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Nath M, Barh A, Sharma A, Verma P, Bairwa RK, Kamal S, Sharma VP, Annepu SK, Sharma K, Bhatt D, Bhatt P, Gupta D, Singh AR. Identification of Eight High Yielding Strains via Morpho-Molecular Characterization of Thirty-Three Wild Strains of Calocybe indica. Foods 2023; 12:foods12112119. [PMID: 37297361 DOI: 10.3390/foods12112119] [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: 04/26/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Calocybe indica, generally referred as milky mushroom, is one of the edible mushroom species suitable for cultivation in the tropical and sub-tropical regions of the world. However, lack of potential high yielding strains has limited its wider adaptability. To overcome this limitation, in this study, the germplasms of C. indica from different geographical regions of India were characterized based on their morphological, molecular and agronomical attributes. Internal transcribed spacers (ITS1 and ITS4)-based PCR amplification, sequencing and nucleotide analysis confirmed the identity of all the studied strains as C. indica. Further, evaluation of these strains for morphological and yield parameters led to the identification of eight high yielding strains in comparison to the control (DMRO-302). Moreover, genetic diversity analysis of these thirty-three strains was performed using ten sequence-related amplified polymorphism (SRAP) markers/combinations. The Unweighted Pair-group Method with Arithmetic Averages (UPGMA)-based phylogenetic analysis categorized the thirty-three strains along with the control into three clusters. Cluster I possesses the maximum number of strains. Among the high yielding strains, high antioxidant activity and phenol content was recorded in DMRO-54, while maximum protein content was observed in DMRO-202 and DMRO-299 as compared with the control strain. The outcome of this study will help the mushroom breeders and growers in commercializing C. indica.
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Affiliation(s)
- Manoj Nath
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Anupam Barh
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
- ICAR-Indian Institute of Soil and Water Conservation, Dehradun 248 195, India
| | - Annu Sharma
- Department of Plant Pathology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan 173 230, India
| | - Parul Verma
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | | | - Shwet Kamal
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | | | - Sudheer Kumar Annepu
- ICAR-Indian Institute of Soil and Water Conservation, Research Center, Ooty 643 006, India
| | - Kanika Sharma
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Deepesh Bhatt
- Department of Biotechnology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Faculty of Science, Sarvajanik University, Surat 395 001, India
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Dharmesh Gupta
- Department of Plant Pathology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan 173 230, India
| | - Akoijam Ratankumar Singh
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre Lamphelpat, Imphal 795 004, India
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Liu C, Guo M, Wang J, Sun Y, Bian Y, Xu Z. Prevalence and diversity of mycoviruses occurring in Chinese Lentinula edodes germplasm resource. Virology 2023; 582:71-82. [PMID: 37030155 DOI: 10.1016/j.virol.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Incidence and banding patterns of virus-like dsRNA elements in 215 Chinese genetically diverse Lentinula edodes strains collected from wide geographic distribution (or producing areas) were first investigated, and 17 viruses were identified including eight novel viruses. The results revealed a 63.3% incidence of dsRNA elements in the cultivated strains and a 67.2% incidence in the wild strains. A total of 10 distinguishable dsRNAs ranging from 0.6 to 12 kbp and 12 different dsRNA patterns were detected in the positive strains. The molecular information of these dsRNA elements was characterized, and the molecular information of the other 12 different viral sequences with (+) ssRNA genome was revealed in four L. edodes strains with complex dsRNA banding patterns. RT-PCR was also done to verify the five dsRNA viruses and 12 (+) ssRNA ones. The results presented may enrich our understanding of L. edodes virus diversity, and will promote further research on virus-host interactions. IMPORTANCE: Viral infections involve complicated interactions including benign, harmful or possibly beneficial to hosts. Sometimes environment could lead to a transition in lifestyles from persistent to acute, resulting in a disease phenotype. The quality of spawn, such as the vulnerability to infection of viruses, is therefore important for mushroom production. Lentinula edodes, a wood rot basidiomycete fungus, was widely cultivated in the world for its edible and medicinal properties. In this study, the profile of dsRNA elements from Chinese genetically diverse L. edodes strains collected from wide geographic distribution or producing areas was first investigated. The molecular information of the dsRNA elements was characterized. Additionally, 12 different viral sequences with (+) ssRNA genome from four L. edodes strains with complex dsRNA banding patterns were identified. The results presented here will broaden our knowledge about mushroom viruses, and promote further studies of L. edodes production and the interaction between viruses and L. edodes.
