Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.

Wild species of Oryza are extremely valuable sources of genetic material that can be used to broaden the genetic background of cultivated rice, and to increase its resistance to abiotic and biotic stresses. Until recently, there was no sequence information for the BBCC Oryza genome; therefore, no sp...

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Autores principales:	Caihong Wang, Xiaojiao Liu, Suotang Peng, Qun Xu, Xiaoping Yuan, Yue Feng, Hanyong Yu, Yiping Wang, Xinghua Wei
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e501201c11fe4916a82f83e09f632489
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spelling	oai:doaj.org-article:e501201c11fe4916a82f83e09f6324892021-11-18T08:27:58ZDevelopment of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.1932-620310.1371/journal.pone.0091826https://doaj.org/article/e501201c11fe4916a82f83e09f6324892014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24632997/?tool=EBIhttps://doaj.org/toc/1932-6203Wild species of Oryza are extremely valuable sources of genetic material that can be used to broaden the genetic background of cultivated rice, and to increase its resistance to abiotic and biotic stresses. Until recently, there was no sequence information for the BBCC Oryza genome; therefore, no special markers had been developed for this genome type. The lack of suitable markers made it difficult to search for valuable genes in the BBCC genome. The aim of this study was to develop microsatellite markers for the BBCC genome. We obtained 13,991 SSR-containing sequences and designed 14,508 primer pairs. The most abundant was hexanuclelotide (31.39%), followed by trinucleotide (27.67%) and dinucleotide (19.04%). 600 markers were selected for validation in 23 accessions of Oryza species with the BBCC genome. A set of 495 markers produced clear amplified fragments of the expected sizes. The average number of alleles per locus (Na) was 2.5, ranging from 1 to 9. The genetic diversity per locus (He) ranged from 0 to 0.844 with a mean of 0.333. The mean polymorphism information content (PIC) was 0.290, and ranged from 0 to 0.825. Of the 495 markers, 12 were only found in the BB genome, 173 were unique to the CC genome, and 198 were also present in the AA genome. These microsatellite markers could be used to evaluate the phylogenetic relationships among different Oryza genomes, and to construct a genetic linkage map for locating and identifying valuable genes in the BBCC genome, and would also for marker-assisted breeding programs that included accessions with the AA genome, especially Oryza sativa.Caihong WangXiaojiao LiuSuotang PengQun XuXiaoping YuanYue FengHanyong YuYiping WangXinghua WeiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e91826 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Caihong Wang Xiaojiao Liu Suotang Peng Qun Xu Xiaoping Yuan Yue Feng Hanyong Yu Yiping Wang Xinghua Wei Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
description	Wild species of Oryza are extremely valuable sources of genetic material that can be used to broaden the genetic background of cultivated rice, and to increase its resistance to abiotic and biotic stresses. Until recently, there was no sequence information for the BBCC Oryza genome; therefore, no special markers had been developed for this genome type. The lack of suitable markers made it difficult to search for valuable genes in the BBCC genome. The aim of this study was to develop microsatellite markers for the BBCC genome. We obtained 13,991 SSR-containing sequences and designed 14,508 primer pairs. The most abundant was hexanuclelotide (31.39%), followed by trinucleotide (27.67%) and dinucleotide (19.04%). 600 markers were selected for validation in 23 accessions of Oryza species with the BBCC genome. A set of 495 markers produced clear amplified fragments of the expected sizes. The average number of alleles per locus (Na) was 2.5, ranging from 1 to 9. The genetic diversity per locus (He) ranged from 0 to 0.844 with a mean of 0.333. The mean polymorphism information content (PIC) was 0.290, and ranged from 0 to 0.825. Of the 495 markers, 12 were only found in the BB genome, 173 were unique to the CC genome, and 198 were also present in the AA genome. These microsatellite markers could be used to evaluate the phylogenetic relationships among different Oryza genomes, and to construct a genetic linkage map for locating and identifying valuable genes in the BBCC genome, and would also for marker-assisted breeding programs that included accessions with the AA genome, especially Oryza sativa.
format	article
author	Caihong Wang Xiaojiao Liu Suotang Peng Qun Xu Xiaoping Yuan Yue Feng Hanyong Yu Yiping Wang Xinghua Wei
author_facet	Caihong Wang Xiaojiao Liu Suotang Peng Qun Xu Xiaoping Yuan Yue Feng Hanyong Yu Yiping Wang Xinghua Wei
author_sort	Caihong Wang
title	Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
title_short	Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
title_full	Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
title_fullStr	Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
title_full_unstemmed	Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
title_sort	development of novel microsatellite markers for the bbcc oryza genome (poaceae) using high-throughput sequencing technology.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/e501201c11fe4916a82f83e09f632489
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Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.

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