosynthesis. However, little is known about the alliin content under abiotic stress or the mechanism by which it is synthesized. RESULTS The findings revealed that the content of alliin was lowest in the garlic roots, and highest in the buds. Furthermore, alliin levels decreased in mature leaves following wounding. Transcriptome data generated over time after wounding further revealed significant up-regulation of genes integral to the biosynthetic pathways of cysteine and serine in mature garlic leaves. CONCLUSIONS The findings suggest that differential expression of cysteine, serine and sulfide-related genes underlies the accumulation of alliin and its precursors in garlic, providing a basis for further analyses of alliin biosynthesis.
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Affiliation(s)
- Xuqin Yang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Yiren Su
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Jiaying Wu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Wen Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Huijian Chen
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - Xiaoying Cao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Junjuan Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Zhong Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Youzhi Wang
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - Deliang Ma
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - G J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China.
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Jiang X, Chi X, Zhou R, Li Y, Li W, Liu Q, Wang K, Liu Q. Transcriptome profiling to identify tepal cell enlargement and pigmentation genes and the function of LtEXLB1 in Lilium tsingtauense. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:241-256. [PMID: 33059816 DOI: 10.1071/fp20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
To understand the molecular mechanism underlying tepal development and pigmentation in Lilium tsingtauense Gilg, we performed whole-transcriptome profiles from closed buds at the greenish tepal stage (CBS), the full-bloom with un-horizontal tepal stage (UFS), and the completely opened bud with reflected tepal stage (RFS) of L. tsingtauense. More than 95699 transcripts were generated using a de novo assembly approach. Gene ontology and pathway analysis of the assembled transcripts revealed carbon metabolism is involved in tepal development and pigmentation. In total, 8171 differentially expression genes (DEGs) in three tepal stages were identified. Among these DEGs, ~994 genes putatively encoded transcription factors (TFs), whereas 693 putatively encoded protein kinases. Regarding hormone pathways, 51 DEGs involved in auxin biosynthesis and signalling and 10 DEGs involved in ethylene biosynthesis and signalling. We also isolated seven LtEXPANSINs, including four EXPAs, one EXPB, one EXLA and one EXLB. LtEXLB1 (GenBank: MN856627) was expressed at higher levels in UFS and RFS, compared with CBS. Silencing LtEXLB1 in leaf discs and tepals by virus-induced gene silencing significantly decreased cell expansion under rehydration conditions. Further analysis revealed that more cell numbers were existed in the abaxial and adaxial subepidermis in the silenced LtEXLB1 samples. As the first transcriptome of L. tsingtauense, the unigenes are a valuable resource for future studies on tepal development, and LtEXLB1 functions in cell expansion.
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Affiliation(s)
- Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Xiufeng Chi
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Rui Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Yanshuo Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Qingchao Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Kuiling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Qinghua Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China; and Corresponding author.
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Tang N, Liu W, Zhang W, Tang D. Integrative analysis of transcriptomic and proteomic changes related to male sterility in Tagetes erecta. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2061-2074. [PMID: 33088050 PMCID: PMC7548268 DOI: 10.1007/s12298-020-00886-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/24/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Male sterile and male fertile two-type lines are important in heterosis utilization and breeding in Tagetes erecta, but the genes and pathways involved in male sterility are poorly understood. To explore these topics, transcriptome data (by RNA-seq) and proteome data (by iTRAQ) were gathered from flower buds of the male sterile line 'MS2-2' and male fertile line 'MF2-2' and integrated for a better understanding of the underlying molecular mechanisms of male sterility in T. erecta. The RNA-seq procedure generated 285,139,740 clean reads and 63359 unigenes and 6640 differentially expressed genes (DEGs) were identified, of which 4136 were downregulated and 2504 were upregulated in 'MS2-2'. DEGs related to flower development, pollen development, pollen wall assembly, endogenous hormones and transcription factors were identified. The iTRAQ analysis identified 3950 proteins in total; 789 were differentially expressed proteins (381 upregulated, 408 downregulated), which were mainly annotated to the Ribosome, Carbon metabolism and Biosynthesis of amino acids pathways. An association analysis revealed strong correlation (r Pearson = 0.6019) between the transcriptomic and proteomic data, and 256 and 34 proteins showed the same and opposite expression patterns with regard to their transcripts, respectively. Pathways such as photosynthesis, fatty acid biosynthesis and phenylpropanoid biosynthesis which influence tapetum and pollen development in male sterile plants, were significantly enriched at the transcript and protein levels. Most genes involved in these pathways were downregulated in 'MS2-2'. The low expression of these genes or functional loss of proteins could be associated with flower development, pollen development and related to changes in fertility in T. erecta. This study provided transcriptomic and proteomic information for T. erecta that could illuminate the mechanism of male sterility.
