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Molecular Markers in Salvia L.: Past, Present and Future

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Salvia Biotechnology

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 on DMs 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.

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Abbreviations

2b-RAD-Seq:

Type IIB restriction enzyme digestion restriction site associated DNA sequencing

2-D PAGE:

Two-dimensional polyacrylamide gel electrophoresis

6-PGD:

6-phosphogluconate dehydrogenase

AAT:

Aspartate aminotransferase

ABI:

Applied biosystem instruments

ABS:

Amplicon based sequencing

AFLP:

Amplified fragment length polymorphism

AMP:

Adenosine monophosphate

AMP-PCR:

Anchored microsatellite-primed PCR

AP-PCR:

Arbitrarily primed PCR

APS:

Adenosine-5′-phosphosulfate

ASB:

Allele-specific blocker

ASP:

Allele-specific primer

AS-PCR:

Allele-specific PCR

ASSRs:

Anchored simple sequence repeats

ATP:

Adenosine triphosphate

BEAMing:

Beads, emulsions, amplification and magnetics-based cloning

bPCR:

Bridge PCR

BSA:

Bulked segregant analysis

CAPS:

Cleaved amplified polymorphic sequence

CBD:

CAAT box-derived marker

CCD:

Charge-coupled device

CDDP:

Conserved DNA-derived polymorphism

cDNA:

Complementary deoxyribonucleic acid

CE:

Capillary electrophoresis

CFLP:

Cleavase fragment length polymorphism

CMOS:

Complementary metal-oxide-semiconductor

CNV:

Copy numbers variation

CoRAP:

Conserved region amplification polymorphism

COS:

Conserved orthologous set

cPAL:

Combinatorial probe-anchor ligation

CRISPR/Cas9:

Clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9

CRoPS:

Complexity reduction of polymorphic sequences

D/TGGE:

Denaturing/temperature gradient gel electrophoresis

DAF:

DNA amplification fingerprinting

DAMD:

Directed amplification of minisatellite DNA

DAMD-PCR:

Directed amplification of minisatellite DNA-PCR

DArT:

Diversity array technology

dATP:

Deoxyadenosine triphosphate

dATPαS:

Deoxyadenosine α-thiotriphosphate

dCAPS:

Derived cleaved amplified polymorphic sequence

dCTP:

Deoxycytidine triphosphate

ddNTPs:

Dideoxynucleotide triphosphates

ddRAD:

Double-digest restriction site-associated DNA

ddRAD-seq:

Double digestion restriction site associated DNA sequencing

DFDMs:

Direct functional DNA markers

DGGE:

Denaturing gradient gel electrophoresis

dGTP:

Deoxyguanosine triphosphate

dHPLC:

Denaturing high-performance liquid chromatography

DMs:

DNA markers

DNA:

Deoxyribonucleic acid

DNBS:

DNA nanoball sequencing

dNTPs:

Deoxyribonucleotide triphosphates

dRAMPs:

Digested random amplified microsatellite polymorphism markers

dsDNA:

Double-stranded DNA

dTTP:

Deoxythymidine triphosphate

dXTP:

Deoxynucleoside triphosphate

EDTA:

Ethylenediaminetetraacetic acid

ELIDA:

Enzymatic luminometric inorganic pyrophosphate detection assay

emPCR:

Emulsion PCR

eSSRs:

Expressed simple sequence repeats

EST:

Expressed sequence tag

EST-SSRs:

Expressed sequence tag based simple sequence repeat markers

ezRAD:

Standard Illumina TruSeq library preparation kits restriction site associated DNA sequencing

FDMs:

Functional DNA markers

FEN:

Flap endonuclease

FGS:

First generation sequencing

FRET:

Fluorescence resonance energy transfer

GAB:

Genomics-assisted breeding

GBS:

Genotyping by sequencing

GC:

Gas chromatography

GS:

Genome sequencer

GT-seq:

Genotyping-in-thousands by sequencing

HGP:

Human genome project

HPLC:

High performance liquid chromatography

HRM:

High resolution melting analysis

IBM:

International business machines

IDH:

Isocitrate dehydrogenase

IFDMs:

Indirect functional DNA markers

IMP:

Inter-MITE polymorphism

InDels:

Insertions/deletions

IRAP:

Inter-retrotransposon amplified polymorphism

iRRL:

Improved reduced-representation librarys

ISA:

Inter-simple sequence repeats amplification

ISSR:

Inter simple sequence repeats

ISTR:

Inverse sequence tagged repeat

ITP:

Intron-targeting polymorphism

ITS:

Internal transcribed spacer

KASP:

Kompetitive allele specific PCR

KASPar:

Competitive allele specific PCR

LTRs:

Long terminal repeats

MAAP:

Multiple arbitrary amplicon profiling

MALDI-TOF MS:

Matrix assisted laser desorption ionization time of flight mass spectrometry

MAS:

Marker-assisted selection

MDH:

Malate dehydrogenase

MEGA-AFLP:

Multiplex-endonuclease genotyping approach amplified fragment length polymorphism

MIPs:

Molecular inversion probes

MITE-AFLP:

Miniature inverted repeat transposable elements-amplified fragment length polymorphism

MITEs:

Miniature inverted repeat transposable elements

MLP:

