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Savoia MA, Del Faro L, Turco A, Fanelli V, Venerito P, Montemurro C, Sabetta W. Biodiversity Evaluation and Preservation of Italian Stone Fruit Germplasm (Peach and Apricot) in Southern Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1279. [PMID: 36986967 PMCID: PMC10055517 DOI: 10.3390/plants12061279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The Prunus genus encompasses a group of economically important and closely related crops, sharing an essentially common genome and, thereby, a high level of conserved and transferable microsatellite (SSR) loci. In Southern Italy, many of the local and/or neglected varieties are abandoned and at risk of extinction due to the high degree of urbanization and agricultural intensification, despite their value as genetic resources for crop improvement. This research aimed to genetically and morphologically characterize the traditional apricot (P. armenica) and peach (P. persica) germplasms collected in old family orchards. Most of the official descriptor categories were scored, thus revealing a rather high level of phenotypic variation in both collections. Genetic data allowed the discovery of diversity masked by morphological traits. Genotyping in 15 and 18 SSRs, eight of which were transferable across both species, showed an average polymorphic informativeness (PIC) of 0.44 and 0.59 for apricot and peach, respectively, and a total of 70 and 144 alleles. A reliable identification of each genotype was achieved, and the presence of possible mislabeling and/or erroneous denominations was solved. These results are encouraging for the valorization of the still poorly explored Italian Prunus germplasm, with significant economic consequences for bioresource conservation and management.
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Affiliation(s)
- Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Loredana Del Faro
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Andrea Turco
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Pasquale Venerito
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council (IPSP-CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Wilma Sabetta
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Via Amendola 165/A, 70126 Bari, Italy
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Reim S, Schiffler J, Braun-Lüllemann A, Schuster M, Flachowsky H, Höfer M. Genetic and Pomological Determination of the Trueness-to-Type of Sweet Cherry Cultivars in the German National Fruit Genebank. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010205. [PMID: 36616334 PMCID: PMC9823723 DOI: 10.3390/plants12010205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 05/14/2023]
Abstract
Genebank collections preserve many old cultivars with ancient breeding history. However, often, cultivars with synonymous or incorrect names are maintained in multiple collections. Therefore, pomological and genetic characterization is an essential prerequisite for confirming trueness-to-type of cultivars in gene bank collections. In our study, 1442 single sweet cherry (Prunus avium L.) trees of the German Fruit Genebank were evaluated according to their trueness-to-type. For this purpose, pomological analysis was performed, in which the accessions were assigned totheir historical cultivar names. The pomological identifications were based on several historical reference sources, such as fruit references from historical cherry cultivar and fruit-stone collections, as well as historical pomological literature sources. In addition, the cherry trees were genetically analyzed for cultivar identity using 16 SSR markers. Based on pomological characterization and genetic analysis for the majority of the trees (86%), cultivar authenticity could be confirmed. Most markers were highly discriminating and powerful for cultivar identification. The cherry collection showed a high degree of genetic diversity, with an expected heterozygosity He = 0.67. Generally, high genetic admixture between cultivars of different geographic origin and year of origin was obtained after STRUCTURE analysis, demonstrating the extensive exchange of genetic information between cherry cultivars in the collection over time. However, the phylogenetic tree calculated by DARwin reflected the geographic origin of selected cherry cultivars. After parentage analysis with CERVUS, paternity could not be confirmed for three cultivars, indicating the necessity of further pedigree analysis for these cultivars. The results of our study underlined the general importance of evaluating the authenticity of cultivars in genebank collections based on genetic and pomological characterization.
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Affiliation(s)
- Stefanie Reim
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
- Correspondence: (S.R.); (M.H.)
| | - Juliane Schiffler
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | | | - Mirko Schuster
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Monika Höfer
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
- Correspondence: (S.R.); (M.H.)
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Anatov DM, Suprun II, Stepanov IV, Tokmakov SV. Genetic diversity analysis of apricots from Dagestan using SSR markers. PROCEEDINGS ON APPLIED BOTANY, GENETICS AND BREEDING 2022. [DOI: 10.30901/2227-8834-2022-4-132-140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background. This publication presents the results of a study into the genetic structure of apricot genotypes from Dagestan using the SSR genotyping technique. The importance of the study is seen in the still underexplored gene pool of Dagestani apricot at the genetic level. With this in view, an assessment of the Dagestani apricot genetic diversity, followed by an analysis of its genetic structure, is of theoretical and practical interest.Materials and methods. The study included 27 apricot genotypes of Dagestani origin: 9 advanced contemporary cultivars and hybrids, 15 seed selections and landraces, and 3 wild forms. Eight SSR markers were used for the genetic diversity analysis: H1-3, A1-91, H2-79, H1-26-2, H2-16, A1-17, RPPG1-032, and RPPG3-026.Results. The UPGMA and NJ dendrogram construction techniques revealed the genetic similarity among the Dagestani apricots, confirmed by a low level of cluster significance. The tendency towards setting apart the genotypes of hybrid origin (obtained from free pollination of introduced cultivars) from the locally selected cultivars was observed by comparing the results of Bayesian analysis and the K-means approach using the Structure and Statistica software. Such isolation is partial, being obviously affected by constant integration of new apricot genotypes into the local gene pool and its enrichment with new alleles at the genetic level.Conclusion. The contemporary assortment of apricots in Dagestan was formed on the basis of both the local autochthonous gene pool and Central Asian and European cultivars introduced into this area. The obtained data will enrich the knowledge about the genetic diversity of apricots in Dagestan and serve as the platform for further studies into the florigenetic links of the North Caucasus with other regions.
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Affiliation(s)
- D. M. Anatov
- Caspian Institute of Bioresources, Dagestan Federal Scientific Center, Russian Academy of Sciences
| | - I. I. Suprun
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making
| | - I. V. Stepanov
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making
| | - S. V. Tokmakov
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making
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Jiang Q, Xu Q, Pan J, Yao X, Cheng Z. Impacts of Chronic Habitat Fragmentation on Genetic Diversity of Natural Populations of Prunus persica in China. PLANTS (BASEL, SWITZERLAND) 2022; 11:1458. [PMID: 35684230 PMCID: PMC9183131 DOI: 10.3390/plants11111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Wild peach is an important resource for improving existing peach varieties. However, the extant populations of wild peach show fragmented distribution due to human disturbance and geographic isolation. In this study, we used natural populations (or wild populations) of Prunus persica (Rosaceae) to assess the genetic effects of habitat fragmentation. A total of 368 individuals sampled from 16 natural populations were analyzed using 23 polymorphic simple sequence repeat (SSR) markers. Prunus persica maintained low within-population genetic variation and high level of genetic differentiation. Two genetic clusters were revealed based on three different methods (UPGMA, PCoA, and STRUCTURE). All populations showed a significant heterozygosity deficiency and most extant populations experienced recent reduction in population size. A significant isolation by distance (IBD) was observed with Mantel's test. Compared to historical gene flow, contemporary gene flow was restricted among the studied populations, suggesting a decrease in gene flow due to habitat fragmentation. Habitat fragmentation has impacted population genetic variation and genetic structure of P. persica. For breeding and conservation purpose, collecting as many individuals as possible from multiple populations to maximize genetic diversity was recommended during the process of germplasm collection. In addition, populations from central China had higher genetic diversity, suggesting these populations should be given priority for conservation and germplasm collection.