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Development of a novel SRAP-SCAR marker for rapid identification of lager and ale types in brewer's yeast. Mol Biol Rep 2023; 50:1943-1948. [PMID: 36380024 DOI: 10.1007/s11033-022-08058-w] [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: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Beer is a globally consumed and universally popular beverage. According to the fermentation conditions of brewer's yeast, ale yeast and lager yeast are the two major varieties. Normal phenotypic and genotypic approaches are insufficient and time-consuming for identifying these two forms of yeast. Therefore, a method for the rapid and cost-effective identification of lager and ale-type brewer's yeasts is necessary. METHODS AND RESULTS In this study, we analysed the genetic diversity of 23 industrial brewer's yeasts from around the world using sequence-related amplified polymorphism (SRAP) markers and produced stable sequence characteristic amplification region (SCAR) markers. The specific DNA fragments identified by the SRAP marker were sequenced and primers were constructed; the resultant SCAR marker (757 bp) was then confirmed against the indicated brewer's yeast type. CONCLUSION The development of SRAP-SCAR marker is more economical, simple, and fast compared to morphological markers.
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Liu JH, Ding FH, Song HY, Chen MH, Hu DM. Analysis of genetic diversity among Chinese Cyclocybe chaxingu strains using ISSR and SRAP markers. PeerJ 2022; 10:e14037. [PMID: 36196401 PMCID: PMC9527026 DOI: 10.7717/peerj.14037] [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: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 01/19/2023] Open
Abstract
Background Cyclocybe chaxingu is an edible and medicinal fungal species commonly cultivated in China. The major problems currently facing by growers of C. chaxingu is the random labeling of strains and strains aging and degeneration. Therefore, an evaluation of genetic diversity is essential for the conservation and reproducing programs of this species. Methods In the present study, 24 widely cultivated strains were collected from the main producing areas of China, and the genetic diversity analysis was performed. DNA polymorphism among these Chinese C. chaxingu strains was analyzed using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Results Eight ISSR primers amplified a total of 75 DNA fragments of which 61 (81.33%) were polymorphic. Fifteen SRAP primer combinations amplified 166 fragments of which 132 (79.52%) were polymorphic. Cluster analysis showed that the C. chaxnigu strains fall into five groups with a genetic distance values ranging from 0.06 to 0.60 by ISSR analysis, while the SRAP analysis divided the test strains into four groups within the range of genetic distance from 0.03 to 0.57. The results of the present study reveal a high level of genetic diversity among the widely cultivated C. chaxingu strains.
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Affiliation(s)
- Jin-Hao Liu
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
| | - Fang-Hui Ding
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China
| | - Hai-Yan Song
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Ministry of Education of the P.R. China, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Nanchang, China
| | - Ming-Hui Chen
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
| | - Dian-Ming Hu
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
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Sun Y, Guo M, Wang J, Bian Y, Xu Z. Curing two predominant viruses occurring in Lentinula edodes by chemotherapy and mycelial fragmentation methods. J Virol Methods 2021; 300:114370. [PMID: 34813824 DOI: 10.1016/j.jviromet.2021.114370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/02/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
Abstract
Previous research has established that Lentinula edodes mycovirus HKB (LeV-HKB) and L. edodes partitivirus 1(LePV1) are major mycoviruses identified in L.edodes germplasm. In this paper, two different methods for curing these two dsRNA mycoviruses, ribavirin treatment and mycelial fragmentation, were evaluated for the first time. Mycelial fragmentation was found to resulted in LeV-HKB- and LePV1-cured fungal strains, whereas ribavirin treatment could eliminate LeV-HKB only. Although no LePV1-cured strain was obtained via ribavirin treatment by the end of the experiment, the relative LePV1 concentration in the eighth successive subcultures was lower than that of the untreated control. The culture features of several virus-cured strains had faster mycelial growth rate and higher colony density than the infected ones. It was also suggested that LeV-HKB infection may affect the pigmentation in plate- and bag-cultivated mycelia of L. edodes strain L135.
