DNA Barcoding and Its Applications in Horticultural Crops
Deepu Mathew, DNA Barcoding and its applications in Horticultural crops. In: Peter, K.V. (Ed.), Biotechnology in Horticulture: Methods and Applications, New India Publishing Agency, New Delhi, (ISBN: 9789381450918), pp.25-50. doi: 10.5281/zenodo.836319, 2013
26 Pages Posted: 11 Jun 2020
Date Written: June 10, 2013
DNA bar-coding is a supplementary tool in plant, insect and microbial systematics. In general the chloroplast and mitochondrial genic loci are used for DNA bar-coding. There are three distinct advantages of using plastid DNA in bar-coding:
(i) The locus is maternally inherited. Since there will be no recombination, the mutations resulted during the evolution will be accumulated and the evolutionary history and phylogenetic relations will be better represented.
(ii) The locus will be always homozygous condition. So during sequence analysis, there will be no question as which nucleotide to be considered at heterozygous SNPs
(iii) The genes will be devoid of introns.
The entire regions sequenced on a gene will be representing the protein coding regions and hence the annotation and analysis will be easier.
This chapter details the DNA bar-coding procedures starting from the selection of loci in plants. In general, the genes used in angiosperms are matK, rpoC1, rpoB, accD, YCF5 and ndhJ whereas in non-angiosperms matK, rpoC1, rpoB, accD, and ndhJ are used (http://www.rbgkew.org.uk/barcoding/index.html). The DNA bar-code in animals consists of a 648 bp region 58-705 from the 5’-end of the CoI gene using the mouse mitochondrial genome as a reference. The list of primer combinations for each locus is given.Additionally, the procedure for sequence analysis and submission to BOLD Systems are also described.
Keywords: Plant Biotechnology, Plant Molecular Biology, Plant Systematics, Taxonomy, Molecular Systematics, Bar-codes
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