Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).

<h4>Background</h4>It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgress...

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Autores principales:	Zhenying Dong, Hongyan Wang, Yuzhu Dong, Yongming Wang, Wei Liu, Gaojian Miao, Xiuyun Lin, Daqing Wang, Bao Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7037fc7ffb95452ebacfc8ff5d1d4b42
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spelling	oai:doaj.org-article:7037fc7ffb95452ebacfc8ff5d1d4b422021-11-18T07:47:58ZExtensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).1932-620310.1371/journal.pone.0062317https://doaj.org/article/7037fc7ffb95452ebacfc8ff5d1d4b422013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23638037/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars.<h4>Methodology</h4>Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed.<h4>Results/conclusions</h4>Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the introgression lines.Zhenying DongHongyan WangYuzhu DongYongming WangWei LiuGaojian MiaoXiuyun LinDaqing WangBao LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e62317 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhenying Dong Hongyan Wang Yuzhu Dong Yongming Wang Wei Liu Gaojian Miao Xiuyun Lin Daqing Wang Bao Liu Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
description	<h4>Background</h4>It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars.<h4>Methodology</h4>Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed.<h4>Results/conclusions</h4>Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the introgression lines.
format	article
author	Zhenying Dong Hongyan Wang Yuzhu Dong Yongming Wang Wei Liu Gaojian Miao Xiuyun Lin Daqing Wang Bao Liu
author_facet	Zhenying Dong Hongyan Wang Yuzhu Dong Yongming Wang Wei Liu Gaojian Miao Xiuyun Lin Daqing Wang Bao Liu
author_sort	Zhenying Dong
title	Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
title_short	Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
title_full	Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
title_fullStr	Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
title_full_unstemmed	Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
title_sort	extensive microsatellite variation in rice induced by introgression from wild rice (zizania latifolia griseb.).
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7037fc7ffb95452ebacfc8ff5d1d4b42
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Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).

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