RAPD-SCAR Markers for Genetically Improved NEW GIFT Nile Tilapia (<I>Oreochromis niloticus niloticus</I> L.) and Their Application in Strain Identification

Abstract

Abstract:The NEW GIFT Nile tilapia (Oreochromis niloticus niloticus L.) is a nationally certificated new strain selected over 14 years and 9 generations from the base strain of GIFT Nile tilapia, introduced in 1994. This new variety has been extended in most of areas of China. The management of genetically improved strains, including the genetic markers for identification is needed urgently. RAPD analysis was conducted and their conversion to SCAR markers was developed. From NEW GIFT Nile tilapia, two strain-specific RAPD bands, S 304 624 bp and S 36 568 bp were identified. The strain-specific RAPD bands were gel-purified, cloned, and sequenced. Locus-specific primers were then designed to amplify the strain-specific bands. PCR amplification was conducted to test the variations in allele frequencies of two converted SCAR markers among the NEW GIFT Nile tilapia and its base strains, as well as 7 additional farmed strains worldwide. The frequency of SCAR marker I (553 bp) was 85.7% in NEW GIFT Nile tilapia, but 16.7% in the base strain. The frequency of SCAR marker II (558 bp) was 91.4% in NEW GIFT Nile tilapia, but 0% − 70% in the 7 other strains. In order to confirm the utility of these two markers, an examination was conducted for a wild population from Egypt, resulted the frequency of SCAR I and II was 10% and 70%, respectively, much lower than that of New GIFT strain. The increase in allele frequency of these two SCAR markers suggests that these markers might be genetically linked to the quantitative trait loci (QTL) underlining the performance traits by long term selection, and indicate the bright potential of SCAR marker technology for tracking generations during selection progress and for distinguishing among genetically improved strain and other strains.

Review of Molecular Techniques for the Identification of Bacterial Communities in Biological Effluent Treatment Facilities at Pulp and Paper Mills

“…The major disadvantage to RAPD-PCR is its inability to yield reproducible polymorphism under varying laboratory conditions (Srivastava et al 2012). To overcome this problem, it is necessary to develop co-dominant markers from dominant markers to avoid lengthy RAPD reaction (Li et al 2010). Such markers are typical oligonucleotides designed from the sequences of the amplicon of RAPD, and they mostly have a high probability of producing polymorphic amplicons (Cheng et al 2015).…”

Development of two novel specific SCAR markers by cloning improved RAPD fragments from the medicinal mushroom Ganoderma lucidium (Leysser: Fr) Karst

“…These techniques are generally used for genetic characterization of organisms. The sequencecharacterized amplified region (SCAR) marker is one of the stable markers that is generally derived from RAPD (Dnyaneshwar et al, 2006;Li et al, 2010;Rajesh et al, 2013;Fu et al, 2015;Zhang et al, 2015;Mei et al, 2015;Cheng et al, 2016). These markers reveal higher levels of polymorphism due to higher annealing temperatures and longer primer sequence specificity (Kumla et al, 2012;Yang et al, 2013).…”

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning

“…A combination of SCAR and RAPD has significantly improved the stability and authenticity of the technique (Dnyaneshwar et al, 2006;Su et al, 2007;Li et al, 2010;Kumla et al, 2012;Rajesh et al, 2013;Fu et al, 2013;Noormohammadi et al, 2013;Mei et al, 2014a,b). Previous studies successfully developed RAPD markers for different species of animals, plants, and microbes (Lee et al, 2013;Yang et al, 2013Yang et al, , 2014Dutta et al, 2014).…”

“…The sequence characterized amplified region (SCAR) marker is another molecular marker, which is more stable and is generally derived from RAPD or intersimple sequence repeat (Dnyaneshwar et al, 2006;Su et al, 2007;Li et al, 2010;Kumla et al, 2012;Rajesh et al, 2013). When SCAR with RAPD are combined, molecular analysis is simplified, in which PCR primers are designed from the sequence of the RAPD amplicon to develop SCAR markers (Kumla et al, 2012;Rajesh et al, 2013).…”