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Genes
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Genetic Mapping in Plants
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Genetic Mapping in Plants

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

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 5022

Special Issue Editor

Prof. Dr. José M. Leitão

E-Mail Website
Guest Editor
MED-Mediterranean Institute for Agriculture, Environment and Development, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005‐139 Faro, Portugal
Interests: molecular biology; plant genetics; plant genomics; plant biotechnology; plant breeding; genotyping; epigenetics; plant tissue culture; genetic diversity; molecular markers development; plant disease resistance; marker assisted selection; legumes; linkage analysis; experimental mutagenesis; DNA repair; plant cytogenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic mapping, a research approach conceived one century ago during the juvenile period of the novel science of genetics, is still, today, one of the most powerful methods for identification of genes for which the only available information is their impact in the phenotype.

It is amazing that our predecessors, based on the phenotypic analysis of progenies obtained by controlled crosses, could have identified in eukaryote genomes, the relative order, and in-between genetic distance of biological features relatively well understood today, but at that time absolute black boxes: genes.

Despite the enormous amount of accumulated genomic knowledge and the most recent developments in genomic research, including the impressive improvements in genome sequencing, the establishment of an unequivocal cause–effect relationship between a phenotypic trait and a genomic feature still requires the previous genome location of that feature, either via classical mapping or by genome-wide genetic association studies.

This Special Issue is dedicated to articles reporting the genome location and identification of novel genes that determine qualitative or quantitative plant traits.

Prof. Dr. José M. Leitão
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic mapping of genes of interest
  • genome location of genes of interest
  • genome wide association studies
  • identification of plant QTLs
  • pseudo-testcross
  • genomic libraries
  • next generation sequencing

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Published Papers (2 papers)

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19 pages, 14611 KiB  
Article
Inheritance and Quantitative Trait Loci Mapping of Aromatic Compounds from Clementine (Citrus × clementina Hort. ex Tan.) and Sweet Orange (C. × sinensis (L.) Osb.) Fruit Essential Oils
by Vincent Ferrer, Gilles Costantino, Noémie Paymal, Carole Quinton, Estefania Carrillo Perdomo, Mathieu Paoli, Pierre Mournet, Patrick Ollitrault, Félix Tomi and François Luro
Genes 2023, 14(9), 1800; https://doi.org/10.3390/genes14091800 - 14 Sep 2023
Viewed by 1082
Abstract
Despite their importance in food processing, perfumery and cosmetics, the inheritance of sweet orange aromatic compounds, as well as their yield in the fruit peel, has been little analyzed. In the present study, the segregation of aromatic compounds was studied in an F1 [...] Read more.
Despite their importance in food processing, perfumery and cosmetics, the inheritance of sweet orange aromatic compounds, as well as their yield in the fruit peel, has been little analyzed. In the present study, the segregation of aromatic compounds was studied in an F1 population of 77 hybrids resulting from crosses between clementine and blood sweet orange. Fruit-peel essential oils (PEOs) extracted by hydrodistillation were analyzed by gas chromatography coupled with flame ionization detection. Genotyping by sequencing was performed on the parents and the hybrids. The resulting “clementine × sweet blood orange” genetic map consists of 710 SNP markers distributed in nine linkage groups (LGs), representing the nine citrus chromosomes, and spanning 1054 centimorgans. Twenty quantitative trait loci (QTLs) were identified, explaining between 20.5 and 55.0% of the variance of the major aromatic compounds and PEO yield. The QTLs for monoterpenes and aliphatic aldehydes predominantly colocalized on LGs 5 and 8, as did the two QTLs for PEO yield. The sesquiterpene QTLs were located on LGs 1, 3, 6 and 8. The detection of major QTLs associated with the synthesis of aliphatic aldehydes, known for their strong aromatic properties, open the way for marker-assisted selection. Full article
(This article belongs to the Special Issue Genetic Mapping in Plants)
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Review

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15 pages, 1728 KiB  
Review
k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives
by Benjamin Karikari, Marc-André Lemay and François Belzile
Genes 2023, 14(7), 1439; https://doi.org/10.3390/genes14071439 - 13 Jul 2023
Cited by 3 | Viewed by 3521
Abstract
Genome-wide association studies (GWAS) have allowed the discovery of marker–trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, [...] Read more.
Genome-wide association studies (GWAS) have allowed the discovery of marker–trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation. Full article
(This article belongs to the Special Issue Genetic Mapping in Plants)
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