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Affiliation(s)
- Yijia Sun
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mengpei Guo
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jinjie Wang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Ma X, Fan X, Wang G, Xu R, Yan L, Zhou Y, Gong Y, Xiao Y, Bian Y. Enhanced Expression of Thaumatin-like Protein Gene ( LeTLP1) Endows Resistance to Trichoderma atroviride in Lentinula edodes. Life (Basel) 2021; 11:863. [PMID: 34440607 PMCID: PMC8398078 DOI: 10.3390/life11080863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 01/17/2023] Open
Abstract
Lentinula edodes (shiitake mushrooms) is heavily affected by the infection of Trichoderma atroviride, causing yield loss and decreases quality in shiitake mushrooms. The selection and breeding of fungal-resistant L. edodes species are an important approach to protecting L. edodes from T. atroviride infection. Herein, a highly resistant L. edodes strain (Y3334) and a susceptible strain (Y55) were obtained by using a resistance evaluation test. Transcriptome analyses and qRT-PCR detection showed that the expression level of LeTLP1 (LE01Gene05009) was strongly induced in response to T. atroviride infection in the resistant Y3334. Then, LeTLP1-silenced and LeTLP1-overexpression transformants were obtained. Overexpression of LeTLP1 resulted in resistance to T. atroviride. Compared with the parent strain Y3334, LeTLP1-silenced transformants had reduced resistance relative to T. atroviride. Additionally, the LeTLP1 protein (Y3334) exhibited significant antifungal activity against T. atroviride. These findings suggest that overexpression of LeTLP1 is a major mechanism for the resistance of L. edodes to T. atroviride. The molecular basis provides a theoretical basis for the breeding of resistant L. edodes strains and can eventually contribute to the mushroom cultivation industry and human health.
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Affiliation(s)
- Xiaolong Ma
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Xiaolin Fan
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Gangzheng Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Ruiping Xu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Lianlian Yan
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yan Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yuhua Gong
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yang Xiao
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
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Mycoviral diversity and characteristics of a negative-stranded RNA virus LeNSRV1 in the edible mushroom Lentinula edodes. Virology 2020; 555:89-101. [PMID: 33308828 DOI: 10.1016/j.virol.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/04/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022]
Abstract
Bioinformatics and RT-PCR analysis of RNA from four Lentinula edodes samples identified 22 different virus-like contigs comprising 15 novel and 3 previously reported viruses. We further investigated the Lentinula edodes negative-stranded RNA virus 1 (LeNSRV1) isolated from a symptomatic sample, whose virion is a filamentous particle with a diameter of ~15 nm and a length of ~1200 nm. RT-PCR analysis detected LeNSRV1 in 10 of the 56 Chinese L. edodes core collection strains and 6 of the 22 monokaryotic strains from the L. edodes strain HNZMD. Genetic variation analysis showed that the sequences encoding the nucleocapsid protein (ORF2) from all the aforementioned LeNSRV1 positive strains are very conservative. The results presented here may enrich our understanding of L. edodes virus diversity and the characteristics of LeNSRV1, and will promote further research on virus-host interaction in L. edodes.
