Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

Tamura, Ken-ichi; Yonemaru, Jun-ichi; Hisano, Hiroshi; Kanamori, Hiroyuki; King, Julie; King, Ian P.; Tase, Kazuhiro; Sanada, Yasuharu; Komatsu, Toshinori; Yamada, Toshihiko

Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

Tamura, Ken-ichi; Yonemaru, Jun-ichi; Hisano, Hiroshi et al.

Theoretical and Applied Genetics, 2009, 118(8), 1549-1560

Permalink : https://hdl.handle.net/2115/43023

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アクセス権	open access
URI	https://hdl.handle.net/2115/43023
タイトル	Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information
著者	Tamura, Ken-ichi ; Yonemaru, Jun-ichi ; Hisano, Hiroshi ; Kanamori, Hiroyuki ; King, Julie ; King, Ian P. ; Tase, Kazuhiro ; Sanada, Yasuharu ; Komatsu, Toshinori ; Yamada, Toshihiko
著者名 Tamura, Ken-ichi
著者名 Yonemaru, Jun-ichi
著者名 Hisano, Hiroshi
著者名 Kanamori, Hiroyuki
著者名 King, Julie
著者名 King, Ian P.
著者名 Tase, Kazuhiro
著者名 Sanada, Yasuharu
著者名 Komatsu, Toshinori
e-Rad_Researcher 70343952 著者名 Yamada, Toshihiko
言語	英語
キーワード	intergeneric (interspecific) hybrid
	intron polymorphisms
	insertion-deletion (indel)
	specificity to species
	rice genome
	comparative genomics
発行日	2009-05
出版者	Springer
収録物名	Theoretical and Applied Genetics
巻(号)	118(8)
ページ	1549-1560
抄録	DNA markers able to distinguish species or genera with high specificity are valuable in the identification of introgressed regions in interspecific or intergeneric hybrids. Intergeneric hybridization between the genera of Lolium and Festuca, leading to the reciprocal introgression of chromosomal segments, can produce novel forage grasses with unique combinations of characteristics. To characterize Lolium/Festuca introgressions, novel PCR-based expression sequence tag (EST) markers were developed. These markers were designed around intronic regions which show higher polymorphism than exonic regions. Intronic regions of the grass genes were predicted from the sequenced rice genome. Two hundred and nine primer sets were designed from Lolium/Festuca ESTs that showed high similarity to unique rice genes dispersed uniformly throughout the rice genome. We selected 61 of these primer sets as insertion-deletion (indel)-type markers and 82 primer sets as cleaved amplified polymorphic sequence (CAPS) markers to distinguish between Lolium perenne and Festuca pratensis. Specificity of these markers to each species was evaluated by the genotyping of four cultivars and accessions (32 individuals) of L. perenne and F. pratensis respectively. Evaluation using specificity indices proposed in this study suggested that many indel-type markers had high species specificity to L. perenne and F. pratensis, including 15 markers completely specific to both species. Forty-nine of the CAPS markers completely distinguish between the two species at bulk level. Chromosome mapping of these markers using a Lolium/Festuca substitution line revealed syntenic relationships between Lolium/Festuca and rice largely consistent with previous reports. This intron-based marker system that shows a high level of polymorphisms between species in combination with high species specificity will consequently be a valuable tool in Festulolium breeding.
資源タイプ	学術雑誌論文
出版タイプ	Accepted Manuscript
権利情報	The original publication is available at www.springerlink.com
PISSN	0040-5752
EISSN	1432-2242
NCID	AA00862655
関連情報 (isVersionOf)	出版社版DOI https://doi.org/10.1007/s00122-009-1003-8