Se-Won Chun1, Jei-Wan Lee1, Ji-Young Ahn2. 1. Division of Forest Bio Resources, National Institute of Forest Science, Suwon, Republic of Korea. 2. Division of Forest Bio Resources, National Institute of Forest Science, Suwon, Republic of Korea. gee330@korea.kr.
Abstract
BACKGROUND: Tilia amurensis (Malvaceae) is a deciduous broad-leaved tree distributed in Korea, China, and Japan. T. amurensis is used as a honey tree and also as a material for furniture, carving, and pulp. This study aimed to develop and characterize novel microsatellite markers using next-generation sequencing (NGS) of T. amurensis. METHODS AND RESULTS: NGS analysis using GS-FLX Titanium obtained 629,273 reads, of which 15,795 contigs were assembled with an average length of 830 bp. A total of 4774 microsatellite regions were detected in 3602 of 15,795 contigs. In total, 360 primer sets were designed based on the microsatellite regions. Among them, 15 primer sets were selected as reproducible polymorphic markers and were characterized for three populations of T. amurensis in Korea. The average number of alleles (NA) was 3.5 in Mt. Hambaek (HB), 3.7 in Mt. Odae (OD), and 3.8 in Mt. Sobaek (SB). The average observed heterozygosity (HO) and expected heterozygosity (HE) values were 0.497 and 0.370 in the HB population, 0.470 and 0.372 in the OD population, and 0.524 and 0.410 in the SB population, respectively. The average polymorphic information content (PIC) value of the 15 microsatellite markers was 0.686. CONCLUSIONS: The novel microsatellite markers will be useful for further studies on genetic diversity evaluation to conserve the genetic resources and natural populations of T. amurensis.
BACKGROUND: Tilia amurensis (Malvaceae) is a deciduous broad-leaved tree distributed in Korea, China, and Japan. T. amurensis is used as a honey tree and also as a material for furniture, carving, and pulp. This study aimed to develop and characterize novel microsatellite markers using next-generation sequencing (NGS) of T. amurensis. METHODS AND RESULTS: NGS analysis using GS-FLX Titanium obtained 629,273 reads, of which 15,795 contigs were assembled with an average length of 830 bp. A total of 4774 microsatellite regions were detected in 3602 of 15,795 contigs. In total, 360 primer sets were designed based on the microsatellite regions. Among them, 15 primer sets were selected as reproducible polymorphic markers and were characterized for three populations of T. amurensis in Korea. The average number of alleles (NA) was 3.5 in Mt. Hambaek (HB), 3.7 in Mt. Odae (OD), and 3.8 in Mt. Sobaek (SB). The average observed heterozygosity (HO) and expected heterozygosity (HE) values were 0.497 and 0.370 in the HB population, 0.470 and 0.372 in the OD population, and 0.524 and 0.410 in the SB population, respectively. The average polymorphic information content (PIC) value of the 15 microsatellite markers was 0.686. CONCLUSIONS: The novel microsatellite markers will be useful for further studies on genetic diversity evaluation to conserve the genetic resources and natural populations of T. amurensis.
Authors: Juan E Zalapa; Hugo Cuevas; Huayu Zhu; Shawn Steffan; Douglas Senalik; Eric Zeldin; Brent McCown; Rebecca Harbut; Philipp Simon Journal: Am J Bot Date: 2011-12-20 Impact factor: 3.844