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Affiliation(s)
- Nan Tang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 People’s Republic of China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001 People’s Republic of China
| | - Wei Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471003 People’s Republic of China
| | - Wuhua Zhang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
| | - Daocheng Tang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
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Khandagale K, Krishna R, Roylawar P, Ade AB, Benke A, Shinde B, Singh M, Gawande SJ, Rai A. Omics approaches in Allium research: Progress and way ahead. PeerJ 2020; 8:e9824. [PMID: 32974094 PMCID: PMC7486827 DOI: 10.7717/peerj.9824] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. METHOD In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. RESULTS Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. CONCLUSION All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.
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Affiliation(s)
- Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Praveen Roylawar
- Department of Botany, S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Avinash B. Ade
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ashwini Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Bharat Shinde
- Vidya Pratishthans’s Arts Science and commerce college, Baramati, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | | | - Ashutosh Rai
- Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
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Ghodke P, Khandagale K, Thangasamy A, Kulkarni A, Narwade N, Shirsat D, Randive P, Roylawar P, Singh I, Gawande SJ, Mahajan V, Solanke A, Singh M. Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress. PLoS One 2020; 15:e0237457. [PMID: 32780764 PMCID: PMC7418993 DOI: 10.1371/journal.pone.0237457] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
Onion (Allium cepa L.) is an important vegetable crop widely grown for diverse culinary and nutraceutical properties. Being a shallow-rooted plant, it is prone to drought. In the present study, transcriptome sequencing of drought-tolerant (1656) and drought-sensitive (1627) onion genotypes was performed to elucidate the molecular basis of differential response to drought stress. A total of 123206 and 139252 transcripts (average transcript length: 690 bases) were generated after assembly for 1656 and 1627, respectively. Differential gene expression analyses revealed upregulation and downregulation of 1189 and 1180 genes, respectively, in 1656, whereas in 1627, upregulation and downregulation of 872 and 1292 genes, respectively, was observed. Genes encoding transcription factors, cytochrome P450, membrane transporters, and flavonoids, and those related to carbohydrate metabolism were found to exhibit a differential expression behavior in the tolerant and susceptible genotypes. The information generated can facilitate a better understanding of molecular mechanisms underlying drought response in onion.