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Affiliation(s)
- Quan Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, China; (Q.J.); (J.P.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Xu
- Shangrao Vocational and Technical College, Shangrao 334109, China;
| | - Junfeng Pan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, China; (Q.J.); (J.P.)
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, China; (Q.J.); (J.P.)
| | - Zhongping Cheng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, China; (Q.J.); (J.P.)
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Molecular Characterization of Prunus Cultivars from Romania by Microsatellite Markers. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, 11 apricot and 5 nectarine cultivars. The average number of alleles per locus (Na = 1.958), in addition to overall observed (Ho = 0.299) and expected heterozygosity (He = 0.286) were lower or comparable to those reported in similar studies, probably explained by the smaller number of analyzed cultivars restricted to a smaller geographic area. Among 26 genotypes a total of 101 alleles were identified, of which 46 alleles were in peach, 55 in apricot and 40 in nectarine, respectively. Six alleles from six loci (CPPCT-030, Pchgms-003, Pchgms-004, Pchgms-010, UDP97-401, UDP98-405) were common to all taxonomic groups. The most informative loci were BPPCT-025, Pchgms-021 and UDP96-001 in peach; BPPCT-025, BPPCT-001 and UDP96-001 in nectarine; and BPPCT-002, BPPCT-025, Pchgms-004, Pchgms-020 and Pchgms-021 in apricot. Clustering and genetic similarity analysis indicated that the degree of interspecific divergence in peach and nectarine cultivars was less than that in peach and apricot. These results will be useful to prevent confusion between cultivars, to improve breeding strategies and to benefit the management of Prunus cultivars bred in Romania.
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Savoia MA, Del Faro L, Venerito P, Gaeta L, Palasciano M, Montemurro C, Sabetta W. The Relevance of Discovering and Recovering the Biodiversity of Apulian Almond Germplasm by Means of Molecular and Phenotypic Markers. PLANTS 2022; 11:plants11040574. [PMID: 35214907 PMCID: PMC8879738 DOI: 10.3390/plants11040574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2022]
Abstract
Almond cultivation has great traditional and economic relevance in Southern Italy, especially in the Apulia region, where almond trees feature an ample and ancient varietal richness. To contrast the loss of plant genetic erosion and to safeguard the available bioresources, as well as to reinforce the local production, the regional Re.Ge.Fru.P. project aimed to re-evaluate, identify, and characterize the Apulian almond germplasm that is still uncharacterized and not jet studied using a dual (genetic and morphological) approach. Collection was conducted in the regional territory of 187 among the most widespread and minor or marginalized genotypes that were molecularly fingerprinted by means of 18 nuclear microsatellites (simple sequence repeats, SSRs). The high number of scored alleles reflected the great level of diversification within the Apulian germplasm, as also confirmed by neighbor joining and structure analysis, that clearly distinguished different genotype clusters. The phenotypic characterization using 17 morphological and phenological descriptors mirrored the genetic results, revealing a high degree of variability. The morphological traits with the best discriminatory ability were nut ventral suture, shell softness and shape and petal color. This work emphasizes the importance of recovering the genetic variability of Apulian almond germplasm, and the need to promote added value and enhance the local agri-food economy.
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Affiliation(s)
- Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
| | - Loredana Del Faro
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy; (L.D.F.); (P.V.)
| | - Pasquale Venerito
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy; (L.D.F.); (P.V.)
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Agriculture and Environment Research Centre (CREA-AA), Via Celso Ulpiani 5, 70125 Bari, Italy;
| | - Marino Palasciano
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council (IPSP-CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Wilma Sabetta
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Via Amendola 165/A, 70126 Bari, Italy
- Correspondence:
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Sheikh ZN, Sharma V, Shah RA, Raina S, Aljabri M, Mir JI, AlKenani N, Hakeem KR. Elucidating Genetic Diversity in Apricot ( Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers. PLANTS (BASEL, SWITZERLAND) 2021; 10:2668. [PMID: 34961139 PMCID: PMC8707356 DOI: 10.3390/plants10122668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/27/2021] [Accepted: 11/28/2021] [Indexed: 05/18/2023]
Abstract
Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program.
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Affiliation(s)
- Zahid Nabi Sheikh
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu 180009, J&K, India; (Z.N.S.); (S.R.)
| | - Vikas Sharma
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu 180009, J&K, India; (Z.N.S.); (S.R.)
| | - Rafiq Ahmad Shah
- Ambri Apple Research Center, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir 190025, J&K, India;
| | - Shilpa Raina
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu 180009, J&K, India; (Z.N.S.); (S.R.)
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 21421, Saudi Arabia;
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21421, Saudi Arabia
| | - Javid Iqbal Mir
- Indian Council of Agricultural and Research Central Institute of Temperate Horticulture, Old Airport Road, Rangreth, Srinagar 190007, J&K, India;
| | - Naser AlKenani
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Princess Dr. NajlaBint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers. PLANTS 2021; 10:plants10122609. [PMID: 34961080 PMCID: PMC8704053 DOI: 10.3390/plants10122609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection.
