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Fabriki-Ourang S, Yousefi-Azarkhanian M. Genetic variability and relationships among Salvia ecotypes/species revealed by TRAP-CoRAP markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1534555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Sedigheh Fabriki-Ourang
- Department of Genetics and Plant Breeding, Faculty of Agriculture and Natural Resources, Imam Khomeini International University, Qazvin, Iran
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Xiao Y, Cheng X, Liu J, Li C, Nong W, Bian Y, Cheung MK, Kwan HS. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China. Sci Rep 2016; 6:36789. [PMID: 27830835 PMCID: PMC5103288 DOI: 10.1038/srep36789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023] Open
Abstract
The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.
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Affiliation(s)
- Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Xuanjin Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Jun Liu
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
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Genetic diversity and population structure of Chinese Lentinula edodes revealed by InDel and SSR markers. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1183-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Liu J, Wang ZR, Li C, Bian YB, Xiao Y. Evaluating genetic diversity and constructing core collections of ChineseLentinula edodescultivars using ISSR and SRAP markers. J Basic Microbiol 2015; 55:749-60. [DOI: 10.1002/jobm.201400774] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/07/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Jun Liu
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Zhuo-Ren Wang
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Chuang Li
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Yin-Bing Bian
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Yang Xiao
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
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Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism. ScientificWorldJournal 2014; 2014:619746. [PMID: 25013861 PMCID: PMC4071973 DOI: 10.1155/2014/619746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 11/17/2022] Open
Abstract
Hypsizygus marmoreus is an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis of H. marmoreus sequences from GenBank database. The genomic DNA extracted from H. marmoreus was amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains of H. marmoreus were classified into two main groups.
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Li L, Fan XZ, Liu W, Xiao Y, Bian YB. Comparative analysis on the diversity of Auricularia auricula-judae by physiological characteristics, somatic incompatibility and TRAP fingerprinting. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0671-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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