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Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers
- Source :
- PLoS ONE, Vol 16, Iss 11 (2021), PLoS ONE, PLoS ONE, Vol 16, Iss 11, p e0260097 (2021)
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- Prunus sibirica is an economically important tree species that occurs in arid and semi-arid regions of northern China. For this species, creation of a core collection is critical for future ecological and evolutionary studies, efficient economic utilization, and development and management of the broader collection of its germplasm resources. In this study, we sampled 158 accessions of P. sibirica from Russia and China using 30 pair of simple sequence repeat molecular markers and 30 different schemes to identify candidate core collections. The 30 schemes were based on combinations of two different sampling strategies, three genetic distances, and five different sample sizes of the complete germplasm resource. We determined the optimal core collection from among the 30 results based on maximization of genetic diversity among groups according to Number of observed alleles (Na), Number of effective alleles (Ne), Shannon’s information index (I), Polymorphic information content (PIC), Nei gene diversity (H) and compared to the initial collection of 158 accessions. We found that the optimal core collection resulted from preferred sampling at 25% with Nei & Li genetic distance these ratios of Na, Ne, I, PIC and H to the complete 158 germplasm resources were 73.0%, 113%, 102%, 100% and 103%, respectively, indicating that the core collection comprised a robust representation of genetic diversity in P. sibirica. The proposed core collection will be valuable for future molecular breeding of this species and management of its germplasm resources.
- Subjects :
- Germplasm
Prunus armeniaca
Cluster Analysis
Data Management
Molecular breeding
Multidisciplinary
Ecology
biology
Sampling (statistics)
Agriculture
Phylogenetic Analysis
Biological Evolution
Phylogenetics
Phenotypes
Shannon Index
Medicine
Prunus
Desert Climate
Research Article
Computer and Information Sciences
Conservation of Natural Resources
Ecological Metrics
Science
Specimen Handling
Genetics
Evolutionary Systematics
Allele
Alleles
Selection (genetic algorithm)
Taxonomy
Evolutionary Biology
Genetic diversity
Population Biology
Ecology and Environmental Sciences
Prunus sibirica
Biology and Life Sciences
Genetic Variation
Species Diversity
biology.organism_classification
Agronomy
Plant Breeding
Genetic distance
Genetic Loci
Seed Bank
Evolutionary biology
Sample Size
Genetic Polymorphism
Population Genetics
Biomarkers
Microsatellite Repeats
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 16
- Issue :
- 11
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....85a7399a3d1c76e60484be038878117e