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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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Autochthonous Austrian Varieties of Prunus avium L. Represent a Regional Gene Pool, Assessed Using SSR and AFLP Markers. Genes (Basel) 2021; 12:genes12030322. [PMID: 33668196 PMCID: PMC7995972 DOI: 10.3390/genes12030322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/31/2021] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
Sweet cherry production faces new challenges that necessitate the exploitation of genetic resources such as varietal collections and landraces in breeding programs. A harmonized approach to characterization is key for an optimal utilization of germplasm in breeding. This study reports the genotyping of 63 sweet cherry accessions using a harmonized set of 11 simple sequence repeat (SSR) markers optimized in two multiplexed PCR reactions. Thirty-eight distinct allelic profiles were identified. The set of SSR markers chosen proved highly informative in these germplasm; an average of 6.3 alleles per locus, a PIC value of 0.59 and above-average expected and observed heterozygosity levels were detected. Additionally, 223 amplified fragment length polymorphism (AFLP) markers derived from eight selective primer combinations were employed to further differentiate 17 closely related accessions, confirming the SSR analysis. Genetic relationships between internationally known old cultivars were revealed: SSR fingerprints of “Schneiders Späte Knorpelkirsche” and “Germersdorfer” were found to be identical to those of the standard cultivar “Noire de Meched”, among others, whereas four accessions known as “Hedelfinger Riesenkirsche” and four known as “Große Schwarze Knorpelkirsche” showed allelic differences at various loci. The genetic diversity of locally-grown cultivars worldwide might be currently underestimated. Several autochthonous Austrian sweet cherry germplasm accessions were genotyped for the first time and their genetic relationships analyzed and discussed. Interestingly, seven Austrian sweet cherry landraces were shown to be clearly genetically separated from international and modern varieties, indicating that Austrian germplasm could include valuable genetic resources for future breeding efforts.
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Berni R, Charton S, Planchon S, Legay S, Romi M, Cantini C, Cai G, Hausman JF, Renaut J, Guerriero G. Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics. HORTICULTURE RESEARCH 2021; 8:12. [PMID: 33384418 PMCID: PMC7775447 DOI: 10.1038/s41438-020-00445-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Bank of the CNR-IBE in Follonica (Italy) and sampled ca. 60 days post-anthesis over three consecutive years (2016-2017-2018). We adopted an approach merging genotyping and targeted gene expression profiling with metabolomics. To complement the data, a study of the soluble proteomes was also performed on two varieties showing the highest content of flavonoids. Metabolomics identified the presence of flavanols and proanthocyanidins in highest abundance in the varieties Morellona and Crognola, while gene expression revealed that some differences were present in genes involved in the phenylpropanoid pathway during the 3 years and among the varieties. Finally, proteomics on Morellona and Crognola showed variations in proteins involved in stress response, primary metabolism and cell wall expansion. To the best of our knowledge, this is the first multi-pronged study focused on Tuscan sweet cherry varieties providing insights into the differential abundance of genes, proteins and metabolites.
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Affiliation(s)
- Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Sophie Charton
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg
| | - Sébastien Planchon
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg
| | - Sylvain Legay
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg
| | - Marco Romi
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
| | - Claudio Cantini
- Istituto per la BioEconomia (IBE CNR), Dipartimento di Scienze BioAgroAlimentari, via Aurelia 49, 58022, Follonica, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100, Siena, Italy
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41, Rue du Brill, L-4422, Belvaux, Luxembourg.
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940, Hautcharage, Luxembourg.
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12
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Abdallah D, Baraket G, Perez V, Salhi Hannachi A, Hormaza JI. Self-compatibility in peach [ Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles. HORTICULTURE RESEARCH 2020; 7:170. [PMID: 33082976 PMCID: PMC7527504 DOI: 10.1038/s41438-020-00392-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 05/07/2023]
Abstract
Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
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Affiliation(s)
- Donia Abdallah
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Ghada Baraket
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Veronica Perez
- Laboratorio de Agrobiología Juan José Bravo Rodríguez (Cabildo Insular de La Palma), Unidad Técnica del Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38700 S/C La Palma, Canary Islands, Spain
| | - Amel Salhi Hannachi
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Jose I. Hormaza
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM La Mayora-UMA-CSIC), 29750 Algarrobo-Costa, Malaga Spain
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13
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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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14
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Development of 85 SNP markers for the endangered plant species Prunus mira (Rosaceae) based on restriction site-associated DNA sequencing (RAD-seq). CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01140-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Muranty H, Denancé C, Feugey L, Crépin JL, Barbier Y, Tartarini S, Ordidge M, Troggio M, Lateur M, Nybom H, Paprstein F, Laurens F, Durel CE. Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC PLANT BIOLOGY 2020; 20:2. [PMID: 31898487 PMCID: PMC6941274 DOI: 10.1186/s12870-019-2171-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 11/27/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. RESULTS Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. CONCLUSIONS The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.
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Affiliation(s)
- Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Laurence Feugey
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Jean-Luc Crépin
- Les Croqueurs de Pommes du Confluent Ain-Isère-Savoie, Les Avenières, France
| | - Yves Barbier
- Les Croqueurs de Pommes du Confluent Ain-Isère-Savoie, Les Avenières, France
| | - Stefano Tartarini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, UK
| | - Michela Troggio
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Gembloux, Belgium
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Balsgård, Kristianstad, Sweden
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czech Republic
| | - François Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
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16
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Das R, Arora V, Jaiswal S, Iquebal MA, Angadi UB, Fatma S, Singh R, Shil S, Rai A, Kumar D. PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data. FRONTIERS IN PLANT SCIENCE 2019; 9:1966. [PMID: 30687361 PMCID: PMC6337687 DOI: 10.3389/fpls.2018.01966] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.
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Affiliation(s)
- Ritwika Das
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - MA Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - UB Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samar Fatma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sandip Shil
- Research Center, ICAR-Central Plantation Crops Research Institute, Jalpaiguri, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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17
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Güney M, Kafkas S, Keles H, Aras S, Ercişli S. Characterization of hawthorn ( Crataegus spp.) genotypes by SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1221-1230. [PMID: 30425436 PMCID: PMC6214427 DOI: 10.1007/s12298-018-0604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023]
Abstract
Hawthorn (Crataegus spp.) is an edible wild fruit that is used in traditional medicine, landscape studies, and food and beverage industries in many countries. It is an important wild plant species in Turkey and is numerous in the Yozgat Province. Genetic and breeding studies on hawthorn are very limited. Therefore, we aimed to characterize 91 hawthorn genotypes using simple sequence repeat (SSR) markers. The SSRs were developed from apple and pear and were screened in hawthorn for amplification and polymorphisms. A total of 265 alleles were detected from thirty-two SSR primer pairs, and those were used to identify genetic relationships. The number of alleles ranged from 2 to 21 alleles per locus with a mean value of 8.28. The Hi05b09 locus showed the highest allele number (Na = 21). The polymorphism information content (PIC) values ranged from 0.16 (CH03d10) to 0.89 (C6554) with a mean value of 0.60. An Unweighted Pair Group Method with Arithmetic Average method was used to cluster the genotypes, and four major clusters were obtained from the amplification of the SSRs. STRUCTURE software identified four populations (ΔK = 4) and eight sub-populations (ΔK = 8), and four major clusters similar results to UPGMA analysis. Our study showed that the SSR markers could be utilized as a reliable tool for the determination of genetic variations and relationships of hawthorn genotypes. A basic molecular analysis on the hawthorn genotypes identified in this study will promote the collection of germplasm collection and the selection of parents' in future cross-breeding studies.
