A review on SNP and other types of molecular markers and their use in animal genetics

By A. Vignal, D. Milan, M. Sancristobal, A. Eggen. Genetics Selection Evolution, 2002

1,160 citations recorded by the source corpus.

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9748085031ae327ff61b0acb137a86178c5b7b1f

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. M. Thomson
2. K. Semagn
3. Å. Bjornstad
4. G. Eizenga
5. A. McClung
6. Per Kryger
7. R. Neira
8. Maria Alice Pinto

In Molecular Biology

1. R. Neira
2. Å. Bjornstad
3. S. Cloutier
4. Patricia Iturra
5. Haiyan Wang
6. Santosh Kumar
7. A. Ismail
8. R. Bijlsma

Citations in the corpus

• An overview of molecular marker methods for plants (2006, methodology): “…denaturing gradient gel electrophoresis (DGGE), 6: denaturing high performance liquid chromatography (DHPLC), 7: Pyrosequencing, 8: SNP it, 9: exonuclease detection (Taqman), 10: Invader Assay, 11: Microarray or DNA chips (Vignal et al., 2002). accuracy, throughput and price (Tost and Gut, 2002).”
• Standard methods for characterising subspecies and ecotypes of Apis mellifera (2013, background): “…level, the genome-wide coverage (coding and non-coding regions), ubiquity, codominance, and conformation to infinite sites model of evolution (Vignal et al., 2002) facilitate employment of more powerful and robust approaches, potentially leading to more reliable identification and more…”
• High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform (2011, background): “Further facilitating computational analysis is the fact that SNPs are usually bi-allelic (having two alleles per locus) due to the low frequency of single nucleotide substitutions at SNP loci and a bias towards transitions over transversions (Vignal et al. 2002).”
• Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges (2007, background): “SNPs hold the potential to signiWcantly expand our ability to survey both neutral (non-coding region) variation as well as genes under selection (coding region) in natural populations, providing also broader genome coverage as compared to mitochondrial DNA or microsatellites ( Vignal et al. 2002; M”
• SNP Discovery through Next-Generation Sequencing and Its Applications (2012, background): “The advantage of SNPs over microsatellites and mitochondrial DNA resides in the fact that SNPs represent single base nucleotide substitutions and, as such, they are less a ff ected by homoplasy because their origin can be explained by mutation models [140].”
• A review of methods for discrimination of honey bee populations as applied to European beekeeping (2011, background): “Thanks to high-throughput genotyping technology, a new generation of molecular markers, called single nucleotide polymorphisms (SNPs), are available (Vignal et al., 2002).”
• Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes (2011, background): “They have a codominant inheritance pattern, are adaptable to automated genotyping, and reveal hidden polymorphisms not detected with other markers and methods (Stickney et al. 2002; Vignal et al. 2002; Liu and Cordes 2004).”
• Identification of Crassostrea ariakensis and Related Oysters by Multiplex Species-Specific PCR (2008, methodology): “SNPs can be genotyped by several methods including single-base primer extension, allele-specific extension, and microarrays (Holloway et al. 1999, Hacia & Collins 1999, Vignal et al. 2002, Ye et al. 2001, Brightwell et al. 2002, Palmer et al. 2003).”
• Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement (2013, neutral): “position (Vignal et al. 2002).”
• DNA marker technologies and their applications in aquaculture genetics. (2004, background): “As this review focuses on DNA markers and their applications in aquaculture, and our point of view could be biased by our research experience, readers are referred to other reviews concerning application of DNA marker technologies (Rafalski and Tingey, 1993; Buitkamp and Epplen, 1996; Dodgson et al.”