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Affiliation(s)
- Pranjali Ghodke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Kiran Khandagale
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - A. Thangasamy
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Abhijeet Kulkarni
- Department of Bioinformatics, Savitribai Phule Pune University, Pune, India
| | - Nitin Narwade
- Department of Bioinformatics, Savitribai Phule Pune University, Pune, India
| | - Dhananjay Shirsat
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Pragati Randive
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Praveen Roylawar
- S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Isha Singh
- School of Biomolecular Science, University College, Dublin, Ireland
| | - Suresh J. Gawande
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Vijay Mahajan
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | | | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
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Ben Michael TE, Faigenboim A, Shemesh-Mayer E, Forer I, Gershberg C, Shafran H, Rabinowitch HD, Kamenetsky-Goldstein R. Crosstalk in the darkness: bulb vernalization activates meristem transition via circadian rhythm and photoperiodic pathway. BMC PLANT BIOLOGY 2020; 20:77. [PMID: 32066385 PMCID: PMC7027078 DOI: 10.1186/s12870-020-2269-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 01/29/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Geophytes possess specialized storage organs - bulbs, tubers, corms or rhizomes, which allow their survival during unfovarable periods and provide energy support for sprouting and sexual and vegetative reproduction. Bulbing and flowering of the geophyte depend on the combined effects of the internal and external factors, especially temperature and photoperiod. Many geophytes are extensively used in agriculture, but mechanisms of regulation of their flowering and bulbing are still unclear. RESULTS Comparative morpho-physiological and transcriptome analyses and quantitative validation of gene expression shed light on the molecular regulation of the responses to vernalization in garlic, a typical bulbous plant. Long dark cold exposure of bulbs is a major cue for flowering and bulbing, and its interactions with the genetic makeup of the individual plant dictate the phenotypic expression during growth stage. Photoperiod signal is not involved in the initial nuclear and metabolic processes, but might play role in the later stages of development, flower stem elongation and bulbing. Vernalization for 12 weeks at 4 °C and planting in November resulted in flower initiation under short photoperiod in December-January, and early blooming and bulbing. In contrast, non-vernalized plants did not undergo meristem transition. Comparisons between vernalized and non-vernalized bulbs revealed ~ 14,000 differentially expressed genes. CONCLUSIONS Low temperatures stimulate a large cascades of molecular mechanisms in garlic, and a variety of flowering pathways operate together for the benefit of meristem transition, annual life cycle and viable reproduction results.The circadian clock appears to play a central role in the transition of the meristem from vegetative to reproductive stage in bulbous plant, serving as integrator of the low-temperature signals and the expression of the genes associated with vernalization, photoperiod and meristem transition. The reserved photoperiodic pathway is integrated at an upstream point, possibly by the same receptors. Therefore, in bulb, low temperatures stimulate cascades of developmental mechanisms, and several genetic flowering pathways intermix to achieve successful sexual and vegetative reproduction.
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Affiliation(s)
- Tomer E Ben Michael
- Institute of Plant Sciences, ARO, The Volcani Center, Rishon LeZion, Israel
- Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO, The Volcani Center, Rishon LeZion, Israel
| | | | - Itzhak Forer
- Institute of Plant Sciences, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Chen Gershberg
- Institute of Plant Sciences, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Hadass Shafran
- Institute of Plant Sciences, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Haim D Rabinowitch
- Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Mehra R, Jasrotia RS, Mahajan A, Sharma D, Iquebal MA, Kaul S, Dhar MK. Transcriptome analysis of Snow Mountain Garlic for unraveling the organosulfur metabolic pathway. Genomics 2020; 112:99-107. [DOI: 10.1016/j.ygeno.2019.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/05/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
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19
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Xue Y, Ma J, He Y, Yu S, Lin Z, Xiong Y, Rafique F, Jiang F, Sun L, Ma M, Zhou Y, Li X, Huang Z. Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus. PeerJ 2019; 7:e7261. [PMID: 31333908 PMCID: PMC6626515 DOI: 10.7717/peerj.7261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/20/2022] Open
Abstract
Background Ananas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood. Methods Comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed. Results In total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves.