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Affiliation(s)
- Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Cukurova, Adana, Turkey
| | - Hakan Keles
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Servet Aras
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, University of Atatürk, Erzurum, Turkey
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18
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Hamadeh B, Chalak L, Coppens d’Eeckenbrugge G, Benoit L, Joly HI. Evolution of almond genetic diversity and farmer practices in Lebanon: impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation. BMC PLANT BIOLOGY 2018; 18:155. [PMID: 30081821 PMCID: PMC6080396 DOI: 10.1186/s12870-018-1372-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 07/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Under cultivation, many outcrossing fruit tree species have switched from sexual reproduction to vegetative propagation. Traditional production systems have persisted, where cultivar propagation is based on a mixed reproductive system. For millenia, almond, Prunus dulcis, has been propagated by seeds. Almond grafting remained of little importance until recently. In Lebanon, both sexual and clonal reproductions are used for almond propagation. We used 15 microsatellite markers to investigate the effect of introducing graft-propagated cultivars and associated practices, on the structure of the genetic diversity among and within the two main Lebanese cultivars. RESULTS As expected, the sexually propagated cultivar Khachabi exhibited more genotypic and genetic diversity than the vegetatively propagated cultivar Halwani. It also exhibited lower differentiation among populations. The distribution of clones showed that propagation modes were not exclusive: farmers have introduced clonal propagation in the seed-propagated cultivar while they have maintained a diversity of genotypes within populations that were mostly graft-propagated. These practices are also important to avoid mate limitations that hamper fruit production in a self-incompatible species. 'Khachabi' is structured into two gene pools separated by the Lebanese mountains. As to 'Halwani', two different gene pools were introduced. The most ancient one shares the same geographic range as 'Khachabi'; longtime coexistence and sexual reproduction have resulted in admixture with 'Khachabi'. In contrast, the more recent introduction of the second gene pool in the Bekaa region followed an evolution towards more extensive clonal propagation of 'Halwani' limiting hybridizations. Furthermore, some pairs of geographically distant 'Halwani' orchards, exhibited low genetic distances, suggesting that a network of exchanges between farmers was effective on a large scale and/or that farmers brought clonal plant material from a common source. CONCLUSIONS Almond diversification in Lebanon is clearly related to the evolution of propagation practices adapted to self-incompatible cultivars. The comparison between both cultivars demonstrated the genetic effects of the introduction of a new cultivar and the associated grafting propagation practices. Our study provided information to develop a strategy for in situ conservation of cultivars and to limit gene flow from introduced material to ancient orchards.
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Affiliation(s)
- Bariaa Hamadeh
- Lebanese Agricultural Research Institute, Fanar, Lebanon
- Université Montpellier 2, UMR CEFE, 34293 Montpellier Cedex, France
- Doctoral School of Sciences and Technologies, Lebanese University, Hadath, Lebanon
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Lamis Chalak
- Faculty of Agriculture, Lebanese University, Dekwaneh, Lebanon
| | - Geo Coppens d’Eeckenbrugge
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Laure Benoit
- CIRAD, UMR CBGP, F-34398 Montpellier, France
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Hélène I. Joly
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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19
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Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics 2018; 19:235. [PMID: 29618324 PMCID: PMC5885378 DOI: 10.1186/s12864-018-4633-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yuewen Wang
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Peizi He
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, 34134, South Korea
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Bao W, Wuyun T, Li T, Liu H, Jiang Z, Zhu X, Du H, Bai YE. Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies. PLoS One 2017; 12:e0188685. [PMID: 29186199 PMCID: PMC5706700 DOI: 10.1371/journal.pone.0188685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 11/11/2017] [Indexed: 02/01/2023] Open
Abstract
Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.
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Affiliation(s)
- Wenquan Bao
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Tana Wuyun
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
- * E-mail:
| | - Tiezhu Li
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Huimin Liu
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Zhongmao Jiang
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Xuchun Zhu
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Hongyan Du
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Yu-e Bai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res 2017; 24:499-508. [PMID: 28541388 PMCID: PMC5737369 DOI: 10.1093/dnares/dsx020] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site–associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kanji Isuzugawa
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Mitsunobu Ikenaga
- Central Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan
| | - Yutaro Saito
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8605, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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22
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Li XW, Meng XQ, Jia HJ, Yu ML, Ma RJ, Wang LR, Cao K, Shen ZJ, Niu L, Tian JB, Chen MJ, Xie M, Arus P, Gao ZS, Aranzana MJ. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genet 2013; 14:84. [PMID: 24041442 PMCID: PMC3848491 DOI: 10.1186/1471-2156-14-84] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 09/11/2013] [Indexed: 12/03/2022] Open
Abstract
Background Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. Results In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: ‘Yu Lu’ and ‘Hakuho’. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the ‘Yu Lu’ subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. Conclusions Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.
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Affiliation(s)
- Xiong-wei Li
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou 310058, China.
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23
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Cidade FW, Vigna BBZ, de Souza FHD, Valls JFM, Dall’Agnol M, Zucchi MI, de Souza-Chies TT, Souza AP. Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus. BMC Genet 2013; 14:50. [PMID: 23759066 PMCID: PMC3682885 DOI: 10.1186/1471-2156-14-50] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 05/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. RESULTS Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). CONCLUSIONS The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.
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Affiliation(s)
- Fernanda W Cidade
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), CP 6010, Campinas, SP CEP 13083-875, Brazil
| | - Bianca BZ Vigna
- Brazilian Agricultural Research Corporation (Embrapa) Southeast Livestock, CP 339, São Carlos, SP CEP 13560-970, Brazil
| | - Francisco HD de Souza
- Brazilian Agricultural Research Corporation (Embrapa) Southeast Livestock, CP 339, São Carlos, SP CEP 13560-970, Brazil
| | - José Francisco M Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica - PqEB, CP 02372, Brasília, DF CEP 70770-917, Brasil
| | - Miguel Dall’Agnol
- Faculty of Agronomy, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 7712 Agronomia, Porto Alegre, Rio Grande do Sul CEP 91501-970, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios/APTA, Km 30, CP 28, Pólo Regional Centro Sul, Rodovia SP127, Piracicaba, SP CEP13400-970, Brazil
| | - Tatiana T de Souza-Chies
- Department of Botany, Prédio 43433, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500 Agronomia, Porto Alegre, Rio Grande do Sul, CEP 91501-970, Brazil
| | - Anete P Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), CP 6010, Campinas, SP CEP 13083-875, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), CP 6109 Campinas, SP, CEP 13083-875, Brazil
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Jolivet C, Rogge M, Degen B. Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium. Heredity (Edinb) 2012; 110:439-48. [PMID: 23211795 DOI: 10.1038/hdy.2012.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.
