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Zhang Y, Niu N, Li S, Liu Y, Xue C, Wang H, Liu M, Zhao J. Virus-Induced Gene Silencing (VIGS) in Chinese Jujube. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112115. [PMID: 37299093 DOI: 10.3390/plants12112115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Virus-induced gene silencing (VIGS) is a fast and efficient method for assaying gene function in plants. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully practiced in some species such as cotton and tomato. However, little research of VIGS systems has been reported in woody plants, nor in Chinese jujube. In this study, the TRV-VIGS system of jujube was firstly investigated. The jujube seedlings were grown in a greenhouse with a 16 h light/8 h dark cycle at 23 °C. After the cotyledon was fully unfolded, Agrobacterium mixture containing pTRV1 and pTRV2-ZjCLA with OD600 = 1.5 was injected into cotyledon. After 15 days, the new leaves of jujube seedlings showed obvious photo-bleaching symptoms and significantly decreased expression of ZjCLA, indicating that the TRV-VIGS system had successfully functioned on jujube. Moreover, it found that two injections on jujube cotyledon could induce higher silencing efficiency than once injection. A similar silencing effect was then also verified in another gene, ZjPDS. These results indicate that the TRV-VIGS system in Chinese jujube has been successfully established and can be applied to evaluate gene function, providing a breakthrough in gene function verification methods.
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Affiliation(s)
- Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Nazi Niu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Shijia Li
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Yin Liu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
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Sareen A, Sharma V, Gupta RC. Assessment of genetic diversity and population structure in wild Ziziphus species from northwest India using SSR marker technique. J Genet Eng Biotechnol 2023; 21:4. [PMID: 36637660 PMCID: PMC9839936 DOI: 10.1186/s43141-022-00458-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Ziziphus species particularly Ziziphus mauritiana and Ziziphus nummularia constitute an important part of genetic resources in India. They contribute economically as a fruit crop with lots of morphological and pomological variability. In current study, 48 accessions belonging to two wild Ziziphus species, i.e., Z. mauritiana and Z. nummularia, were characterized using SSR markers. In addition, external features were also examined using stereomicroscope. RESULTS Present investigation was done to explore the genetic structure of North Indian jujube. In total, 23 SSR markers detected 57 SSR alleles with an average of 2.47 alleles. Highest number of alleles (4) were detected by three primers, namely BFU1178, BFU479, and ZCMS14, while lowest number of alleles (2) were detected by fifteen primers. Highest Polymorphism Information Content (PIC) was 0.500 and shown by two primers, namely BFU528 and BFU1248, while lowest PIC (0.041) was observed in primers BFU286 with mean value of 0.443. Similarly, highest value of marker index (MI) was detected by primer BFU1178 i.e. 1.969, and lowest value of marker index was observed in primer BFU286 i.e. 0.021. Dendrogram generated using SSR markers data and principal component analysis showed two major groups of the analyzed germplasm with intermixing. STRUCTURE analysis also clustered all the accessions into two groups. We did not found correlation between geographic and genetic distances. CONCLUSIONS The preliminary results suggest that there is high level of gene pool mixing in these species which can be attributed to their cross-pollination habit. However, more such studies with large numbers of samples are required in future to gain concrete insights of the genetic structure in these species.
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Affiliation(s)
- Amit Sareen
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
| | - Vikas Sharma
- Department of Agriculture, Sant Baba Bhag Singh University Khiala, Jalandhar, 144030 India
| | - Raghbir Chand Gupta
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
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Saina JK, Gichira AW, Ngarega BK, Li ZZ, Gituru RW, Hu GW, Liao K. Development and utilization of microsatellite markers to assess genetic variation coupled with modelling range shifts of Dodonaea viscosa (L.) Jacq. in isolated Taita Hills and Mount Kenya forests. Mol Biol Rep 2021; 49:917-929. [PMID: 34741709 DOI: 10.1007/s11033-021-06911-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Understanding genetic variation is critical for the protection and maintenance of fragmented and highly disturbed habitats. The Taita Hills of Kenya are the northernmost part of the Eastern Arc Mountains and have been identified as one of the world's top ten biodiversity hotspots. Over the past century the current forests in the Taita Hills have become highly fragmented. In order to appraise the influence of anthropological disturbance and fragmentation on plant species in these mountains, we studied the genetic variation and population structure of Dodonaea viscosa (L.) Jacq. (Sapindaceae), using newly developed microsatellite (SSR) markers, combined with ecological niche modelling analyses (ENMs). METHODS AND RESULTS We utilized the Illumina paired-end technology to sequence D. viscosa's genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed, and 49,836 SSRs were identified from 42,638 sequences. A total of 18 out of 25 randomly selected primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within populations and only 20% among the eight populations. According to ENM results, D. viscosa's suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of (representative concentration pathway) RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments. CONCLUSIONS In the present study, we successfully developed and tested SSR markers for D. viscosa. Study results indicate that fragmentation would constitute a severe threat to plant forest species. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.
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Affiliation(s)
- Josphat K Saina
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Andrew W Gichira
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Boniface K Ngarega
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Robert W Gituru
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya
| | - Guang-Wan Hu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kuo Liao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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Li B, Lin F, Huang P, Guo W, Zheng Y. Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biol Res 2020; 53:21. [PMID: 32410692 PMCID: PMC7227249 DOI: 10.1186/s40659-020-00289-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/29/2020] [Indexed: 01/25/2023] Open
Abstract
Background Liriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm. Results We performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79. Conclusions The genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Wenying Guo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China. .,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.
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Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis). FORESTS 2020. [DOI: 10.3390/f11010061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.
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Li J, Liu XB, Zhao ZW, Yang ZL. Genetic diversity, core collection and breeding history of Pleurotus ostreatus in China. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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