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Liu J, Li X, Liu Y, Xing C, Xie Y, Cai G, Lu J. Evaluation of genetic diversity and development of core collections of industrial brewing yeast using ISSR markers. Arch Microbiol 2020; 203:1001-1008. [PMID: 33112996 DOI: 10.1007/s00203-020-02091-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Germplasm of industrial brewing yeast of the worldwide have a richer diversity, and various successes in improving the performance of brewing yeasts. However, they are limited in that they have relatively low odds of combining desirable traits in a correct manner. To improve germplasm resource preservation, management, and utilization efficiency. In this study, the genetic diversity of 35 industrial brewing yeasts were analyzed based upon inter simple sequence repeat (ISSR) markers, in which 151 out of 167 SSR loci (90.42%) were polymorphic between two or more strains. Three preliminary core collections were established using ISSR data, and based on three different strategies as follows: an advanced maximization (M) strategy, an allele preferred sampling (A) strategy, and a random sampling (R) strategy. Comparison of genetic parameters, including polymorphic information content, Nei's genetic diversity (H), effective allele number, observed allele number, Shannon's index (I), and principal coordinate analyses, confirmed that all the core collections accurately recapitulated the diversity of the initial germplasm. Considering the loci retention ratio and trait coverage efficiency, Core1 was considered the best core collection.
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Affiliation(s)
- Jun Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Xiaomin Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Yueqin Liu
- China Resources Snow Breweries's Technical Center, China Resources Building, No. 8 Jianguomen North Avenue, Beijing, 100005, People's Republic of China
| | - Chengyu Xing
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Ying Xie
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Guolin Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
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Genetic diversity analysis of Corynespora cassiicola isolates on the rubber tree (Hevea brasiliensis) in Vietnam using ribosomal DNA internal transcribed spacer (rDNA-ITS) sequences and sequence-related amplified polymorphism (SRAP). J RUBBER RES 2020. [DOI: 10.1007/s42464-020-00047-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Effects of Medium Composition and Genetic Background on Agrobacterium-Mediated Transformation Efficiency of Lentinula edodes. Genes (Basel) 2019; 10:genes10060467. [PMID: 31248134 PMCID: PMC6627104 DOI: 10.3390/genes10060467] [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: 05/17/2019] [Revised: 06/08/2019] [Accepted: 06/14/2019] [Indexed: 11/28/2022] Open
Abstract
The establishment of genetic transformation method is crucial for the functional genomics research in filamentous fungi. Although the transformation method has been developed in several types of fungi, a highly efficient and convenient transformation system is desperately needed in Lentinula edodes. Present work established the Agrobacterium-mediated transformation (ATMT) of basidiomycete L. edodes in both monokaryon and dikaryon mycelia by using constructed binary plasmid pCAMBIA-1300-GFP. Then, the transformation efficiency of ATMT was evaluated by using different mediums for recipient incubation and different varieties of L. edodes. The results showed that in dikaryon strain W1, the positive hygromycin-resistant transformants was observed in all medium with the positive frequency of selected transformants that ranged from 0 to 30%. While in the monokaryon strain W1-26, only the millet medium group obtained positive transformants with a positive frequency of 75.48%. Moreover, three dikaryotic wild strains (YS55, YS3334, and YS3357) and two dikaryotic cultivated strains (W1 and S606) showed the highest transformation efficiency, with 32.96% of the germination frequency, and 85.12% of positive frequency for hygromycin-resistant transformants. This work demonstrated that Agrobacterium-mediated transformation was successfully performed in L. edodes, and the genotype of recipients as well as the medium for mycelial incubation were suggested to play key roles in determining the transformation efficiency. These findings may provide new avenues for the genetic modification of edible mushroom and may extend the cognition of DNA-mediated transformation in filamentous fungi.