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Affiliation(s)
- C Jolivet
- Johann Heinrich von Thünen Institut vTI, Institute of Forest Genetics, D-22927 Grosshansdorf, Germany.
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25
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Shoda M, Urasaki N, Sakiyama S, Terakami S, Hosaka F, Shigeta N, Nishitani C, Yamamoto T. DNA profiling of pineapple cultivars in Japan discriminated by SSR markers. BREEDING SCIENCE 2012; 62:352-9. [PMID: 23341750 PMCID: PMC3528333 DOI: 10.1270/jsbbs.62.352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/11/2012] [Indexed: 05/07/2023]
Abstract
We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of 'N67-10' and 'Hawaiian Smooth Cayenne'. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders' rights.
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Affiliation(s)
- Moriyuki Shoda
- Okinawa Prefectural Agricultural Research Center Nago Branch, 4605-3 Nago, Nago, Okinawa 905-0012, Japan
| | - Naoya Urasaki
- Okinawa Prefectural Agricultural Research Center, 820 Makabe, Itoman, Okinawa 901-0336, Japan
| | - Sumisu Sakiyama
- Okinawa Prefectural Agricultural Research Center Nago Branch, 4605-3 Nago, Nago, Okinawa 905-0012, Japan
| | - Shingo Terakami
- Naro Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Fumiko Hosaka
- Naro Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Narumi Shigeta
- Naro Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Chikako Nishitani
- Naro Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Toshiya Yamamoto
- Naro Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
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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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27
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Delplancke M, Alvarez N, Espíndola A, Joly H, Benoit L, Brouck E, Arrigo N. Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers. Evol Appl 2011; 5:317-29. [PMID: 25568053 DOI: 10.1111/j.1752-4571.2011.00223.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 11/02/2011] [Indexed: 11/30/2022] Open
Abstract
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.
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Affiliation(s)
- Malou Delplancke
- Université Montpellier 2, Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 Montpellier cedex, France
| | - Nadir Alvarez
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne Lausanne, Switzerland
| | - Anahí Espíndola
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne Lausanne, Switzerland
| | - Hélène Joly
- CIRAD, Centre d'Ecologie Fonctionnelle et Evolutive Montpellier cedex, France
| | - Laure Benoit
- CIRAD, Centre d'Ecologie Fonctionnelle et Evolutive Montpellier cedex, France
| | - Elise Brouck
- Université Montpellier 2, Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 Montpellier cedex, France
| | - Nils Arrigo
- Department of Ecology & Evolutionary Biology, University of Arizona Tucson, AZ, USA
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28
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Kato S, Iwata H, Tsumura Y, Mukai Y. Genetic structure of island populations of Prunus lannesiana var. speciosa revealed by chloroplast DNA, AFLP and nuclear SSR loci analyses. JOURNAL OF PLANT RESEARCH 2011; 124:11-23. [PMID: 20512520 DOI: 10.1007/s10265-010-0352-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 04/01/2010] [Indexed: 05/29/2023]
Abstract
The wild flowering cherry Prunus lannesiana var. speciosa is highly geographically restricted, being confined to the Izu Islands and neighboring peninsulas in Japan. In an attempt to elucidate how populations of this species have established we investigated the genetic diversity and differentiation in seven populations (sampling 408 individuals in total), using three kinds of genetic markers: chloroplast DNA (cpDNA), amplified fragment length polymorphisms (AFLPs), and 11 nuclear SSR polymorphic loci. Eight haplotypes were identified based on the cpDNA sequence variations, 64 polymorphic fragments were scored for the AFLP markers, and a total of 154 alleles were detected at the 11 nuclear SSR loci. Analysis of molecular variance showed that among-population variation accounted for 16.55, 15.04 and 7.45% of the total detected variation at the cpDNA, AFLPs, and SSR loci, respectively. Thus, variation within populations accounted for most of the genetic variance for all types of markers, although the genetic differentiation among populations was also highly significant. For cpDNA variation, no clear structure was found among the populations, except that of the most distant island, although an "isolation by distance" pattern was found for each marker. Both neighbor-joining trees and structure analysis indicate that the genetic relationships between populations reflect geological variations between the peninsula and the islands and among the islands. Furthermore, hybridization with related species may have affected the genetic structure, and some genetic introgression is likely to have occurred.
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Affiliation(s)
- Shuri Kato
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki 305-8687, Japan.
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29
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Christelová P, Valárik M, Hřibová E, Van den houwe I, Channelière S, Roux N, Doležel J. A platform for efficient genotyping in Musa using microsatellite markers. AOB PLANTS 2011; 2011:plr024. [PMID: 22476494 PMCID: PMC3185971 DOI: 10.1093/aobpla/plr024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 08/16/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Bananas and plantains (Musa spp.) are one of the major fruit crops worldwide with acknowledged importance as a staple food for millions of people. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changed farming practices, and the need for its characterization and preservation is urgent. With the aim of providing a simple and robust approach for molecular characterization of Musa species, we developed an optimized genotyping platform using 19 published simple sequence repeat markers. METHODOLOGY The genotyping system is based on 19 microsatellite loci, which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. This genotyping platform was tested and optimized on a set of 70 diploid and 38 triploid banana accessions. PRINCIPAL RESULTS The marker set used in this study provided enough polymorphism to discriminate between individual species, subspecies and subgroups of all accessions of Musa. Likewise, the capability of identifying duplicate samples was confirmed. Based on the results of a blind test, the genotyping system was confirmed to be suitable for characterization of unknown accessions. CONCLUSIONS Here we report on the first complex and standardized platform for molecular characterization of Musa germplasm that is ready to use for the wider Musa research and breeding community. We believe that this genotyping system offers a versatile tool that can accommodate all possible requirements for characterizing Musa diversity, and is economical for samples ranging from one to many accessions.
