Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences

Lidia Skuza

doi:10.1007/978-1-0716-1799-1_6

Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences

Methods Mol Biol. 2022:2392:83-91. doi: 10.1007/978-1-0716-1799-1_6.

Author

Lidia Skuza^{1

2}

Affiliations

¹ Institute of Biology, University of Szczecin, Szczecin, Poland. lidia.skuza@usz.edu.pl.
² The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland. lidia.skuza@usz.edu.pl.

PMID: 34773616
DOI: 10.1007/978-1-0716-1799-1_6

Abstract

Noncoding regions of the chloroplast (cpDNA) and mitochondrial (mtDNA) genomes are commonly used in plant phylogenetic and population studies. Consensus primers, which are homologous to most coding regions, but amplify variable noncoding regions, are very useful for this purpose. However, high genetic diversity of plants poses a problem in developing molecular methods that require conserved DNA sequences between species.This chapter describes the protocol for designing PCR primers suitable for analysis of closely related plant species. As an example, we used PCR primer design for cpDNA noncoding regions of the rye (Secale).

Keywords: Noncoding sequences; Primer design; Related species; Species identification; cpDNA1; mtDNA.

MeSH terms

Chloroplasts / genetics
DNA, Chloroplast / genetics
DNA, Mitochondrial / genetics
Mitochondria* / genetics
Phylogeny
Plants / genetics
Secale / genetics

Substances

DNA, Chloroplast
DNA, Mitochondrial