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Anisimova OK, Kochieva EZ, Shchennikova AV, Filyushin MA. Thaumatin-like Protein (TLP) Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Expression in Response to Fusarium proliferatum Infection. PLANTS 2022; 11:plants11060748. [PMID: 35336630 PMCID: PMC8949454 DOI: 10.3390/plants11060748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022]
Abstract
Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, we identified 32 TLP homologs in the A. sativum cv. Ershuizao genome, which may function in the defense against Fusarium attack. The promoters of A. sativumTLP (AsTLP) genes contained cis-acting elements associated with hormone signaling and response to various types of stress, including those caused by fungal pathogens and their elicitors. The expression of AsTLP genes in Fusarium-resistant and -susceptible garlic cultivars was differently regulated by F. proliferatum infection. Thus, in the roots the mRNA levels of AsTLP7–9 and 21 genes were increased in resistant and decreased in susceptible A. sativum cultivars, suggesting the involvement of these genes in the garlic response to F. proliferatum attack. Our results provide insights into the role of TLPs in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.
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Gao Y, Zhang Y, Feng C, Chu H, Feng C, Wang H, Wu L, Yin S, Liu C, Chen H, Li Z, Zou Z, Tang L. A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis. Comput Struct Biotechnol J 2022; 20:1002-1011. [PMID: 35242290 PMCID: PMC8860920 DOI: 10.1016/j.csbj.2022.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 11/17/2022] Open
Abstract
Amorphophallus konjac, a perennial herb in the Araceae family, is a cash crop that can produce a large amount of konjac glucomannan. To explore mechanisms underlying such large genomes in the genus Amorphophallus as well as the gene regulation of glucomannan biosynthesis, we present a chromosome-level genome assembly of A. konjac with a total genome size of 5.60 Gb and a contig N50 of 1.20 Mb. Comparative genomic analysis reveals that A. konjac has undergone two whole-genome duplication (WGD) events in quick succession. Two recent bursts of transposable elements are identified in the A. konjac genome, which contribute greatly to the large genome size. Our transcriptomic analysis of the developmental corms characterizes key genes involved in the biosynthesis of glucomannan and related starches. High expression of cellulose synthase-like A, Cellulose synthase-like D, mannan-synthesis related 1, GDP-mannose pyrophosphorylase and phosphomannomutase fructokinase contributes to glucomannan synthesis during the corm expansion period while high expression of starch synthase, starch branching enzyme and phosphoglucomutase is responsible for starch synthesis in the late corm development stage. In conclusion, we generate a high-quality genome of A. konjac with different sequencing technologies. The expansion of transposable elements has caused the large genome of this species. And the identified key genes in the glucomannan biosynthesis provide valuable candidates for molecular breeding of this crop in the future.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Yanan Zhang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Chen Feng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Honglong Chu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Haibo Wang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Lifang Wu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Chao Liu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Huanhuan Chen
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Zhumei Li
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Zhengrong Zou
- College of Lifesciences, Jiangxi Normal University, Nanchang 330022, China
- Corresponding authors.
| | - Lizhou Tang
- College of Lifesciences, Jiangxi Normal University, Nanchang 330022, China
- Corresponding authors.
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Wu J, Niu Z, Lu X, Tang X, Qiao X, Ma L, Liu C, Li N. Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic ( Allium sativum) Greening. Front Nutr 2021; 8:764133. [PMID: 34790689 PMCID: PMC8591526 DOI: 10.3389/fnut.2021.764133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/14/2021] [Indexed: 12/03/2022] Open
Abstract
Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.
