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:	Yongqiang Sun, Shengjun Dong, Quangang Liu, Jianhua Chen, Jingjing Pan, Jian Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9f258f07a74148f093ac8041f0858ca2
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spelling	oai:doaj.org-article:9f258f07a74148f093ac8041f0858ca22021-11-25T06:19:31ZSelection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers1932-6203https://doaj.org/article/9f258f07a74148f093ac8041f0858ca22021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8604298/?tool=EBIhttps://doaj.org/toc/1932-6203Prunus 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.Yongqiang SunShengjun DongQuangang LiuJianhua ChenJingjing PanJian ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yongqiang Sun Shengjun Dong Quangang Liu Jianhua Chen Jingjing Pan Jian Zhang Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers
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 (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.
format	article
author	Yongqiang Sun Shengjun Dong Quangang Liu Jianhua Chen Jingjing Pan Jian Zhang
author_facet	Yongqiang Sun Shengjun Dong Quangang Liu Jianhua Chen Jingjing Pan Jian Zhang
author_sort	Yongqiang Sun
title	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_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_sort	selection of a core collection of prunus sibirica l. germplasm by a stepwise clustering method using simple sequence repeat markers
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/9f258f07a74148f093ac8041f0858ca2
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Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers

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