Molecular Markers in Plant Genetics and Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (10 June 2023) | Viewed by 4422

Special Issue Editor


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Guest Editor
Department of Biology, IPB University, Bogor 16680, Indonesia
Interests: molecular marker; plant improvement; gene cloning; abiotic stress

Special Issue Information

Dear Colleagues,

Molecular markers have significantly contributed to plant improvement through their application in plant genetics and breeding, facilitating the detection of specific-sequence polymorphisms in DNA among individuals in a population. Since the RLFP marker was invented in 1984 by the English scientist Alec Jeffreys, numerous molecular markers, such as RAPD, AFLP, SSR, and SNP, were developed and used in many areas of plant science. The advances in genomic technology, particularly genome sequencing, have facilitated the discovery and application of SNP markers, the most prefered markers, in plant genetics and plant breeding.  Molecular markers have been applied in plant genetics to assess genetic diversity, probe the gene, construct a genetic map, and identify monogenic and quantitative trait loci (QTL), whereas molecular markers have been applied in marker-assisted breeding (MAB) in plant breeding to perform a genetic selection. The use of molecular markers in MAB can speed up the plant breeding process for several economic crops. However, the application of molecular markers in the integration of identified QTL into a breeding program, especially breeding for quantitative traits, such as yield and tolerant traits to environmental stresses, is still a challenge with slow progress. The Special Issue aims to gather and publish inventions and innovations in new marker development, beyond the existing molecular markers, and their application in plant/crop genetics and breeding.

In this Special Issue, we would like to invite submissions of high-quality original research or review articles on topics related to the development and application of molecular markers in the field of plant/crop genetics and molecular breeding.

Prof. Dr. M. Miftahudin
Guest Editor

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Keywords

  • molecular marker
  • plant genetic
  • breeding
  • mapping
  • QTL
  • GWAS
  • marker-assisted selection

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Published Papers (2 papers)

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Research

10 pages, 854 KiB  
Article
ITS1 Barcode and Phytochemical Analysis by Gas Chromatography–Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru
by Alexandra López-Barrera, Efrén Santos-Ordóñez, Ricardo Pacheco-Coello, Liliana Villao-Uzho, Migdalia Miranda, Yamilet Gutiérrez, Iván Chóez-Guaranda and Segundo Guillermo Ruiz-Reyes
Genes 2023, 14(1), 88; https://doi.org/10.3390/genes14010088 - 28 Dec 2022
Viewed by 2055
Abstract
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be [...] Read more.
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography–mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products. Full article
(This article belongs to the Special Issue Molecular Markers in Plant Genetics and Breeding)
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10 pages, 2510 KiB  
Article
Chromosomal Location of Pm12—A Novel Powdery Mildew Resistance Gene from Avena sterilis
by Tomasz Ociepa and Sylwia Okoń
Genes 2022, 13(12), 2409; https://doi.org/10.3390/genes13122409 - 19 Dec 2022
Cited by 4 | Viewed by 1562
Abstract
Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of [...] Read more.
Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F2 individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F3. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8–111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection. Full article
(This article belongs to the Special Issue Molecular Markers in Plant Genetics and Breeding)
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