A Comparison of Old and Modern Type DNA Marker Technologies and Their Impact on Animal Breeding Programs

Abstract

In recent years, molecular genetic technologies allowed to identify genetic structure in farm animals have great advantages for animal breeding. Especially, in developed countries these methods began to be widely used to assist animal breeding studies. It can be said that there are various molecular genetic markers. These markers can be classified by taking into consideration a number of factors such as the principle of the detection technique, type of polymorphism. Although old type molecular genetic markers such as RFLP, AFLP, microsatellites are widely used today, the information obtained from them is more limited than modern molecular genetic markers. SNP chip technologies, which known as modern molecular markers and are one of the most important developments in the molecular genetics field, have provided genomic breeding value estimation and genomic selection in farm animals. In this review, old and new types of molecular markers were compared and their usage in animal breeding were discussed.

Overview of Marker-assisted Selection in Animal Breeding

“…DNA markers in molecular genetics can be divided into three primary groups based on the kind of information they offer at a particular locus: Bi-allelic dominant: Random Amplification of Polymorphic DNA (RAPDs ), and AFLPs (Amplified Fragment Length Polymorphism), Biallelic co-dominant: Examples include RFLPs (Restriction Fragment Length Polymorphism), SSCPs (Single Stranded Conformation Polymorphism), and Multi-allelic co-dominant: For instance, microsatellites [21,22].…”

“…Various factors, including the quality of the DNA template, PCR conditions, reagents, and equipment, can contribute to the amplification or failure of any band using RAPDs [8]. Despite their somewhat lower reliability, RAPDs find widespread use in measuring population inbreeding, assessing genetic diversity and similarity, and generating genomic maps for agricultural animals [22,29,[30][31][32][33][34].…”

“…AFLP is a crucial technique for identifying genetic diversity and allows the detection of changes originating from Single Nucleotide Polymorphisms (SNPs) and insertions/deletions (indels) [22]. This versatility has made AFLP popular in various applications, including linkage mapping, Quantitative Trait Loci (QTL) analysis, genetic relationship research, and investigating genetic diversity in cDNA for gene expression profiling [38][39][40][41][42][43]22].…”

“…The Restriction Fragment Length Polymorphisms (RFLP) technique, established in 1974 following the discovery of restriction endonucleases in the 1960s [22,44], is a practical method for detecting mutations. RFLP analysis involves the use of enzymes with recognition sequences generated by mutations.…”

Short tandem repeats (STR) in cattle genomics and breeding

“…STR are di-, tri-, or tetra nucleotide tandem repeats in tandemly repeated DNA sequences that are present in variable copy numbers at each locus and throughout the genome (Ashley and Dow, 1994;Forbes et al, 1995;Bruford et al, 1996;Ellegren et al, 1997;Montaldo and Meza-Herrera, 1998;Schlötterer, 1998;Schmid et al, 1999;Toth et al, 2000;Beuzen et al, 2000;Teneva, 2009 ;Teneva and Petrovic 2010;Teneva et al, 2013;Gündüz et al, 2016). PCR-amplified microsatellite repeats in the alleles can be detected using fragment analysis and other methods.…”