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Bourguiba H, Batnini MA, Naccache C, Zitouna N, Trifi-Farah N, Audergon JM, Krichen L. Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems. Genetica 2021; 149:239-251. [PMID: 34231081 DOI: 10.1007/s10709-021-00127-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia.
| | - Mohamed-Amine Batnini
- Department of Plant Pathology, OARDC/OSU, 120 Selby, 1680 Madison Ave, Wooster, OH, 44691, USA
| | - Chahnez Naccache
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Biochimie et Biotechnology (LR01ES05), Tunis, Tunisia
| | - Nadia Zitouna
- LR16IPT05, Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
| | - Jean-Marc Audergon
- INRAe Centre PACA, UR 1052 GAFL, Domaine St Maurice, 67, allée des chênes, CS60094, 84143, Montfavet Cedex, France
| | - Lamia Krichen
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia. Biochem Genet 2021; 59:1065-1087. [PMID: 34132957 PMCID: PMC8249305 DOI: 10.1007/s10528-021-10090-7] [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: 10/31/2019] [Accepted: 05/28/2021] [Indexed: 11/18/2022]
Abstract
Polyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.
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Yi X, Chen J, Zhu H, Li Y, Li X, Li M, Duan Y, Chen L, Wang X. Phylogeography and the population genetic structure of flowering cherry Cerasus serrulata (Rosaceae) in subtropical and temperate China. Ecol Evol 2020; 10:11262-11276. [PMID: 33144963 PMCID: PMC7593168 DOI: 10.1002/ece3.6765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 06/10/2020] [Indexed: 11/24/2022] Open
Abstract
Cerasus serrulata (Rosaceae) is an important flowering cherry resource which is valuable for developing new cultivars of flowering cherries. It is broadly distributed and possesses abundant variations. In this study, phylogeographic analysis was conducted to reveal the evolutionary history to better understand the genetic diversity and genetic structure of C. serrulata so as to provide more accurate molecular insights into better conservation and utilization of the germplasm resources. A total of 327 individuals from 18 wild populations were collected. Three chloroplast DNA (cpDNA) fragments (matK, trnD-E, and trnS-G) and the nuclear internal transcribed spacer (ITS) were utilized. The results showed a high genetic diversity at both species level and population level of C. serrulata. High genetic differentiation and the existence of the phylogeographic structure were detected. No significant expansion events were discovered. Two geographic lineages were inferred. One was confined to the Qinling Mountains and the Taihang Mountains. The other was from the Wuling Mountains to the Jiangnan Hilly Regions and then went northeast to the coast of Asia. In addition, some taxonomic treatments of the C. serrulata complex are discussed and reconsidered. Conservation and utilization strategies of wild C. serrulata germplasm resources were recommended.
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Affiliation(s)
- Xian‐Gui Yi
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Jie Chen
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Hong Zhu
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Yong‐Fu Li
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Xue‐Xia Li
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Meng Li
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Yi‐Fan Duan
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Lin Chen
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
| | - Xian‐Rong Wang
- Co‐Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research CenterCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingJiangsuChina
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Bourguiba H, Scotti I, Sauvage C, Zhebentyayeva T, Ledbetter C, Krška B, Remay A, D’Onofrio C, Iketani H, Christen D, Krichen L, Trifi-Farah N, Liu W, Roch G, Audergon JM. Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin. FRONTIERS IN PLANT SCIENCE 2020; 11:638. [PMID: 32523597 PMCID: PMC7261834 DOI: 10.3389/fpls.2020.00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/24/2020] [Indexed: 05/22/2023]
Abstract
The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (FST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ivan Scotti
- INRA Centre PACA, UR 629 URFM, Avignon, France
| | | | - Tetyana Zhebentyayeva
- Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Craig Ledbetter
- San Joaquin Valley Agricultural Sciences Center, Crop Diseases, Pests & Genetics, Parlier, CA, United States
| | - Boris Krška
- Department of Fruit Growing, Faculty of Horticulture, Mendel University, Lednice, Czechia
| | | | - Claudio D’Onofrio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Pisa, Italy
| | - Hiroyuki Iketani
- National Agriculture and Food Research Organization (NARO) Institute of Fruit Tree Science, Tsukuba, Japan
| | - Danilo Christen
