Functional Domain Marker (FDM): an In Silico Demonstration in Solanaceae Using Simple Sequence Repeats (SSRs)

被引：20

作者：

Yu, Ju-Kyung ^{[1
]}

Paik, Hyojung ^{[2
]}

Choi, Jae Pil ^{[2
]}

Han, Jung-Heon ^{[3
]}

Choe, Jun-Kyoung ^{[2
]}

Hur, Cheol-Goo ^{[2
]}

机构：

[1] Syngenta Seeds Inc, Stanton Minnesota, MN 55018 USA

[2] Korea Res Inst Biotechnol & Biosci, Bioinformat Res Ctr, Taejon 305806, South Korea

[3] Seoul Natl Univ, Pepper & Breeding Inst Business Incubator, Coll Agr & Life Sci, Suwon 441853, South Korea

来源：

PLANT MOLECULAR BIOLOGY REPORTER | 2010年 / 28卷 / 02期

关键词：

Bioinformatic tool; Sequence analysis; Gene annotation; Biological database; Functional marker development; CHITINASE;

D O I：

10.1007/s11105-009-0154-8

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A simple sequence repeat-functional domain marker (SSR-FDM) relies on development of molecular markers for putative functional domains using simple sequence repeats and in silico annotated information of those sequences using biological databases. A total of 148,921 tomato ESTs and 115,598 pepper ESTs were analyzed, resulting in the identification of 439 tomato SSR-FDMs and 489 pepper SSR-FDMs. Among them, 54 pepper SSR-FDMs were tested on pepper. Several genomic databases were used for the in silico annotation of the SSR-FDM sequences that revealed a wide range of candidate genes. This study demonstrates that SSR-FDMs provide information regarding transcribed genetic markers and putative function as a genomic resource database for Solanaceae. This system could be applied to the development of a functional marker database for any crop species.

引用

页码：352 / 356

页数：5

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