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Nybom H, Ruan C, Rumpunen K. The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review. Genes (Basel) 2023; 14:2120. [PMID: 38136942 PMCID: PMC10743242 DOI: 10.3390/genes14122120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, 29194 Kristianstad, Sweden
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China;
| | - Kimmo Rumpunen
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden;
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Donkpegan ASL, Bernard A, Barreneche T, Quero-García J, Bonnet H, Fouché M, Le Dantec L, Wenden B, Dirlewanger E. Genome-wide association mapping in a sweet cherry germplasm collection ( Prunus avium L.) reveals candidate genes for fruit quality traits. HORTICULTURE RESEARCH 2023; 10:uhad191. [PMID: 38239559 PMCID: PMC10794993 DOI: 10.1093/hr/uhad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/12/2023] [Indexed: 01/22/2024]
Abstract
In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP-trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.
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Affiliation(s)
- Armel S L Donkpegan
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
- UMR BOA, SYSAAF, Centre INRAE Val de Loire, 37380
Nouzilly, France
| | - Anthony Bernard
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Teresa Barreneche
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - José Quero-García
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Hélène Bonnet
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Mathieu Fouché
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Loïck Le Dantec
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Bénédicte Wenden
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Elisabeth Dirlewanger
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
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Li R, Huang Y, Yang X, Su M, Xiong H, Dai Y, Wu W, Pei X, Yuan Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2876. [PMID: 37571029 PMCID: PMC10421310 DOI: 10.3390/plants12152876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.
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Affiliation(s)
- Rongju Li
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Yinling Huang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinsen Yang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Meng Su
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Huaiyang Xiong
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Yang Dai
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Wei Wu
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qianhua Yuan
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
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Wang X, Wang L, Sun Y, Chen J, Liu Q, Dong S. Genetic diversity and conservation of Siberian apricot (Prunus sibirica L.) based on microsatellite markers. Sci Rep 2023; 13:11245. [PMID: 37433853 DOI: 10.1038/s41598-023-37993-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Siberian apricot (Prunus sibirica L.) is a woody tree species of ecological, economic, and social importance. To evaluate the genetic diversity, differentiation, and structure of P. sibirica, we analyzed 176 individuals from 10 natural populations using 14 microsatellite markers. These markers generated 194 alleles in total. The mean number of alleles (13.8571) was higher than the mean number of effective alleles (6.4822). The average expected heterozygosity (0.8292) was higher than the average observed heterozygosity (0.3178). Shannon information index and polymorphism information content were separately 2.0610 and 0.8093, demonstrating the rich genetic diversity of P. sibirica. Analysis of molecular variance revealed that 85% of the genetic variation occurred within populations, with only 15% among them. The genetic differentiation coefficient and gene flow were separately 0.151 and 1.401, indicating a high degree of genetic differentiation. Clustering results showed that a genetic distance coefficient of 0.6 divided the 10 natural populations into two subgroups (subgroups A and B). STRUCTURE and principal coordinate analysis divided the 176 individuals into two subgroups (clusters 1 and 2). Mantel tests revealed that genetic distance was correlated with geographical distance and elevation differences. These findings can contribute to the effective conservation and management of P. sibirica resources.
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Affiliation(s)
- Xinxin Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China
| | - Li Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China
| | - Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, 110866, Liaoning, China.
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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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Palasciano M, Zuluaga DL, Cerbino D, Blanco E, Aufiero G, D’Agostino N, Sonnante G. Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers. PLANTS (BASEL, SWITZERLAND) 2022; 12:136. [PMID: 36616264 PMCID: PMC9824393 DOI: 10.3390/plants12010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.
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Affiliation(s)
- Marino Palasciano
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Diana L. Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Domenico Cerbino
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA) Pollino, C.da Piano Incoronata, 85048 Rotonda, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Gaetano Aufiero
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
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Armbruster GF, Lucek K, Willi Y. Cryptic population structure at the northern range margin of the service tree Sorbus domestica. PeerJ 2022; 10:e14397. [PMID: 36523464 PMCID: PMC9745788 DOI: 10.7717/peerj.14397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Climate change has aroused interest in planting warm- and drought-adapted trees in managed forests and urban areas. An option is to focus on tree species that occur naturally, but have centers of distribution in warmer and drier areas. However, in order to protect the species pool of genetic diversity, efforts of planting and promotion should be informed by knowledge on the local genetic diversity. Here, we studied the macro- and micro-scale population genetic structure of the rare European fruit tree Sorbus domestica at its northern range margin, in western Switzerland. New microsatellite data were combined with published data from across the European distribution of the species. Analyses revealed the presence of mainly one of two species-wide ancestral clusters, i.e., the western European cluster, with evidence that it consists of two cryptic sub-clusters. Average pairwise F ST of 0.118 was low across the range, and only allelic richness was reduced in the northern margin compared to more southern and southeastern areas of Europe. Based on our finding of considerable genetic diversity of the species in western and northern Switzerland, we suggest that a national propagation program should focus on collecting seeds from natural, high-density tree stands and propagate locally. More generally, our study shows that rare tree species in marginal areas of their distributions do not necessarily have low genetic diversity or heightened levels of inbreeding, and in those cases probably need no assisted migration in efforts to propagate them.
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Affiliation(s)
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, BS, Switzerland
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, BS, Switzerland
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