- Département Fédéral de L’économie DFE, Station de Recherche Agroscope Changins-Wädenswil ACW, Centre de Recherche Conthey, Conthey, Switzerland
| | - Lamia Krichen
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Weisheng Liu
- Liaoning Institute of Pomology, Yingkou City, China
| | - Guillaume Roch
- INRA Centre PACA, UR 1052 GAFL, Montfavet, France
- CEP Innovation, Lyon, France
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High genetic diversity and differentiation of an extremely narrowly distributed and critically endangered decaploid rose (Rosa praelucens): implications for its conservation. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1052-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Jian H, Zhang Y, Qiu X, Yan H, Wang Q, Zhang H, Sun H. Yalongjiang River Has Had an Important Role in the Dispersal and Divergence of Rosa soulieana in the Hengduan Mountains of China. PLoS One 2016; 11:e0158586. [PMID: 27355209 PMCID: PMC4927166 DOI: 10.1371/journal.pone.0158586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/17/2016] [Indexed: 11/18/2022] Open
Abstract
The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity (Ht), Shannon index (I), and heterozygosity value within populations (Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient (Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River.
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Affiliation(s)
- Hongying Jian
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonghong Zhang
- Life Science Department, Yunnan Normal University, Kunming, China
| | - Xianqin Qiu
- National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Huijun Yan
- National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qigang Wang
- National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hao Zhang
- National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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Chen T, Chen Q, Luo Y, Huang ZL, Zhang J, Tang HR, Pan DM, Wang XR. Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:787-97. [PMID: 25521479 DOI: 10.1111/plb.12294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 12/10/2014] [Indexed: 05/16/2023]
Abstract
Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (GST = 0.215; NST = 0.256) and nuclear DNA (GST = 0.146; NST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.
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Affiliation(s)
- T Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Q Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Y Luo
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Z-L Huang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - J Zhang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - H-R Tang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - D-M Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - X-R Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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Murata H, Yamada A, Yokota S, Maruyama T, Endo N, Yamamoto K, Ohira T, Neda H. Root endophyte symbiosis in vitro between the ectomycorrhizal basidiomycete Tricholoma matsutake and the arbuscular mycorrhizal plant Prunus speciosa. MYCORRHIZA 2014; 24:315-321. [PMID: 24158697 DOI: 10.1007/s00572-013-0534-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/09/2013] [Indexed: 06/02/2023]
Abstract
We previously reported that Tricholoma matsutake and Tricholoma fulvocastaneum, ectomycorrhizal basidiomycetes that associate with Pinaceae and Fagaceae, respectively, in the Northern Hemisphere, could interact in vitro as a root endophyte of somatic plants of Cedrela odorata (Meliaceae), which naturally harbors arbuscular mycorrhizal fungi in South America, to form a characteristic rhizospheric colony or "shiro". We questioned whether this phenomenon could have occurred because of plant-microbe interactions between geographically separated species that never encounter one another in nature. In the present study, we document that these fungi formed root endophyte interactions and shiro within 140 days of inoculation with somatic plants of Prunus speciosa (=Cerasus speciosa, Rosaceae), a wild cherry tree that naturally harbors arbuscular mycorrhizal fungi in Japan. Compared with C. odorata, infected P. speciosa plants had less mycelial sheath surrounding the exodermis, and the older the roots, especially main roots, the more hyphae penetrated. In addition, a large number of juvenile roots were not associated with hyphae. We concluded that such root endophyte interactions were not events isolated to the interactions between exotic plants and microbes but could occur generally in vitro. Our pure culture system with a somatic plant allowed these fungi to express symbiosis-related phenotypes that varied with the plant host; these traits are innately programmed but suppressed in nature and could be useful in genetic analyses of plant-fungal symbiosis.