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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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12
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Du J, Guo HB, Li Q, Forsythe A, Chen XH, Yu XD. Genetic diversity of Lepista nuda (Agaricales, Basidiomycota) in Northeast China as indicated by SRAP and ISSR markers. PLoS One 2018; 13:e0202761. [PMID: 30148893 PMCID: PMC6110484 DOI: 10.1371/journal.pone.0202761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/07/2018] [Indexed: 01/03/2023] Open
Abstract
Lepista nuda is a popular wild edible mushroom that grows in China. In this study, we used ISSR and SRAP molecular markers to analyze the genetic diversity of 72 samples of L. nuda from eight populations in Northeast China. In total, six ISSR primers and five pairs of SRAP primers that produced clear and polymorphic banding profiles were selected for assessing L. nuda genetic diversity. The results revealed a high level of genetic variation among the 72 samples (94.4% polymorphism) but a low degree of gene flow among the populations. Among L. nuda populations, genetic distance was not correlated significantly with geographic distance. The antioxidant activity of the samples from each population was also tested and the result showed that all the selected samples had more than 60% DPPH scavenging activities. Nonetheless, the antioxidant activity diversity is not coincident with both the genetic diversity and the geographic distribution. The results indicate that ISSR and SRAP molecular markers are useful for studying the genetic diversity of L. nuda. The results also suggest that L. nuda populations in Northeast China require protection.
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Affiliation(s)
- Jing Du
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hong-Bo Guo
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, China
- College of Life Engineering, Shenyang Institute of Technology, Fushun, Liaoning, China
| | - Qi Li
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Adrian Forsythe
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Xu-Hui Chen
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiao-Dan Yu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
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Wang J, Guo M, Sun Y, Bian Y, Zhou Y, Xu Z. Genetic variation and phylogenetic analyses reveal transmission clues of Lentinula edodes partitivirus 1 (LePV1) from the Chinese L. edodes core collection. Virus Res 2018; 255:127-132. [DOI: 10.1016/j.virusres.2018.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/14/2018] [Accepted: 07/19/2018] [Indexed: 11/28/2022]
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14
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Liu XB, Li J, Yang ZL. Genetic diversity and structure of core collection of winter mushroom ( Flammulina velutipes) developed by genomic SSR markers. Hereditas 2017; 155:3. [PMID: 28690478 PMCID: PMC5496253 DOI: 10.1186/s41065-017-0038-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
Background A core collection is a subset of an entire collection that represents as much of the genetic diversity of the entire collection as possible. The establishment of a core collection for crops is practical for efficient management and use of germplasm. However, the establishment of a core collection of mushrooms is still in its infancy, and no established core collection of the economically important species Flammulina velutipes has been reported. Results We established the first core collection of F. velutipes, containing 32 strains based on 81 genetically different F. veltuipes strains. The allele retention proportion of the core collection for the entire collection was 100%. Moreover, the genetic diversity parameters (the effective number of alleles, Nei’s expected heterozygosity, the number of observed heterozygosity, and Shannon’s information index) of the core collection showed no significant differences from the entire collection (p > 0.01). Thus, the core collection is representative of the genetic diversity of the entire collection. Genetic structure analyses of the core collection revealed that the 32 strains could be clustered into 6 groups, among which groups 1 to 3 were cultivars and groups 4 to 6 were wild strains. The wild strains from different locations harbor their own specific alleles, and were clustered stringently in accordance with their geographic origins. Genetic diversity analyses of the core collection revealed that the wild strains possessed greater genetic diversity than the cultivars. Conclusion We established the first core collection of F. velutipes in China, which is an important platform for efficient breeding of this mushroom in the future. In addition, the wild strains in the core collection possess favorable agronomic characters and produce unique bioactive compounds, adding value to the platform. More attention should be paid to wild strains in further strain breeding. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao Bin Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jing Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China.,University of Chinese Academy of Sciences, Beijing, 100049 China.,State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, Yunnan 650091 China
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
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15
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Chen R, Hara T, Ohsawa R, Yoshioka Y. Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction. BREEDING SCIENCE 2017; 67:239-247. [PMID: 28744177 PMCID: PMC5515314 DOI: 10.1270/jsbbs.16192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 05/23/2023]
Abstract
Diversity analysis of rapeseed accessions preserved in the Japanese Genebank can provide valuable information for breeding programs. In this study, 582 accessions were genotyped with 30 SSR markers covering all 19 rapeseed chromosomes. These markers amplified 311 alleles (10.37 alleles per marker; range, 3-39). The genetic diversity of Japanese accessions was lower than that of overseas accessions. Analysis of molecular variance indicated significant genetic differentiation between Japanese and overseas accessions. Small but significant differences were found among geographical groups in Japan, and genetic differentiation tended to increase with geographical distance. STRUCTURE analysis indicated the presence of two main genetic clusters in the NARO rapeseed collection. With the membership probabilities threshold, 227 accessions mostly originating from overseas were assigned to one subgroup, and 276 accessions mostly originating from Japan were assigned to the other subgroup. The remaining 79 accessions are assigned to admixed group. The core collection constructed comprises 96 accessions of diverse origin. It represents the whole collection well and thus it may be useful for rapeseed genetic research and breeding programs. The core collection improves the efficiency of management, evaluation, and utilization of genetic resources.