Major latex-like protein

MNR:

Menadione reductase

MP-PCR:

Microsatellite-primed PCR

MPS:

Massively parallel sequencing

MPSS:

Massively parallel signature sequencing

mRNA:

Messenger RNA

MS:

Mass spectrometry

MSG:

Multiplexed shotgun sequencing

NGS:

Next generation sequencing

NIR:

Near infrared spectroscopy

NMR:

Nuclear magnetic resonance

nsSNP:

Non-synonymous single nucleotide polymorphism

OH:

Hydroxyl

OLA:

Oligonucleotide ligation assay

ONT:

Oxford nanopore technologies

ORF:

Open reading frame

PAGE:

Polyacrylamide gel electrophoresis

paired-end RPLs:

paired-end reduced representation libraries

PAV:

Presence/absence variations

PCR:

Polymerase chain reaction

PCR-RFLP:

Polymerase chain reaction-restriction fragment length polymorphism

pERPLs:

Paired-end reduced representation libraries

Pfu:

DNA polymerase from Pyrococcus furiosus

PGI:

Phosphoglucoisomerase

PGM:

Phosphoglucomutase

PPi:

Pyrophosphate

PTP:

Picotiter plate

qPCR:

Quantitative PCR

QTL:

Quantitative trait loci

RAD:

Restriction site associated DNA

RAD-seq:

Restriction site-associated DNA sequencing

RAMPs:

Random amplified microsatellite polymorphisms

RAPD:

Random amplified polymorphic DNA

RBIP:

Retrotransposon-based insertion polymorphism

rDNA:

Ribosomal DNA

REMAP:

Retrotransposon microsatellite amplified polymorphism

RESTseq:

Restriction fragment sequencing

RFEL:

Restriction fragment end labeling

RFLP:

Restriction fragment length polymorphism

RLGS:

Restriction landmark genome scanning

RNA:

Ribonucleic acid

RNA-seq:

RNA sequencing

RRL:

Reduced-representation library

RRS:

Reduced-representation sequencing

RTEs:

Retrotransposons

RT-PCR:

Reverse transcriptase PCR

SAMPL:

Selective amplification of microsatellite polymorphic loci

SBS:

Sequencing-by-synthesis

SCAR:

Sequence characterized amplified regions

SCoT:

Start codon targeted

SFLA:

Selective fragment length amplification

SFPs:

Single feature polymorphisms

sGBS:

Spiked genotyping-by-sequencing

SGS:

Second generation sequencing

SKDH:

Shikimate dehydrogenase

SkimGBS:

Skim genotyping-by-sequencing

SLAF-Seq:

Specific length amplified fragment sequencing

SMRT:

Single molecule real-time

SMS:

Single molecule sequencing

SNP:

Single nucleotide polymorphism

SOLiD:

Sequencing by oligonucleotide ligation and detection

SPARs:

Single primer amplification reactions

SRAP:

Sequence-related amplified polymorphism

SRFA:

Selective restriction fragment amplification

S-SAP:

Sequence-specific amplification polymorphism

SSCP:

Single-strand conformation polymorphism

ssDNA:

Single-stranded DNA

SSRs:

Simple sequence repeats

STMS:

Sequence-tagged microsatellite site

STRs:

Short tandem repeats

STS:

Sequence tagged sites

synSNP:

Synonymous single nucleotide polymorphism

Taq:

DNA polymerase from Thermus aquaticus

TD:

Transposon display

TDFs:

Transcript-derived fragments

TE:

Transposable element

TE-AFLP:

Three-endonuclease amplified fragment length polymorphism

tGBS-seq:

Tunable genotyping by sequencing

TGGE:

Thermal gradient gel electrophoresis

TGS:

Third generation sequencing

TILLING:

Targeting induced local lesions in genomes

Tm:

Melting temperature

TRAP:

Target region amplification polymorphism

UGMs:

Unigene-derived microsatellites

Vent1:

DNA polymerase from Thermococcus litoralis

VNTRs:

Variable number tandem repeats

WGR:

Whole genome resequencing

WGS:

Whole genome sequencing

ZMW:

Zero-mode waveguide

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Acknowledgements

The authors thank Ph.D. candidates Emine Uygur Gocer and Adnan Aydin for their helps in reference preparation. Finally, we thank our teachers and researchers who contributed and touched our lives.

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Authors and Affiliations

  1. Department of Field Crops, Akdeniz University, 07070, Antalya, Turkey

    Mehmet Karaca

  2. Vocational School of Technical Sciences, Akdeniz University, 07070, Antalya, Turkey

    Ayse Gul Ince

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Correspondence to Mehmet Karaca .

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  1. Laboratory of Applied Biotechnology, The Stephan Angeloff Institute of Microbiology-BAS, Plovdiv, Bulgaria

    Vasil Georgiev

  2. Department of Analytical Chemistry, University of Food Technologies, Plovdiv, Bulgaria

    Atanas Pavlov

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Karaca, M., Ince, A.G. (2017). Molecular Markers in Salvia L.: Past, Present and Future. In: Georgiev, V., Pavlov, A. (eds) Salvia Biotechnology. Springer, Cham. https://doi.org/10.1007/978-3-319-73900-7_9

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