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Affiliation(s)
- Hitoshi Murata
- Department of Applied Microbiology and Mushroom Sciences, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan,
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Population genetic structure in a threatened tree, Pyrus calleryana var. dimorphophylla revealed by chloroplast DNA and nuclear SSR locus polymorphisms. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0489-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Lopez L, Barreiro R. Genetic guidelines for the conservation of the endangered polyploid Centaurea borjae (Asteraceae). JOURNAL OF PLANT RESEARCH 2013; 126:81-93. [PMID: 22678690 DOI: 10.1007/s10265-012-0497-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
Appropriate management of species of conservation concern requires designing strategies that should include genetic information as small population size and restricted geographic range can reduce genetic variation. We used AFLPs to investigate genetic variation within and among populations of the endangered narrow endemic Centaurea borjae, and found no evidence for genetic impoverishment despite its <40 km range and potential for vegetative propagation. Genetic variation was comparable to other plants with similar life history (88 % occurring within populations) and potential clone mates were less frequent than expected. Nonetheless, populations separated by few hundred meters showed signs of significant genetic differentiation suggesting low gene flow between them. Our results suggested that the three geographically closer populations located at the center of the range might be treated as a single management unit, while the remaining ones could be considered independent units. We found evidence of fine-scale spatial genetic structure up to 80 m indicating that the collection of germplasm for ex-situ conservation should focus on individuals separated >80 m to maximize genetic variation.
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Affiliation(s)
- Lua Lopez
- Área de Ecología, Facultad de Ciencias, Universidad da Coruña, Campus A Zapateira s/n, 15071 A Coruña, Spain.
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[Chloroplast DNA trnQ-rps16 variation and genetic structure of nine wild Chinese cherry (Cerasus pseudocerasus Lindl.) populations]. YI CHUAN = HEREDITAS 2012. [PMID: 23208145 DOI: 10.3724/sp.j.1005.2012.01475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chinese cherry (Cerasus pseudocerasus Lindl.) is one of the most economically domestic fruit trees in China. The rich variation of wild Chinese cherry is the most important breeding resource for existing cultivars. In order to reveal the levels and distribution of genetic variation within wild Chinese cherry of Sichuan Province, China, where is rich in wild Chinese cherry, the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacer was analyzed in 145 individuals of all nine existing populations (seven from Sichuan, two from Shanxi and Guizhou provinces) of China. The results showed that trnQ-rps16 sequence were aligned with 13 polymorphic sites (1.87%), including 3 substitutions and 10 indels in 145 individuals, which revealed a low level of genetic diversity (h= 0.562, π= 0.00184). Compared to other regions (h= 0.733, π= 0.00243), a rather lower genetic diversity (h= 0.544, π= 0.00203) was found in the populations from Sichuan, and a large scale of genetic diversity among the seven populations was detected (h= 0-0.708; π= 0-0.00298), ranging from EM (h=0.000, π=0.000) to TL (h=0.708, π=0.00298). The low genetic diversity of populations may be strongly affected by founder effect and bottleneck effect because of the marginal nature, recent reduction, and consequent genetic drift of these populations. In addition, a fairly low genetic differentiation (FST= 0.21573) was found among the studied populations. This suggest that gene flow seems to originate from pronounced seed dispersal abilities of the species and it may play a significant role in shaping such a genetic structure. The long generation cycle of the species may also contribute to this structure. Based on these findings, a conservational plan for sampling or preserving fewer populations but more individuals from each population for the species was proposed.
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12
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Shuri K, Saika K, Junko K, Michiharu K, Nagamitsu T, Iwata H, Tsumura Y, Mukai Y. Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa. Heredity (Edinb) 2012; 109:188-98. [PMID: 22669074 DOI: 10.1038/hdy.2012.29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mating processes of local demes and spatial genetic structure of island populations at the self-incompatibility (S-) locus under negative frequency-dependent selection (NFDS) were evaluated in Prunus lannesiana var. speciosa in comparison with nuclear simple sequence repeat (SSR) loci that seemed to be evolutionarily neutral. Our observations of local mating patterns indicated that male-female pair fecundity was influenced by not only self-incompatibility, but also various factors, such as kinship, pollen production and flowering synchrony. In spite of the mating bias caused by these factors, the NFDS effect on changes in allele frequencies from potential mates to mating pollen was detected at the S-locus but not at the SSR loci, although the changes from adult to juvenile cohorts were not apparent at any loci. Genetic differentiation and isolation-by-distance over various spatial scales were smaller at the S-locus than at the SSR loci, as expected under the NFDS. Allele-sharing distributions among the populations also had a unimodal pattern at the S-locus, indicating the NFDS effect except for alleles unique to individual populations probably due to isolation among islands, although this pattern was not exhibited by the SSR loci. Our results suggest that the NFDS at the S-locus has an impact on both the mating patterns and the genetic structure in the P. lannesiana populations studied.
