Authors: Nupur Mondal1*, Gayacharan2
1 Shivaji College, University of Delhi, New Delhi
2 Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi
Molecular markers can be broadly defined as unique sequence of nucleotides which can identify or differentiate between traits/ individuals. Such markers might not have any phenotypic effect of the individual, but are used for chromosome mapping, DNA fingerprinting, and genetic screening. Molecular markers must have desirable traits like they should be polymorphic, reproducible, evenly distributed across the whole genome (not clustered in particular regions), inexpensive, easy to analyze and co-dominant.
Types of molecular markers
There are a large number of molecular markers which can be classified into three types based upon methodology followed by them. They are:
- First generation markers (Based on hybridization). They are called so because the DNA profile is visualized through hybridization of DNA with radioactively labeled probes of known sequence. Example RFLP (Restriction Fragment Length Polymorphism).
- Second generation markers (Based on PCR), as their assay was carried out through amplification using either arbitrary or sequence specific primers. Example RAPD (Random Amplified Polymorphic DNA), AFLP (Amplified Fragment Length Polymorphism), SSR (Simple Sequence Repeat), VNTR (Variable Number Tandem Repeat) etc.
- Third generation markers (Based on DNA sequencing), their detection requires sequence information. Example SNP (Single Nucleotide Polymorphism).
Single Nucleotide Polymorphism
Single nucleotide polymorphisms, called SNPs (pronounced “snips”), are the most common genetic variation. Each SNP represents a difference in a nucleotide. Example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. If more than 1% of a population does not carry the same nucleotide at a specific position in the DNA sequence, then this variation can be classified as a SNP. Single nucleotide polymorphism can be because of substitution, deletion, or insertion. SNPs occur in both coding and noncoding regions of the genome.
SNP markers in oilseeds
In oilseeds, SNP has been worked upon extensively in last decade. Certain groups preferred whole genome scan over candidate gene approach. In soybean (Zhu et al., 2003; Van et al., 2004; Schmutz et al., 2010) whole genome scan was carried out to find SNP in both coding and non coding regions. On the other hand Jeong and Saghai Maroof (2004) and Shi et al. (2008) worked on candidate genes related to resistance in soybean. Similarly, in Brassica, Trick et al. (2009) and Park et al. (2010) reported SNP present in whole genome while Li et al. (2009) reported SNP markers in candidate genes controlling flowering time and leaf morphological traits. In Arachis, Lopez et al. (2000) and Barkeley et al. (2011) worked on finding SNP in candidate genes delta 12fatty acid desaturase and infatty acid desaturase 2A respectively while Alves et al. (2008) did the same in resistance genes. Bertioli et al. (2009) found SNP in whole genome of Arachis. Xang et al. (2017) worked with 405 oilseed rape cultivars which were genotyped with a 60K Brassica Infinium SNP array in low and high Phosphorus environments. A total of 285 single nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels.
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