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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...

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Autores principales: Sun, Yongqiang, Dong, Shengjun, Liu, Quangang, Chen, Jianhua, Pan, Jingjing, Zhang, Jian
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
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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.
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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
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