Elaeis oleifera genomic-SSR markers: Exploitation in oil palm germplasm diversity and cross-amplification in arecaceae

Noorhariza Mohd Zaki, Rajinder Singh, Rozana Rosli, Ismanizan Ismail

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of dinucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H o) (0.164) and highly positive fixation indices (F is) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.

Original languageEnglish
Pages (from-to)4069-4088
Number of pages20
JournalInternational Journal of Molecular Sciences
Volume13
Issue number4
DOIs
Publication statusPublished - Apr 2012

Fingerprint

Arecaceae
Palm oil
exploitation
Polymorphism
Microsatellite Repeats
markers
Amplification
Oils
oils
Cocos
Genomic Library
Nucleotides
Genetic Markers
Breeding
biological diversity
polymorphism
primers
sequencing
nucleotides
resources

Keywords

  • Elaeis oleifera
  • Genomic library
  • Simple sequence repeat (SSR)
  • Transferability

ASJC Scopus subject areas

  • Computer Science Applications
  • Molecular Biology
  • Catalysis
  • Inorganic Chemistry
  • Spectroscopy
  • Organic Chemistry
  • Physical and Theoretical Chemistry

Cite this

Elaeis oleifera genomic-SSR markers : Exploitation in oil palm germplasm diversity and cross-amplification in arecaceae. / Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan.

In: International Journal of Molecular Sciences, Vol. 13, No. 4, 04.2012, p. 4069-4088.

Research output: Contribution to journalArticle

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