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Affiliation(s)
- Pavla Christelová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc CZ-77200, Czech Republic
| | - Miroslav Valárik
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc CZ-77200, Czech Republic
| | - Eva Hřibová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc CZ-77200, Czech Republic
| | - Ines Van den houwe
- Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, B-3001 Leuven, Belgium
| | - Stéphanie Channelière
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc CZ-77200, Czech Republic
- Corresponding author's e-mail address:
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Bourguiba H, Khadari B, Krichen L, Trifi-Farah N, Santoni S, Audergon JM. Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering. Genetica 2010; 138:1023-32. [PMID: 20838857 PMCID: PMC2948653 DOI: 10.1007/s10709-010-9488-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 08/16/2010] [Indexed: 10/25/2022]
Abstract
Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated 'Bargougs' were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin.
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Affiliation(s)
- Hedia Bourguiba
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 84143 Montfavet, France
- INRA, UMR 1098 Développement et Amélioration des Plantes, Campus CIRAD, TA A96/03 Avenue Agropolis, 34398 Montpellier cedex 5, France
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 El Manar, Tunisia
| | - Bouchaib Khadari
- INRA, UMR 1098 Développement et Amélioration des Plantes, Campus CIRAD, TA A96/03 Avenue Agropolis, 34398 Montpellier cedex 5, France
- Conservatoire Botanique National Méditerranéen, UMR 1098, 34000 Montpellier cedex 1, France
| | - Lamia Krichen
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 El Manar, Tunisia
| | - Neila Trifi-Farah
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 El Manar, Tunisia
| | - Sylvain Santoni
- INRA, UMR 1097 Diversité et Adaptation des Plantes Cultivées, 2 Place Viala, 34060 Montpellier cedex 1, France
| | - Jean-Marc Audergon
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 84143 Montfavet, France
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Tsuda Y, Kimura M, Kato S, Katsuki T, Mukai Y, Tsumura Y. Genetic structure of Cerasus jamasakura, a Japanese flowering cherry, revealed by nuclear SSRs: implications for conservation. JOURNAL OF PLANT RESEARCH 2009; 122:367-375. [PMID: 19340524 DOI: 10.1007/s10265-009-0224-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 02/08/2009] [Indexed: 05/27/2023]
Abstract
The genetic resources of a particular species of flowering cherry, Cerasus jamasakura, have high conservation priority because of its cultural, ecological and economic value in Japan. Therefore, the genetic structures of 12 natural populations of C. jamasakura were assessed using ten nuclear SSR loci. The population differentiation was relatively low (F (ST), 0.043), reflecting long-distance dispersal of seeds by animals and historical human activities. However, a neighbor-joining tree derived from the acquired data, spatial analysis of molecular variance and STRUCTURE analysis revealed that the populations could be divided into two groups: one located on Kyusyu Island and one on Honshu Island. Genetic diversity parameters such as allelic richness and gene diversity were significantly lower in the Kyushu group than the Honshu group. Furthermore, STRUCTURE analysis revealed that the two lineages were admixed in the western part of Honshu Island. Thus, although the phylogeographical structure of the species and hybridization dynamics among related species need to be evaluated in detail using several marker systems, the Kyusyu Island and Honshu Island populations should be considered as different conservation units, and the islands should be regarded as distinct seed transfer zones for C. jamasakura, especially when rapid assessments are required.
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Affiliation(s)
- Yoshiaki Tsuda
- Tree Genetics Laboratory, Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan.
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Mori Y, Nagamitsu T, Kubo T. Clonal growth and its effects on male and female reproductive success in Prunus ssiori (Rosaceae). POPUL ECOL 2008. [DOI: 10.1007/s10144-008-0099-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Li TH, Li YX, Li ZC, Zhang HL, Qi YW, Wang T. Simple sequence repeat analysis of genetic diversity in primary core collection of peach (Prunus persica). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2008; 50:102-110. [PMID: 18666957 DOI: 10.1111/j.1744-7909.2007.00598.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this study, the genetic diversity of 51 cultivars in the primary core collection of peach (Prunus persica (L.) Batsch) was evaluated by using simple sequence repeats (SSRs). The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach > Crisp peach > Flat peach > Nectarine > Honey Peach > Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging (UPGMA) placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.
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Affiliation(s)
- Tian-Hong Li
- Department of Fruit Science, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
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34
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Saddoud O, Chatti K, Salhi-Hannachi A, Mars M, Rhouma A, Marrakchi M, Trifi M. Genetic diversity of Tunisian figs (Ficus carica L.) as revealed by nuclear microsatellites. Hereditas 2007; 144:149-57. [PMID: 17850599 DOI: 10.1111/j.2007.0018-0661.01967.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The present study portrays the achievement of the genetic polymorphism surveying and the establishment of an ecotypes identification key on the basis of simple sequence repeats data. Seventy-two Tunisian fig ecotypes in situ and ex situ conserved were analyzed using six microsatellite loci. A total of 58 alleles and 124 genotypes were revealed and permitted to evidence high degree of genetic diversity mainly explained at the intra group level. Cluster analysis based on genetic distances proved that a typical continuous genetic diversity characterizes the local germplasm. In addition, the microsatellite multilocus genotyping has permitted to unambiguously distinguish 70 well-defined ecotypes (resolving power of 97.22%). Data are discussed in relation with the reliability of the used markers to check the conformity of the plant material and to rationally manage the conservation of this crop.
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Affiliation(s)
- O Saddoud
- Laboratoire de Génétique moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus universitaire, El Manar, Tunis, Tunisia
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35
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Schueler S, Tusch A, Scholz F. Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites. Mol Ecol 2006; 15:3231-43. [PMID: 16968267 DOI: 10.1111/j.1365-294x.2006.03029.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.
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Affiliation(s)
- Silvio Schueler
- Institute for Forest Genetics and Forest Tree Breeding, Federal Research Centre for Forestry and Forest Products, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany.
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Xie H, Sui Y, Chang FQ, Xu Y, Ma RC. SSR allelic variation in almond (Prunus dulcis Mill.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:366-72. [PMID: 16307227 DOI: 10.1007/s00122-005-0138-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Accepted: 10/23/2005] [Indexed: 05/05/2023]
Abstract
Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.