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Affiliation(s)
- Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yehua He
- Horticultural Biotechnology College of South China Agricultural University, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sanmiao Yu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhen Lin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yingyuan Xiong
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fatima Rafique
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fuxing Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lingxia Sun
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingdong Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yujue Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuo Huang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Yang Y, Wei F, Braynen J, Wei X, Tian B, Shi G, Cao G, Yuan J, Zhang X. Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa. Cell Biosci 2019; 9:49. [PMID: 31236208 PMCID: PMC6580506 DOI: 10.1186/s13578-019-0313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background Polyploidy is considered as a basic event in plant speciation and evolution in nature, and the cytological and proteomic profilings of floral buds at meiosis (FAM) would definitely contribute to a better understanding of the polyploid-associated effects during plant reproduction cycle. Results Herein, the cytological investigations demonstrated that chromosome behaviors such as univalent and multivalent at prophase I, chaotic alignments at metaphase, aberrant segregation at telophase, were frequently observed during meiosis in autotetraploid Brassica rapa. The proteomic analysis showed a total of 562 differentially expressed proteins (DEPs) were identified in FAM between autotetraploid and diploid B. rapa. Notably, PARP2 and LIG1 related to base excision repair and BARD1 involved in recombination were significantly down-regulated in autotetraploid B. rapa, which indicated DNA repair pathway were more likely affected during meiosis in autotetraploid B. rapa. The functional analysis showed that DEPs assigned to “chromatin structure and dynamics”, “cell cycle control, cell division, chromosome partitioning” and “cytoskeleton” were preferentially up-regulated, which suggested a robust regulation of cell division in autotetraploid B. rapa. In combination with the floral RNA-seq data released, a number of DEPs were found positively correlated with their transcript abundance, but posttranslational modification of proteins might also play a role in regulating meiosis course after polyploidization. Conclusions In general, this study provides a detailed cytology and proteome landscape of FAM between diploid and autotetraploid B. rapa, which definitely affords us a better understanding of uniformity and discrepancy of meiosis at the plant reproductive stage before and after polyploidization. Electronic supplementary material The online version of this article (10.1186/s13578-019-0313-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Yang
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Fang Wei
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Janeen Braynen
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Xiaochun Wei
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Baoming Tian
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gongyao Shi
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gangqiang Cao
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Jiachen Yuan
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Xiaowei Zhang
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
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Wu Z, Hu K, Yan M, Song L, Wen J, Ma C, Shen J, Fu T, Yi B, Tu J. Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea. BMC Genomics 2019; 20:348. [PMID: 31068124 PMCID: PMC6507029 DOI: 10.1186/s12864-019-5721-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea. Results The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. Conclusions On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liping Song
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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Li B, Chen X, Wu Y, Gu A, Zhang J, Luo S, Gao X, Zhao J, Pan X, Shen S. Gene characterization and molecular pathway analysis of reverse thermosensitive genic male sterility in eggplant ( Solanum melongena L.). HORTICULTURE RESEARCH 2019; 6:118. [PMID: 31700645 PMCID: PMC6823389 DOI: 10.1038/s41438-019-0201-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 06/05/2019] [Accepted: 09/02/2019] [Indexed: 05/02/2023]
Abstract
The naturally occurring mutant eggplant line 05ms was identified with reverse thermosensitive genic male sterility (rTGMS), but its temperature-responsive fertility mechanisms remain largely unknown. Here, we studied the flower morphology, anther cellular structure, and genome-wide gene expression of this rTGMS line. Candidate genes for thermosensitive male sterility during the microspore development of 05ms and the temperature-insensitive line S63 under low-temperature (LT) and high-temperature (HT) conditions were identified. Under LT, tapetum cells were vacuolated and had delayed disintegration in 05ms. RNA-seq analysis indicated that DEGs were enriched in the KEGG pathways 'plant hormone signal transduction', 'starch and sucrose metabolism', and 'phenylpropanoid biosynthesis'. We identified two genes, 4CLL1 (Sme2.5_00368.1_g00010.1) and CKI1 (Sme2.5_10056.1_g00002.1), which could potentially regulate eggplant anther development and may be candidate genes for rTGMS. Finally, we propose a working model of anther abortion for rTGMS in eggplant. CKI1 responds to LT stress and causes expression changes in genes related to anther development, such as 4CLL1, and the cellular structure of the tapetum becomes abnormal, causing male sterility. The findings of this study explain the underlying molecular mechanisms of male sterility in eggplant rTGMS lines.
