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      Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

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          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 di-nucleotides (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.

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          Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

          T Thiel, W Michalek, R. K. Varshney … (2003)
          A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
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            Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.

            Michele Morgante, Michael Hanafey, Wayne Powell (2002)
            Microsatellites are a ubiquitous class of simple repetitive DNA sequence. An excess of such repetitive tracts has been described in all eukaryotes analyzed and is thought to result from the mutational effects of replication slippage. Large-scale genomic and EST sequencing provides the opportunity to evaluate the abundance and relative distribution of microsatellites between transcribed and nontranscribed regions and the relationship of these features to haploid genome size. Although this has been studied in microbial and animal genomes, information in plants is limited. We assessed microsatellite frequency in plant species with a 50-fold range in genome size that is mostly attributable to the recent amplification of repetitive DNA. Among species, the overall frequency of microsatellites was inversely related to genome size and to the proportion of repetitive DNA but remained constant in the transcribed portion of the genome. This indicates that most microsatellites reside in regions pre-dating the recent genome expansion in many plants. The microsatellite frequency was higher in transcribed regions, especially in the untranslated portions, than in genomic DNA. Contrary to previous reports suggesting a preferential mechanism for the origin of microsatellites from repetitive DNA in both animals and plants, our findings show a significant association with the low-copy fraction of plant genomes.
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              Isolation of plant DNA from faesh tissue

              Jeff J. Doyle, JJ DOYLE, J. L. DOYLE … (1990)
              Article 0 comments Cited 293 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: Molecular Diversity Preservation International (MDPI)
                ISSN (Electronic): 1422-0067
                Publication date Collection: 2012
                Publication date (Electronic): 28 March 2012
                Volume: 13
                Issue: 4
                Pages: 4069-4088
                Affiliations
                [1 ]Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, Kuala Lumpur 50720, Malaysia; E-Mails: rajinder@ 123456mpob.gov.my (R.S.); lizana@ 123456mpob.gov.my (R.R.)
                [2 ]School of Bioscience and Biotechnology, Faculty Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; E-Mail: maniz@ 123456ukm.my
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: hariza@ 123456mpob.gov.my ; Tel.: +603-8769-4956; Fax: +603-8926-1995.
                Article
                Publisher ID: ijms-13-04069
                DOI: 10.3390/ijms13044069
                PMC ID: 3344202
                PubMed ID: 22605966
                SO-VID: 56b6fbce-8ba1-41c9-9864-054fbe3a7c3c
                Copyright © © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.
                License:

                This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

                History
                Date received : 23 December 2011
                Date revision received : 08 March 2012
                Date accepted : 08 March 2012
                Categories
                Subject: Article

                ScienceOpen disciplines: Molecular biology
                Keywords: genomic library,elaeis oleifera,simple sequence repeat (ssr),transferability
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: genomic library, elaeis oleifera, simple sequence repeat (ssr), transferability

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