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Affiliation(s)
- Jinxiang Wu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zhonglu Niu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaoming Lu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaozhen Tang
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xuguang Qiao
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Longchuan Ma
- Garlic Science and Technology Research Center of Jinxiang, Jining, China
| | - Chao Liu
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningyang Li
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
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Finkers R, van Kaauwen M, Ament K, Burger-Meijer K, Egging R, Huits H, Kodde L, Kroon L, Shigyo M, Sato S, Vosman B, van Workum W, Scholten O. Insights from the first genome assembly of Onion (Allium cepa). G3 (BETHESDA, MD.) 2021; 11. [PMID: 34544132 DOI: 10.1101/2021.03.05.434149] [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: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 05/18/2023]
Abstract
Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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Affiliation(s)
- Richard Finkers
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Kai Ament
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Karin Burger-Meijer
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Henk Huits
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Laurens Kroon
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ben Vosman
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Olga Scholten
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
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55
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Li M, Zheng Z, Liu J, Yang Y, Ren G, Ru D, Zhang S, Du X, Ma T, Milne R, Liu J. Evolutionary origin of a tetraploid Allium species on the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:5780-5795. [PMID: 34487579 DOI: 10.1111/mec.16168] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/30/2022]
Abstract
Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known members in the subgenus Cyathophora. We found that A. tetraploideum was an obvious allotetrapoploid derived from ancestors including at least two closely related diploid species, A. farreri and A. cyathophorum, from which it differs by multiple ecological and genomic attributes. However, these two species cannot account for the full genome of A. tetraploideum, indicating that at least one extinct diploid is also involved in its ancestry. Furthermore, A. tetraploideum appears to have arisen via homoploid hybrid speciation (HHS) from two extinct allotetraploid parents, which derived in turn from the aforementioned diploids. Other modes of origin were possible, but all were even more complex and involved additional extinct ancestors. Our study together highlights how some polyploid species might have very complex origins, involving both HHS and polyploid speciation and also extinct ancestors.
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Affiliation(s)
- Minjie Li
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Juncheng Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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56
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Finkers R, van Kaauwen M, Ament K, Burger-Meijer K, Egging R, Huits H, Kodde L, Kroon L, Shigyo M, Sato S, Vosman B, van Workum W, Scholten O. Insights from the first genome assembly of Onion (Allium cepa). G3 (BETHESDA, MD.) 2021; 11:jkab243. [PMID: 34544132 PMCID: PMC8496297 DOI: 10.1093/g3journal/jkab243] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022]
Abstract
Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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Affiliation(s)
- Richard Finkers
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Kai Ament
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Karin Burger-Meijer
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Henk Huits
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Laurens Kroon
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ben Vosman
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Olga Scholten
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
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57
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Feng S, Liu Z, Cheng J, Li Z, Tian L, Liu M, Yang T, Liu Y, Liu Y, Dai H, Yang Z, Zhang Q, Wang G, Zhang J, Jiang H, Wei A. Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. HORTICULTURE RESEARCH 2021; 8:205. [PMID: 34480029 PMCID: PMC8417289 DOI: 10.1038/s41438-021-00665-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 05/14/2023]
Abstract
Zanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shanxi, China
| | - Lu Tian
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yonghong Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zujun Yang
- Center for Information in Biology, College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China.
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58
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Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic ( Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin. Int J Mol Sci 2021; 22:ijms22179237. [PMID: 34502163 PMCID: PMC8430937 DOI: 10.3390/ijms22179237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Garlic (Allium sativum L.) is an important vegetable and is cultivated and consumed worldwide for its economic and medicinal values. Garlic cloves, the major reproductive and edible organs, are derived from the axillary meristems. KNOTTED-like homeobox (KNOX) proteins, such as SHOOT MERISTEM-LESS (STM), play important roles in axillary meristem formation and development. However, the KNOX proteins in garlic are still poorly known. Here, 10 AsKNOX genes, scattered on 5 of the 8 chromosomes, were genome-wide identified and characterized based on the newly released garlic genome. The typical conserved domains of KNOX proteins were owned by all these 10 AsKNOX homologs, which were divided into two Classes (Class I and Class II) based on the phylogenetic analysis. Prediction and verification of the subcellular localizations revealed the diverse subcellular localization of these 10 AsKNOX proteins. Cis-element prediction, tissue expression analysis, and expression profilings in responding to exogenous GA3 and 6-BA showed the potential involvement of AsKNOX genes in the gibberellin and cytokinin signaling pathways. Overall, the results of this work provided a better understanding of AsKNOX genes in garlic and laid an important foundation for their further functional studies.
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Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes. Int J Mol Sci 2021; 22:ijms22136791. [PMID: 34202675 PMCID: PMC8268838 DOI: 10.3390/ijms22136791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.
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60
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Anisimova OK, Shchennikova AV, Kochieva EZ, Filyushin MA. Pathogenesis-Related Genes of PR1, PR2, PR4, and PR5 Families Are Involved in the Response to Fusarium Infection in Garlic ( Allium sativum L.). Int J Mol Sci 2021; 22:ijms22136688. [PMID: 34206508 PMCID: PMC8268425 DOI: 10.3390/ijms22136688] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Plants of the genus Allium developed a diversity of defense mechanisms against pathogenic fungi of the genus Fusarium, including transcriptional activation of pathogenesis-related (PR) genes. However, the information on the regulation of PR factors in garlic (Allium sativum L.) is limited. In the present study, we identified AsPR genes putatively encoding PR1, PR2, PR4, and PR5 proteins in A. sativum cv. Ershuizao, which may be involved in the defense against Fusarium infection. The promoters of the AsPR1-5 genes contained jasmonic acid-, salicylic acid-, gibberellin-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with the response to plant parasites. The expression of AsPR1c, d, g, k, AsPR2b, AsPR5a, c (in roots), and AsPR4a(c), b, and AsPR2c (in stems and cloves) significantly differed between garlic cultivars resistant and susceptible to Fusarium rot, suggesting that it could define the PR protein-mediated protection against Fusarium infection in garlic. Our results provide insights into the role of PR factors in A. sativum and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.
