Cargando…
Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers
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 bro...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8604298/ https://www.ncbi.nlm.nih.gov/pubmed/34797843 http://dx.doi.org/10.1371/journal.pone.0260097 |
_version_ | 1784601927870316544 |
---|---|
author | Sun, Yongqiang Dong, Shengjun Liu, Quangang Chen, Jianhua Pan, Jingjing Zhang, Jian |
author_facet | Sun, Yongqiang Dong, Shengjun Liu, Quangang Chen, Jianhua Pan, Jingjing Zhang, Jian |
author_sort | Sun, Yongqiang |
collection | PubMed |
description | 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 (N(a)), Number of effective alleles (N(e)), 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 N(a), N(e), 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. |
format | Online Article Text |
id | pubmed-8604298 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-86042982021-11-20 Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers Sun, Yongqiang Dong, Shengjun Liu, Quangang Chen, Jianhua Pan, Jingjing Zhang, Jian PLoS One Research Article 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 (N(a)), Number of effective alleles (N(e)), 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 N(a), N(e), 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. Public Library of Science 2021-11-19 /pmc/articles/PMC8604298/ /pubmed/34797843 http://dx.doi.org/10.1371/journal.pone.0260097 Text en © 2021 Sun et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Sun, Yongqiang Dong, Shengjun Liu, Quangang Chen, Jianhua Pan, Jingjing Zhang, Jian Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title | Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title_full | Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title_fullStr | Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title_full_unstemmed | Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title_short | Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers |
title_sort | selection of a core collection of prunus sibirica l. germplasm by a stepwise clustering method using simple sequence repeat markers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8604298/ https://www.ncbi.nlm.nih.gov/pubmed/34797843 http://dx.doi.org/10.1371/journal.pone.0260097 |
work_keys_str_mv | AT sunyongqiang selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers AT dongshengjun selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers AT liuquangang selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers AT chenjianhua selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers AT panjingjing selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers AT zhangjian selectionofacorecollectionofprunussibiricalgermplasmbyastepwiseclusteringmethodusingsimplesequencerepeatmarkers |