Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Abstract

The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species

“…Restriction fragments are generated by combining a rare cutter restriction enzyme (6- to 8-base recognition) and a frequent cutter restriction enzyme (4-base recognition). Under proper conditions, enzyme-specific oligonucleotide adapters (10–30 base pairs) form a double-stranded configuration with ends that anneal to the sticky ends of the respective restriction enzyme sites [ 197 ].…”

“…The first selective primer contains a 5′ section complementary to the adapter and the adjacent rare-cutter restriction site sequence with 3′ selective (1–3 bps) nucleotides extension. The second selective primer also has a 5′ end complementary to the adapter and the frequent-cutter recognition site sequence with an additional 3′ selective nucleotides (1–3 bps) extension [ 197 ]. Thus, adjusting the number of selective nucleotides is an essential step toward fingerprints with a manageable number of fragments.…”

Development of Superior Fibre Quality Upland Cotton Cultivar Series ‘Ravnaq’ Using Marker-Assisted Selection

“…The molecular markers, based on the differences in the genetic material (DNA) sequence and closely located by a trait of interest, have evolved because of availability genetic sequence data. Molecular markers vary on types of genetic structure of DNA sequence and detection methods used to generate and record the polymorphisms between genotypes of interest ( Collard et al, 2005 ; Amiteye., 2021 ). DNA markers associated with genomic regions of interest allow breeders to select plants early stage of plant growth based on a marker genotype rather than a phenotype that may get expressed later in plant vegetation.…”

Analysis of Biochemical and Genetic Variability of Pleurotus ostreatus Based on the β-Glucans and CDDP Markers

“…When analyzing the apple CDDP polymorphism, some primer combinations generated identical amplification profiles [ 35 ] such as in the case of our study. CDDP-based fingerprinting was reported to be applicable in the genetic diversity description as well as for germplasm conservation [ 49 ].…”