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Li MJ, Yu HX, Guo XL, He XJ. Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae). AOB PLANTS 2021; 13:plab017. [PMID: 34055281 PMCID: PMC8152445 DOI: 10.1093/aobpla/plab017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai-Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4-3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.
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Affiliation(s)
- Min-Jie Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- Nanjing Institute of Environmental Science, MEE, Nanjing, Jiangsu 210042, P.R. China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
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Liu N, Tong J, Hu M, Ji Y, Wang B, Liang H, Liu M, Wu Z. Transcriptome landscapes of multiple tissues highlight the genes involved in the flavor metabolic pathway in Chinese chive (Allium tuberosum). Genomics 2021; 113:2145-2157. [PMID: 33991618 DOI: 10.1016/j.ygeno.2021.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023]
Abstract
The unique flavor of Allium tuberosum is primarily associated with the hydrolysis of a series of organosulfur compounds, S-alk(en)yl cysteine sulphoxides (CSOs), upon tissue bruising or maceration. To obtain the tissue-specific transcriptomes, 18 RNA-Seq libraries representing leaf, root, stem, mature flower, inflorescence, and seed tissues of A. tuberosum were sequenced, finally yielding 133.7 Gb clean reads. The de novo assembled transcriptomes enabled the identification of 223,529 unigenes, which were functionally annotated and analyzed for the gene ontology and metabolic pathways. Furthermore, to reveal the flavor metabolic pathways, a total of 205 unigenes involved in the sulfur assimilation and CSO biosynthesis were identified, and their expression profiles were analyzed by RNA-Seq and qRT-PCR. Collectively, this study provides a valuable resource for in-depth molecular and functional researches especially on flavor formation, as well as for the development of molecular markers, and other genetic studies in A. tuberosum.
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Affiliation(s)
- Ning Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Jing Tong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Manman Hu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanhai Ji
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Baoju Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hao Liang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Mingchi Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhanhui Wu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of China, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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Genome-Wide Identification and Expression of Chitinase Class I Genes in Garlic ( Allium sativum L.) Cultivars Resistant and Susceptible to Fusarium proliferatum. PLANTS 2021; 10:plants10040720. [PMID: 33917252 PMCID: PMC8068077 DOI: 10.3390/plants10040720] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023]
Abstract
Vegetables of the Allium genus are prone to infection by Fusarium fungi. Chitinases of the GH19 family are pathogenesis-related proteins inhibiting fungal growth through the hydrolysis of cell wall chitin; however, the information on garlic (Allium sativum L.) chitinases is limited. In the present study, we identified seven class I chitinase genes, AsCHI1–7, in the A. sativum cv. Ershuizao genome, which may have a conserved function in the garlic defense against Fusarium attack. The AsCHI1–7 promoters contained jasmonic acid-, salicylic acid-, gibberellins-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with defense against pathogens. The expression of AsCHI2, AsCHI3, and AsCHI7 genes was constitutive in Fusarium-resistant and -susceptible garlic cultivars and was mostly induced at the early stage of F. proliferatum infection. In roots, AsCHI2 and AsCHI3 mRNA levels were increased in the susceptible and decreased in the resistant cultivar, whereas in cloves, AsCHI7 and AsCHI5 expression was decreased in the susceptible but increased in the resistant plants, suggesting that these genes are involved in the garlic response to Fusarium proliferatum attack. Our results provide insights into the role of chitinases in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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Yang QQ, Yang F, Zhao YQ, Lu XJ, Liu CY, Zhang BW, Ge J, Fan JD. Genome-wide identification and functional characterization of WRKY transcription factors involved in the response to salt and heat stress in garlic ( Allium sativum L). BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2022.2045218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Qing-Qing Yang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Feng Yang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Yong-Qiang Zhao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Xin-Juan Lu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Can-Yu Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Bi-Wei Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Jie Ge
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
| | - Ji-De Fan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, Jiangsu, PR China
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