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Affiliation(s)
- Bing Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051 China
| | - Xueping Chen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Yanrong Wu
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051 China
| | - Aixia Gu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Jingjing Zhang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051 China
| | - Shuangxia Luo
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Xiurui Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051 China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Xiuqing Pan
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051 China
| | - Shuxing Shen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
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Egea LA, Mérida-García R, Kilian A, Hernandez P, Dorado G. Assessment of Genetic Diversity and Structure of Large Garlic ( Allium sativum) Germplasm Bank, by Diversity Arrays Technology "Genotyping-by-Sequencing" Platform (DArTseq). Front Genet 2017; 8:98. [PMID: 28775737 PMCID: PMC5517412 DOI: 10.3389/fgene.2017.00098] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/30/2017] [Indexed: 12/20/2022] Open
Abstract
Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.
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Affiliation(s)
- Leticia A. Egea
- Departamento de Bioquímica y Biología Molecular, Campus Rabanales (C6-1-E17), Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de CórdobaCórdoba, Spain
- Instituto de Agricultura Sostenible (IAS-CSIC), Campus Alameda del ObispoCórdoba, Spain
| | - Rosa Mérida-García
- Instituto de Agricultura Sostenible (IAS-CSIC), Campus Alameda del ObispoCórdoba, Spain
| | - Andrzej Kilian
- Diversity Arrays Technology Pty. Ltd., CanberraACT, Australia
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Campus Alameda del ObispoCórdoba, Spain
| | - Gabriel Dorado
- Departamento de Bioquímica y Biología Molecular, Campus Rabanales (C6-1-E17), Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de CórdobaCórdoba, Spain
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Chand SK, Nanda S, Mishra R, Joshi RK. Multiple garlic (Allium sativum L.) microRNAs regulate the immunity against the basal rot fungus Fusarium oxysporum f. sp. Cepae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:9-21. [PMID: 28224922 DOI: 10.1016/j.plantsci.2017.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/21/2016] [Accepted: 01/16/2017] [Indexed: 05/07/2023]
Abstract
The basal plate rot fungus, Fusarium oxysporum f. sp. cepae (FOC), is the most devastating pathogen posing a serious threat to garlic (Allium sativum L.) production worldwide. MicroRNAs (miRNAs) are key modulators of gene expression related to development and defense responses in eukaryotes. However, the miRNA species associated with garlic immunity against FOC are yet to be explored. In the present study, a small RNA library developed from FOC infected resistant garlic line was sequenced to identify immune responsive miRNAs. Forty-five miRNAs representing 39 conserved and six novel sequences responsive to FOC were detected. qRT-PCR analyses further classified them into three classes based on their expression patterns in susceptible line CBT-As11 and in the resistant line CBT-As153. North-blot analyses of six selective miRNAs confirmed the qRT-PCR results. Expression studies on a selective set of target genes revealed a negative correlation with the complementary miRNAs. Furthermore, transgenic garlic plant overexpresing miR164a, miR168a and miR393 showed enhanced resistance to FOC, as revealed by decreased fungal growth and up-regulated expression of defense-responsive genes. These results indicate that multiple miRNAs are involved in garlic immunity against FOC and that the overexpression of miR164a, miR168a and miR393 can augment garlic resistance to Fusarium basal rot infection.
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Affiliation(s)
- Subodh Kumar Chand
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Satyabrata Nanda
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Rukmini Mishra
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Raj Kumar Joshi
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
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Guo J, Liu J, Wei Q, Wang R, Yang W, Ma Y, Chen G, Yu Y. Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias. PLANT PHYSIOLOGY 2017; 173:668-687. [PMID: 27810942 PMCID: PMC5210702 DOI: 10.1104/pp.16.00795] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/02/2016] [Indexed: 05/04/2023]
Abstract
Petal senescence is a complex programmed process. It has been demonstrated previously that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on posttranslational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation. In this study, we first obtained reference petunia (Petunia hybrida) transcriptome data via RNA sequencing. Next, we quantitatively investigated the petunia proteome and ubiquitylome and the association between them in petunia corollas following ethylene treatment. In total, 51,799 unigenes, 3,606 proteins, and 2,270 ubiquitination sites were quantified 16 h after ethylene treatment. Treatment with ethylene resulted in 14,448 down-regulated and 6,303 up-regulated unigenes (absolute log2 fold change > 1 and false discovery rate < 0.001), 284 down-regulated and 233 up-regulated proteins, and 320 up-regulated and 127 down-regulated ubiquitination sites using a 1.5-fold threshold (P < 0.05), indicating that global ubiquitination levels increase during ethylene-mediated corolla senescence in petunia. Several putative ubiquitin ligases were up-regulated at the protein and transcription levels. Our results showed that the global proteome and ubiquitylome were negatively correlated and that ubiquitination could be involved in the degradation of proteins during ethylene-mediated corolla senescence in petunia. Ethylene regulates hormone signaling transduction pathways at both the protein and ubiquitination levels in petunia corollas. In addition, our results revealed that ethylene increases the ubiquitination levels of proteins involved in endoplasmic reticulum-associated degradation.