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Affiliation(s)
- Hua Xie
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Ban-Jing Rd., Hai-Dian District, 100089 Beijing, China
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37
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Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG, Motto M, Quarta R. Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)]xP. ferganensis BC(1)linkage map: saturation and coverage improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1013-21. [PMID: 16088395 DOI: 10.1007/s00122-005-0006-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 05/20/2005] [Indexed: 05/03/2023]
Abstract
A set of 146 single sequence repeats (SSRs) and 14 amplified fragment length polymorphism (AFLP) primer combinations were used to enrich a previously developed linkage map obtained from a (Prunus persicaxP. ferganensis)xP. persica BC(1) progeny. Forty-one SSR primer pairs gave polymorphic patterns detecting 42 loci. The restriction/selective primer AFLP combinations produced a total of 79 segregating fragments. The resulting map is composed of 216 loci covering 665 cM with an average distance of 3.1 cM. Novel regions were covered by the newly mapped loci for a total of 159 cM. Eight linkage groups were assembled instead of the earlier 10 as two small groups (G1a and G8b), previously independent, were joined to their respective major groups (G1b and G8a). Several gaps were also reduced resulting in an improved saturation of the map. Twelve gaps >or=10 cm are still present. A comparative analysis against the Prunus reference map (71 anchor loci) pointed out an almost complete synteny and colinearity. Six loci were not syntenic and only two were not colinear. Genetic distances were significantly longer in our map than in the reference one.
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Affiliation(s)
- I Verde
- Istituto Sperimentale per la Frutticoltura (CRA), Via di Fioranello 52, Ciampino Aeroporto, 00040 Rome, Italy.
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38
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Xu Y, Ma RC, Xie H, Liu JT, Cao MQ. Development of SSR markers for the phylogenetic analysis of almond trees from China and the Mediterranean region. Genome 2005; 47:1091-104. [PMID: 15644967 DOI: 10.1139/g04-058] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expressed sequence tag (EST) derived simple sequence repeats (SSRs, microsatellites) were screened and identified from 3863 almond and 10 185 peach EST sequences, and the spectra of SSRs in the non-redundant EST sequences were investigated after sequence assembly. One hundred seventy-eight (12.07%) almond SSRs and 497 (9.97%) peach SSRs were detected. The EST-SSR occurs every 4.97 kb in almond ESTs and 6.57 kb in peach, and SSRs with di- and trinucleotide repeat motifs are the most abundant in both almond and peach ESTs. Twenty one EST-SSRs were thereafter, developed and used together with 7 genomic SSRs, to study the genetic relationship among 36 almond (P. communis Fritsch.) cultivars from China and the Mediterranean area, as well as 8 accessions of other related species from the genus Prunus. Both EST-derived and genomic SSR markers showed high cross-species transferability in the genus. Out of the 112 polymorphic alleles detected in the 36 cultivated almonds, 28 are specific to Chinese cultivars and 25 to the others. The 44 accessions were clustered into 4 groups in the phylogenetic tree and the 36 almond cultivars formed two distinct subgroups, one containing only Chinese cultivars and one of unknown origin and the other only those originating from the Mediterranean area, indicating that Chinese almond cultivars have a distinct evolutionary history from the Mediterranean almond. Our preliminary results indicated that common almond was more closely related to peach (P. persica (L.) Batsch.) than to the four wild species of almond, (P. mongolica Maxim., P. ledebouriana Schleche, P. tangutica Batal., and P. triloba Lindl.). The implications of these SSR markers for evolutionary analysis and molecular mapping of Prunus species are discussed.
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Affiliation(s)
- Yong Xu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Ban-Jing., Hai-Dian District, Beijing 100089, China
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39
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Jakse J, Satovic Z, Javornik B. Microsatellite variability among wild and cultivated hops (HumuluslupulusL.). Genome 2004; 47:889-99. [PMID: 15499403 DOI: 10.1139/g04-054] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hop (Humulus lupulus L.) is a dioecious perennial plant native to the northern hemisphere cultivated for its use in the brewing industry. To investigate the genetic diversity present in wild hop accessions in comparison with cultivated hops, microsatellite marker variation was assessed at four loci in 124 accessions of wild (from Europe, Asia and from North America) and cultivated (varieties and breeding lines) hops. A total of 63 alleles were identified, with an average of 15.7 alleles per locus and an average PIC of 0.64 over four loci. The average number of alleles per locus in groups of accessions ranged from 5.75 to 8.30, with the highest number detected in groups of wild hops either of European (EU) or North American (NA) origin. Accessions from NA revealed the highest number of unique alleles indicating the high diversity present in this gene pool. Cluster analysis based on the DDor Dswdistance matrix divided accessions into 10 different clusters, which reflect the relationship among geographically diverse wild accessions and hop cultivars. The highest genetic differences were found between NA wild accessions, forming one distant cluster, and all the other accessions. The differentiation between European wild and cultivated accessions was revealed by PCoA based on the DDdistance matrix and by AMOVA results. Cultivated hops differ significantly from wild ones, although most of the variability was found within groups. The molecular variances within groups of cultivated and wild hops were homogeneous, suggesting that a similar level of molecular variability is found in both groups of accessions. The analysis of allele polymorphism and of allele sequences showed that hop germplasm can be differentiated to NA and EU geographic types according to the differences of allele sizes at three loci or by the specific microsatellite repeat type at one locus. The analysis also indicates the different evolutionary dynamics and complex mutations of microsatellite sequences within loci that can be followed in the two biogeographically separated germplasms.Key words: Humulus lupulus L., genetic diversity, germplasm, microsatellites, allele sequence variation.
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Affiliation(s)
- Jernej Jakse
- Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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Quilot B, Wu BH, Kervella J, Génard M, Foulongne M, Moreau K. QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:884-97. [PMID: 15168024 DOI: 10.1007/s00122-004-1703-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 04/02/2004] [Indexed: 05/08/2023]
Abstract
Genetic control of the different attributes involved in peach quality has been investigated in an advanced backcross population derived from a cross between Prunus davidiana clone P1908, a wild parent with poor agronomic performance, and a commercial variety, Summergrand. A total of 24 physical and biochemical traits were investigated. Quantitative trait loci (QTLs) were detected for all the traits studied. We identified alleles from P. davidiana with agronomically favorable effects regarding fruit and stone sizes, sugar and acid concentrations and red flesh coloration, in clear contrast to its phenotype. We identified three main regions of the genome where alleles from P. davidiana had negative effects on multiple traits. In other regions, co-locations of QTLs with opposite effects on quality traits were also detected. We discuss the nature of these co-locations in the light of the probable physiological mechanisms involved. Strategies to cope with negative correlations between favorable traits and co-locations of P. davidiana alleles with negative effects on quality traits and positive effects regarding resistance to powdery mildew are discussed from a breeding point of view.
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Affiliation(s)
- B Quilot
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9, France.
