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

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Title: Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information
Authors: Tamura, Ken-ichi Browse this author
Yonemaru, Jun-ichi Browse this author
Hisano, Hiroshi Browse this author
Kanamori, Hiroyuki Browse this author
King, Julie Browse this author
King, Ian P. Browse this author
Tase, Kazuhiro Browse this author
Sanada, Yasuharu Browse this author
Komatsu, Toshinori Browse this author
Yamada, Toshihiko Browse this author →KAKEN DB
Keywords: intergeneric (interspecific) hybrid
intron polymorphisms
insertion-deletion (indel)
specificity to species
rice genome
comparative genomics
Issue Date: May-2009
Publisher: Springer
Journal Title: Theoretical and Applied Genetics
Volume: 118
Issue: 8
Start Page: 1549
End Page: 1560
Publisher DOI: 10.1007/s00122-009-1003-8
Abstract: 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.
Rights: The original publication is available at
Type: article (author version)
Appears in Collections:北方生物圏フィールド科学センター (Field Science Center for Northern Biosphere) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 山田 敏彦

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