Molecular markers in Salvia L.: Past, present and future

Abstract

Sage (Salvia L.) is one of the largest genera in the family Lamiaceae. Species in the genus are used to preserve foods and a spice for flavoring, ornamental plants in parks and gardens. In addition, several species of this genus are utilized in medicine and fragrance industries. The utilization of molecular markers in Salvia lags behind many other plant species. Molecular markers are proteins/isozymes, secondary metabolites, deoxyribonucleic acid or ribonucleic acid (DNA/RNA) sequences that could be thought as signs or marks differentiation one locus or an individual from others. DNA markers (DMs) define the location of traits, genes or indicate differences within and between genomes of individuals. The earlier application of DMs was the fingerprinting studies and later onDMs were extensively used in plant genetic mapping and gene identification studies. Currently DMs are routinely used in plant variety identification, protection, conservation, genetic stock development, marker-assisted breeding, association and ecological studies. Genotyping by sequencing (GBS), high-throughput marker systems based on next generation sequencing (NGS), makes DMs more effective. Future technologies of molecular markers would not only detect and locate the genome-wide genetic differences at the single nucleotide level, but also will detect the epigenetic differences in the whole genome. DMs will be extensively used in genome mapping and genome selection research in next generation breeding studies. In this chapter, the technical aspects, types and principles of traditional and NGS based DMs used in plant research are briefly introduced. DMs are technically classified as traditional PCR-based, hybridization-based, PCR-restriction enzyme based, PCR-hybridization based and NGS-based GBS markers. DMs are also classified as genetic and genic (functional) markers. Furthermore, DMs could be classified as low-throughput and high-throughput markers. In some other resources, molecular markers are classified as the first, second, third, fourth and next generation marker systems. DMs could be classified as nuclear, plastid (chloroplast), mitochondrial markers, or in silico based markers. In this chapter, DMs are reclassified based on their technical principles and will be revisited emphasizing on their use in Salvia. This chapter also deals with genome-wide genetic markers and molecular markers for secondary metabolites.