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41
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Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N, Claverie M, Voisin R, Poizat C, Lafargue B, Baron O, Laigret F, Kleinhentz M, Arús P, Esmenjaud D. Microsatellite genetic linkage maps of myrobalan plum and an almond-peach hybrid--location of root-knot nematode resistance genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:827-38. [PMID: 15241595 DOI: 10.1007/s00122-004-1694-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Accepted: 03/29/2004] [Indexed: 05/23/2023]
Abstract
Inheritance and linkage studies were carried out with microsatellite [or simple sequence repeat (SSR)] markers in a F(1) progeny including 101 individuals of a cross between Myrobalan plum ( Prunus cerasifera Ehrh) clone P.2175 and the almond (Prunus dulcis Mill.)-peach ( Prunus persica L. Batsch) hybrid clone GN22 ["Garfi" (G) almond x "Nemared" (N) peach]. This three-way interspecific Prunus progeny was produced in order to associate high root-knot nematode (RKN) resistances from Myrobalan and peach with other favorable traits for Prunus rootstocks from plum, peach and almond. The RKN resistance genes, Ma from the Myrobalan plum clone P.2175 and R(MiaNem) from the 'N' peach, are each heterozygous in the parents P.2175 and GN22, respectively. Two hundred and seventy seven Prunus SSRs were tested for their polymorphism. One genetic map was constructed for each parent according to the "double pseudo-testcross" analysis model. The Ma gene and 93 markers [two sequence characterized amplified regions (SCARs), 91 SSRs] were placed on the P.2175 Myrobalan map covering 524.8 cM. The R(MiaNem) gene, the Gr gene controlling the color of peach leaves, and 166 markers (one SCAR, 165 SSRs) were mapped to seven linkage groups instead of the expected eight in Prunus. Markers belonging to groups 6 and 8 in previous maps formed a single group in the GN22 map. A reciprocal translocation, already reported in a G x N F(2), was detected near the Gr gene. By separating markers from linkage groups 6 and 8 from the GN22 map, it was possible to compare the eight homologous linkage groups between the two maps using the 68 SSR markers heterozygous in both parents (anchor loci). All but one of these 68 anchor markers are in the same order in the Myrobalan plum map and in the almond-peach map, as expected from the high level of synteny within Prunus. The Ma and R(MiaNem)genes confirmed their previous location in the Myrobalan linkage group 7 and in the GN22 linkage group 2, respectively. Using a GN22 F(2) progeny of 78 individuals, a microsatellite map of linkage group 2 was also constructed and provided additional evidence for the telomeric position of R(MiaNem) in group 2 of the Prunus genome.
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Affiliation(s)
- E Dirlewanger
- INRA, Unité de Recherches sur les Espèces Fruitières et la Vigne (UREFV), B.P. 81, 33883 Villenave d'Ornon Cedex, France.
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Romero C, Pedryc A, Muñoz V, Llácer G, Badenes ML. Genetic diversity of different apricot geographical groups determined by SSR markers. Genome 2003; 46:244-52. [PMID: 12723040 DOI: 10.1139/g02-128] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forty apricot cultivars with different geographic origins belonging to the germplasm collections of St. Istvan University (Budapest, Hungary) and the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were studied by means of SSR markers. The aim of the study was to determine the genetic relationships among genotypes from different eco-geographical groups. Sixteen primer pairs flanking microsatellite sequences in the peach genome were assayed. Eleven of them were polymorphic in the set of cultivars studied and allowed every genotype to be unambiguously distinguished. Genetic diversity in the population studied was analyzed using several variability parameters. A total of 34 alleles were detected with a mean value of 3.1 alleles/locus. The expected heterozygosity mean was 0.46 and the observed heterozygosity was 32% on an average leading to a high value of the Wright's fixation index (0.32). Additionally, UPGMA cluster analysis based on Nei's genetic distance grouped genotypes according to their geographic origins and pedigrees. SSR markers have proved to be an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in apricot.
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Affiliation(s)
- Carlos Romero
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial 46113 Moncada, Valencia, Spain
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43
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Schueler S, Tusch A, Schuster M, Ziegenhagen B. Characterization of microsatellites in wild and sweet cherry (Prunus avium L.)--markers for individual identification and reproductive processes. Genome 2003; 46:95-102. [PMID: 12669801 DOI: 10.1139/g02-107] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.
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Affiliation(s)
- Silvio Schueler
- Institute for World Forestry, University of Hamburg, c/o Institute for Forest Genetics and Forest Tree Breeding, Sieker Landstr. 2, D-22927 Grosshansdorf, Germany.
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Wünsch A, Hormaza JI. Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences. Heredity (Edinb) 2002; 89:56-63. [PMID: 12080370 DOI: 10.1038/sj.hdy.6800101] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2001] [Accepted: 02/14/2002] [Indexed: 11/09/2022] Open
Abstract
A total of 76 sweet cherry genotypes were screened with 34 microsatellite primer pairs previously developed in peach. Amplification of SSR loci was obtained for 24 of the microsatellite primer pairs, and 14 of them produced polymorphic amplification patterns. On the basis of polymorphism and quality of amplification, a set of nine primer pairs and the resulting 27 informative alleles were used to identify 72 genotype profiles. Of these, 68 correspond to unique cultivar genotypes, and the remaining four correspond to three cultivars that could not be differentiated from the two original genotypes of which they are mutants, and two very closely related cultivars. The mean number of alleles per locus was 3.7 while the mean heterozygosity over the nine polymorphic loci averaged 0.49. The results demonstrate the usefulness of cross-species transferability of microsatellite sequences allowing the discrimination of different genotypes of a fruit tree species with sequences developed in other species of the same genus. UPGMA cluster analysis of the similarity data divided the ancient genotypes studied into two fairly well-defined groups that reflect their geographic origin, one with genotypes originating in southern Europe and the other with the genotypes from northern Europe and North America.
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Affiliation(s)
- A Wünsch
- Unidad de Fruticultura, Servicio de Investigación Agroalimentaria, Campus de Aula Dei, Zaragoza, Spain.
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Dettori MT, Quarta R, Verde I. A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 2001. [DOI: 10.1139/g01-065] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A linkage map was obtained using a BC1 progeny (Prunus persica × (P. persica × P. ferganensis)). The map is composed of 109 loci (74 RFLPs, 17 SSRs, 16 RAPDs, and two morphological traits) distributed in 10 linkage groups. Loci, segregating in five different ratios, were integrated in the map with JoinMap 2.0 software. The map covers 521 cM of the peach genome. The average distance between adjacent loci is 4.8 cM. Two monogenic traits, flesh adhesion (F/f) and leaf glands (E/e), were placed on the map. Thirty-two loci in common with a saturated linkage map of Prunus allowed a comparative analysis to be made between the two maps. Homologies were found among the respective linkage groups. No relevant differences were observed in the linear order of the common loci.Key words: peach, linkage map, Prunus persica, Prunus ferganensis, molecular markers.
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