Genome shotgun sequencing and development of microsatellite markers for gerbera (Gerbera hybrida H.) by 454 GS-FLX

  • Kyoung-In Seo
  • Gi-An Lee
  • Sang-Kun Park
  • Mun-Sup Yoon
  • Kyung-Ho Ma
  • Jung-Ro Lee
  • Yu-Mi Choi
  • Yeon-ju Jung
  • Myung-Chul Lee

Abstract

The objective of this research was to develop and characterize microsatellite markers for gerbera. We used shotgun sequencing with Roche 454 GS-FLX Titanium technology to identify microsatellite loci in gerbera genomic DNA (Gerbera hybrida). The total length of non-redundant sequences obtained was 22,527,019 bp, which consisted of 3,085 contigs and 28,249 singletons. We assembled 61,958 reads into 3,085 contigs, of which 114 (3.70%) contained microsatellite repeats. The average G+C content was 39.3%. Functional annotation to known sequences yielded 14.7% unigenes in the ‘Raon’ cultivar. Analysis of the gerbera genome DNA (‘Raon’) general library showed that sequences of (AT), (AG), (AAG) and (AAT) repeats appeared most often, whereas (AC), (AAC) and (ACC) were the least frequent. Primer pairs were designed for 80 loci. Only eight primer pairs produced reproducible polymorphic bands in the 28 gerbera accessions analyzed. A total of 30 alleles were identified from the eight polymorphic SSR loci, with two to eight alleles per locus (average level of 3.75). These markers will be useful for investigating genetic diversity and differentiation in gerbera.

Keywords: Genetic diversity, genomics, microsatellite isolation, pyrosequencing, SSRs.

African Journal of Biotechnology Vol. 11(29), pp. 7388-7396, 10 April, 2012

Author Biographies

Kyoung-In Seo
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Gi-An Lee
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Sang-Kun Park
Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Suwon, Gyunggi-do, 440-706, Korea
Mun-Sup Yoon
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Kyung-Ho Ma
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Jung-Ro Lee
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Yu-Mi Choi
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Yeon-ju Jung
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Myung-Chul Lee
National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do, 441-707, Korea
Published
2014-04-03
Section
Articles

eISSN: 1684-5315