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Affiliation(s)
- K Shuri
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Japan.
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Yan J, Shang P, Zheng D, Dong Y, Mao J, Wang S, Liu X, Yang S. Effect of simulated space gravity environment on Gibberella moniliformis EZG0807. Curr Microbiol 2012; 64:469-76. [PMID: 22350001 DOI: 10.1007/s00284-012-0097-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 01/24/2012] [Indexed: 11/28/2022]
Abstract
To determine the feasibility of inducing mutation for Gibberella moniliformis EZG0807 with a superconducting magnet, this paper investigated the effects of this instrument on the filamentous fungus G. moniliformis EZG0807. The superconducting magnet could simulate space gravity environment from hypo-gravity (0 g) to hyper-gravity (2 g). After G. moniliformis EZG0807 was exposed to the superconducting magnet for 72 h, the morphological observation, agar diffusion method, and amplified fragment length polymorphism were performed to detect the mutagenic effects in the aspect of morphology, the activity of metabolites, and genomic DNA, respectively. The mutant strain M7212 in 1 g (16 T) was different from the control in the morphology, showing no activity against the four tested bacteria Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Proteus vulgaris, and lost a size of 675 bp band on the genomic DNA. These results indicated that the superconducting magnet could be used to induce mutation for G. moniliformis EZG0807, which enabled improving the production of G. moniliformis EZG0807 and providing an effective approach for fungal breeding.
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Affiliation(s)
- Jvfen Yan
- The Institute of Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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Estimation of genetic diversity and evaluation of relatedness through molecular markers among medicinally important trees: Terminalia arjuna, T. chebula and T. bellerica. Mol Biol Rep 2010; 38:5025-36. [PMID: 21161393 DOI: 10.1007/s11033-010-0649-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 12/04/2010] [Indexed: 10/18/2022]
Abstract
Terminalia trees are being over-exploited because of their medicinal and economical importance leading to loss of valuable genetic resources. For sustainable utilization and conservation, assessment of genetic diversity therefore becomes imperative. We report a comprehensive first study on estimation and analysis of genetic variation through Amplified fragment length polymorphism (AFLP), inter simple sequence repeat polymorphism (ISSR) and random amplification of polymorphic DNA (RAPD) across three species of Terminalia. The study included (i) characterization of genetic diversity at interspecific level, and (ii) comparison of efficiency of the marker systems. That the three species are genetically distinct was revealed by all the three marker systems as unique DNA fingerprints were obtained. This led to identification of several species-specific amplification products. Further analysis helped in species-wise clustering. The species specific bands obtained from the present investigation can be used as diagnostic markers to identify the raw materials for herbal drug preparations for authentication purposes.
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Kim CK, Kikuchi S, Hahn JH, Park SC, Kim YH, Lee BW. Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm. Evol Bioinform Online 2010; 6:133-41. [PMID: 21079756 PMCID: PMC2978937 DOI: 10.4137/ebo.s6077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
This study identifies 2,617 candidate genes related to anthocyanin biosynthesis in rice using microarray analysis and a newly developed maximum boundary range algorithm. Three seed developmental stages were examined in white cultivar and two black Dissociation insertion mutants. The resultant 235 transcription factor genes found to be associated with anthocyanin were classified into nine groups. It is compared the 235 genes by transcription factor analysis and 593 genes from among clusters of COGs related to anthocyanin functions. Total 32 genes were found to be expressed commonly. Among these, 9 unknown and hypothetical genes were revealed to be expressed at each developmental stage and were verified by RT-PCR. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation, our results underline the potential usefulness of the newly developed algorithm.
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Affiliation(s)
- Chang Kug Kim
- Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
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