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Affiliation(s)
- Jianhang Guo
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Qian Wei
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Rongmin Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Yueyue Ma
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Guoju Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
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26
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Chen L, Chen Q, Zhu Y, Hou L, Mao P. Proteomic Identification of Differentially Expressed Proteins during Alfalfa ( Medicago sativa L.) Flower Development. FRONTIERS IN PLANT SCIENCE 2016; 7:1502. [PMID: 27757120 PMCID: PMC5047909 DOI: 10.3389/fpls.2016.01502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/21/2016] [Indexed: 05/23/2023]
Abstract
Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa (Medicago sativa L.) seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1), pollination (S2), and the post-pollination senescence period (S3). Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD). Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs), carbonic anhydrase, and NADPH: quinone oxidoreductase-like protein. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower development and contributes to the understanding of the basic molecular mechanisms during the alfalfa flowering process. These results may offer insight into potential strategies for improving seed yield, quality, and stress tolerance in alfalfa.
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Affiliation(s)
- Lingling Chen
- Beijing Key Laboratory of Grassland Science, Forage Seed Lab, China Agricultural UniversityBeijing, China
- Chifeng Academy of Agricultural and Animal SciencesChifeng, China
| | - Quanzhu Chen
- Chengdu Municipal Development and Reform CommissionChengdu, China
| | - Yanqiao Zhu
- Beijing Key Laboratory of Grassland Science, Forage Seed Lab, China Agricultural UniversityBeijing, China
| | - Longyu Hou
- Beijing Key Laboratory of Grassland Science, Forage Seed Lab, China Agricultural UniversityBeijing, China
| | - Peisheng Mao
- Beijing Key Laboratory of Grassland Science, Forage Seed Lab, China Agricultural UniversityBeijing, China
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Bohra A, Jha UC, Adhimoolam P, Bisht D, Singh NP. Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. PLANT CELL REPORTS 2016; 35:967-93. [PMID: 26905724 DOI: 10.1007/s00299-016-1949-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
A comprehensive understanding of CMS/Rf system enabled by modern omics tools and technologies considerably improves our ability to harness hybrid technology for enhancing the productivity of field crops. Harnessing hybrid vigor or heterosis is a promising approach to tackle the current challenge of sustaining enhanced yield gains of field crops. In the context, cytoplasmic male sterility (CMS) owing to its heritable nature to manifest non-functional male gametophyte remains a cost-effective system to promote efficient hybrid seed production. The phenomenon of CMS stems from a complex interplay between maternally-inherited (mitochondrion) and bi-parental (nucleus) genomic elements. In recent years, attempts aimed to comprehend the sterility-inducing factors (orfs) and corresponding fertility determinants (Rf) in plants have greatly increased our access to candidate genomic segments and the cloned genes. To this end, novel insights obtained by applying state-of-the-art omics platforms have substantially enriched our understanding of cytoplasmic-nuclear communication. Concomitantly, molecular tools including DNA markers have been implicated in crop hybrid breeding in order to greatly expedite the progress. Here, we review the status of diverse sterility-inducing cytoplasms and associated Rf factors reported across different field crops along with exploring opportunities for integrating modern omics tools with CMS-based hybrid breeding.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, India.
| | - Uday C Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Deepak Bisht
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India
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