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Affiliation(s)
- Ruikun Chen
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
| | - Takashi Hara
- Faculty of Life and Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
| | - Ryo Ohsawa
- Faculty of Life and Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
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16
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Guo M, Bian Y, Wang J, Wang G, Ma X, Xu Z. Biological and Molecular Characteristics of a Novel Partitivirus Infecting the Edible Fungus Lentinula edodes. PLANT DISEASE 2017; 101:726-733. [PMID: 30678568 DOI: 10.1094/pdis-07-16-0951-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A new partitivirus named Lentinula edodes partitivirus 1 (LePV1) was isolated from a diseased L. edodes strain with severe degeneration of the mycelium and imperfect browning in bag cultures. The nucleotide sequences of LePV1 dsRNA-1 and dsRNA-2 were determined; they were 2,382 bp and 2,245 bp in length, and each contained a single ORF encoding RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. The purified virus preparation contained isometric particles 34 nm in diameter encapsidating these dsRNAs. Phylogenetic analyses showed LePV1 to be a new member of Betapartitivirus, with the RdRp sequence most closely related to Grapevine partitivirus. RT-PCR analysis showed that 27 of the 56 Chinese L. edodes core collection strains carry LePV1, with the virus being more common in wild strains than cultivated strains. In addition, qPCR analysis suggested that coinfection with L. edodes mycovirus HKB (LeV-HKB) could increase replication of the RdRp gene of LePV1. This study may be essential for the development of more accurate disease diagnostics and the formulation of control strategies for viral diseases in L. edodes.
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Affiliation(s)
- Mengpei Guo
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China, and Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinjie Wang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gangzheng Wang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolong Ma
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China, and Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, China
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17
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Lee HY, Moon S, Shim D, Hong CP, Lee Y, Koo CD, Chung JW, Ryu H. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars. Genes (Basel) 2017; 8:genes8040109. [PMID: 28338645 PMCID: PMC5406856 DOI: 10.3390/genes8040109] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/28/2017] [Accepted: 03/21/2017] [Indexed: 11/16/2022] Open
Abstract
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea.
| | | | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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18
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Jing Y, Peng M, Yang L, Wang Q. Evaluation of genetic diversity among Piptoporus betulinusas revealed by inter simple sequence repeat markers. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2016.1276413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Yanli Jing
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, PR China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Harbin, PR China
| | - Mu Peng
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, PR China
| | - Lixia Yang
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, PR China
- College of Life and Environmental Science, Hulunbuir University, Hulunbuir, PR China
| | - Qiuyu Wang
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, PR China
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19
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Li C, Gong W, Zhang L, Yang Z, Nong W, Bian Y, Kwan HS, Cheung MK, Xiao Y. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom. Front Microbiol 2017; 8:237. [PMID: 28261189 PMCID: PMC5314409 DOI: 10.3389/fmicb.2017.00237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom.
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Affiliation(s)
- Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Wenbing Gong
- Institute of Applied Mycology, Huazhong Agricultural UniversityHubei, China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural SciencesChangsha, China
| | - Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Zhiquan Yang
- College of Informatics, Huazhong Agricultural University Hubei, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Hoi-Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Man-Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
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20
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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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