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Zhang J, Shen N, Li C, Xiang X, Liu G, Gui Y, Patev S, Hibbett DS, Barry K, Andreopoulos W, Lipzen A, Riley R, He G, Yan M, Grigoriev IV, Shan Kwan H, Kit Cheung M, Bian Y, Xiao Y. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. J Adv Res 2021; 38:91-106. [PMID: 35572413 PMCID: PMC9091725 DOI: 10.1016/j.jare.2021.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 02/08/2023] Open
Abstract
We detected three subgroups of L. edodes with robust phenotypic differentiation. The three subgroups were diverged 36,871 generations ago. L. edodes cultivars in China might originate from the vicinity of Northeast China. We dissected the genetic basis of adaptive evolution in L. edodes. Genes related to fruiting body development are involved in adaptive evolution.
Introduction Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
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Salwan R, Katoch S, Sharma V. Recent Developments in Shiitake Mushrooms and Their Nutraceutical Importance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Saito T, Sakuta G, Kobayashi H, Ouchi K, Inatomi S. Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars. MYCOBIOLOGY 2019; 47:466-472. [PMID: 32010468 PMCID: PMC6968638 DOI: 10.1080/12298093.2019.1665331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.
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Affiliation(s)
- Teruaki Saito
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | - Genki Sakuta
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | | | - Kenji Ouchi
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | - Satoshi Inatomi
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
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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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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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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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Molecular identification of lactic acid bacteria in Chinese rice wine using species-specific multiplex PCR. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2193-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Developing an SCAR and ITS reliable multiplex PCR-based assay for safflower adulterant detection in saffron samples. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.07.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mansour H, Mekki LE, Hussein MA. Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers. Pak J Biol Sci 2014; 17:56-61. [PMID: 24783778 DOI: 10.3923/pjbs.2014.56.61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes.
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Development of SCAR markers to determine the mating types of Lepista nuda protoplast monokaryons. Curr Microbiol 2013; 68:536-42. [PMID: 24352297 DOI: 10.1007/s00284-013-0510-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/31/2013] [Indexed: 10/25/2022]
Abstract
Lepista nuda (Bull. ex Fr.) Cooke belongs to Tricholomataceae and is an edible fungus with both economic and medical value. Mycelia were isolated from the fruiting bodies of L. nuda and were used to prepare the protoplast monokaryons. One hundred and fifteen monokaryons were obtained and their mating types were determined using somatic incompatibility tests. Protoplast monokaryons segregated into either the A1B1 or the A2B2 mating types. Inter-simple sequence repeats and sequence-related amplified polymorphism fingerprinting were used to analyse the mating types of these protoplast monokaryons and 16 sequence-characterised amplified region primers were developed to efficiently differentiate between the monokaryon mating types. Multiplex PCR analyses were also established. The data presented here outline a method for the precise and rapid identification of protoplast monokaryon mating types, which has the promise to shorten the period required for conventional crossbreeding.
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PCR-based gene marker with a high efficiency genome scanning (HEGS) system: application for distinguishing among cultivars in Lentinula edodes. World J Microbiol Biotechnol 2012; 28:1315-9. [DOI: 10.1007/s11274-011-0908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 09/22/2011] [Indexed: 10/17/2022]
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Liu JY, Ying ZH, Liu F, Liu XR, Xie BG. Evaluation of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains. Curr Microbiol 2012; 64:317-25. [PMID: 22218569 DOI: 10.1007/s00284-011-0069-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/03/2011] [Indexed: 11/25/2022]
Abstract
In this study, three molecular marker systems including sequence related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and inter-simple sequence repeats (ISSR) were screened to select polymorphisms of 24 main commercial strains of Lentinula edodes cultivated widely in China. Twenty-nine sequence characterized amplified region (SCAR) markers were developed to set up a dendrogram using UPMGA based on nucleotide sequences of some SRAP, RAPD, and ISSR polymorphic fragments. The grouping showed that the 24 strains were apparently clustered into five groups at a level of 0.68 similarity coefficient, and those that have similar breeding background clustered preferentially into the same subgroup. Results also revealed that the 24 strains had a low level of genetic diversity, and the breeding source of L. edodes should be broadened by exploiting wild types and introducing exotic strains. In addition, the tested strains of L. edodes could be clearly distinguished and identified from others by using different combinations of SCAR primers. Thus, results of this work demonstrated that SCAR was an excellent genetic marker system to characterize and investigate genetic diversity of L. edodes. Furthermore, this provided an alternative method to identify the genetic relationship of different strains of other fungi.
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Affiliation(s)
- Jing-Yu Liu
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Construction of a genetic linkage map based on amplified fragment length polymorphism markers and development of sequence-tagged site markers for marker-assisted selection of the sporeless trait in the oyster mushroom (Pleurotus eryngii). Appl Environ Microbiol 2011; 78:1496-504. [PMID: 22210222 DOI: 10.1128/aem.07052-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Quél. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection.
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Development of IRAP-SCAR marker for strain identification in Lentinula edodes. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0626-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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