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Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 January 2025 | Viewed by 2126

Special Issue Editor

Dr. Luigi De Masi

E-Mail Website
Guest Editor
National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Università n. 133, 80055 Portici, Italy
Interests: plant agrobiodiversity; genetic and chemical variability; plant genetic resources; molecular characterization; biomolecular resources; DNA-based molecular markers; biosequences; DNA polymorphisms; bioinformatics; protein function prediction; nutrition and health; natural products; secondary metabolites; bioactive molecules; functional foods and nutraceuticals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular marker technology (MMT) comprises a keystone for modern geneticists and molecular biologists. Since its introduction, MMT has been commonly used for the analysis of genome architecture and polymorphisms in plants, greatly improving our ability to characterize genetic variation. MMT has also revolutionized plant breeding, leading to gene mapping and marker-assisted selection (MAS). MMT can allow for the identification of specific chromosomal regions associated with genes for traits of interest. Then, this information is exploited to transfer quality traits to improved varieties via MAS programs.

DNA polymorphisms have huge potential to detect evolutionary and genetic relationships between and within plant species, and can be useful in conserving biodiversity in natural and domesticated plant populations. Today more than ever, plant biodiversity has a key role in maintaining ecosystemic services and sustainable productions, guaranteeing food security, and increasing resistance and resilience to the global climate change and to invasive/native biotic stresses. In the near future, MMT represents a powerful tool available to perform molecular characterization of natural populations and germplasm collections so that potentially useful genes, new alleles, and genotypes (above all if endangered and rare) can be properly preserved from genetic erosion and exploited by the next generations.

Therefore, DNA polymorphism detection is of paramount importance for conducting natural variation studies and breeding. MMT offers a robust characterization system to increase our knowledge about plant biodiversity, the strength of which comes from the fact it is not influenced by environmental or developmental factors. MMT is mainly based on PCR applications for the detection of polymorphic DNA in plant species of agricultural or ecological interest. Nowadays, there is a wide availability of different types of DNA markers. However, with the aim of accelerating the discovery of DNA polymorphisms, more research should be carried out through the latest technologies, such as next-generation sequencing (NGS), to thoroughly analyse the genetic diversity of natural and cultivated plant species at the highest resolution possible. Indeed, bioinformatic analysis of genome sequences is revealing the impact of DNA polymorphisms on gene function, on the phenotype, and on evolutionary processes in plants.

All this considered, we would like to focus on the discovery, current methodologies, advantages, challenges, and applications of DNA polymorphisms as molecular markers. Reports on bioinformatics tools and biosequence databases are also welcomed. Thus, the aim of this Special Issue is to present relevant studies and recent progress across all aspects of plant biodiversity as seen through the lens of MMT.

Dr. Luigi De Masi
Guest Editor

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • plant biodiversity
  • plant genetic resources
  • genetic variability
  • molecular characterization
  • biomolecular resources
  • DNA-based molecular markers
  • DNA sequencing
  • next generation sequencing
  • biosequences
  • DNA polymorphisms
  • bioinformatics

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Published Papers (2 papers)

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Research

16 pages, 1678 KiB  
Article
MassARRAY and SABER Analyses of SNPs in Embryo DNA Reveal the Abscission of Self-Fertilised Progeny during Fruit Development of Macadamia (Macadamia integrifolia Maiden & Betche)
by Anushika L. De Silva, Wiebke Kämper, Steven M. Ogbourne, Joel Nichols, Jack W. L. Royle, Trent Peters, David Hawkes, Shahla Hosseini Bai, Helen M. Wallace and Stephen J. Trueman
Int. J. Mol. Sci. 2024, 25(12), 6419; https://doi.org/10.3390/ijms25126419 - 11 Jun 2024
Viewed by 612
Abstract
Yield in many crops is affected by abscission during the early stages of fruitlet development. The reasons for fruitlet abscission are often unclear but they may include genetic factors because, in some crops, self-pollinated fruitlets are more likely to abscise than cross-pollinated fruitlets. [...] Read more.
Yield in many crops is affected by abscission during the early stages of fruitlet development. The reasons for fruitlet abscission are often unclear but they may include genetic factors because, in some crops, self-pollinated fruitlets are more likely to abscise than cross-pollinated fruitlets. Pollen parentage can also affect final fruit size and fruit quality. Here, we aimed to understand the effects of pollen parentage on fruitlet retention and nut quality in orchards of macadamia (Macadamia integrifolia Maiden & Betche). We identified the pollen parent of macadamia ‘cultivar ‘816’ embryos by analysing single nucleotide polymorphisms (SNPs) in their DNA using customised MassARRAY and Single Allele Base Extension Reaction (SABER) methods. This allowed us to determine the proportions of self-fertilised and cross-fertilised progeny during premature fruit drop at 6 weeks and 10 weeks after peak anthesis, as well as at nut maturity. We determined how pollen parentage affected nut-in-shell (NIS) mass, kernel mass, kernel recovery, and oil concentration. Macadamia trees retained cross-fertilised fruitlets rather than self-fertilised fruitlets. The percentage of progeny that were cross-fertilised increased from 6% at 6 weeks after peak anthesis to 97% at nut maturity, with each tree producing on average 22 self-fertilised nuts and 881 cross-fertilised nuts. Three of the four cross-pollen parents provided fruit with significantly higher NIS mass, kernel mass, or kernel recovery than the few remaining self-fertilised fruit. Fruit that were cross-fertilised by ‘842’, ‘A4’, or ‘A203’ had 16–29% higher NIS mass and 24–44% higher kernel mass than self-fertilised fruit. Nuts that were cross-fertilised by ‘A4’ or ‘A203’ also had 5% or 6% higher kernel recovery, worth approximately $US460–540 more per ton for growers than self-fertilised nuts. The highly selective abscission of self-fertilised fruitlets and the lower nut quality of self-fertilised fruit highlight the critical importance of cross-pollination for macadamia productivity. Full article
(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)
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18 pages, 3646 KiB  
Article
Development of Genome-Wide Intron Length Polymorphism (ILP) Markers in Tea Plant (Camellia sinensis) and Related Applications for Genetics Research
by Yuan Shen, Xiaoying He, Feng Zu, Xiaoxia Huang, Shihua Yin, Lifei Wang, Fang Geng and Xiaomao Cheng
Int. J. Mol. Sci. 2024, 25(6), 3241; https://doi.org/10.3390/ijms25063241 - 13 Mar 2024
Viewed by 938
Abstract
The market value of tea is largely dependent on the tea species and cultivar. Therefore, it is important to develop efficient molecular markers covering the entire tea genome that can be used for the identification of tea varieties, marker-assisted breeding, and mapping important [...] Read more.
The market value of tea is largely dependent on the tea species and cultivar. Therefore, it is important to develop efficient molecular markers covering the entire tea genome that can be used for the identification of tea varieties, marker-assisted breeding, and mapping important quantitative trait loci for beneficial traits. In this study, genome-wide molecular markers based on intron length polymorphism (ILP) were developed for tea trees. A total of 479, 1393, and 1342 tea ILP markers were identified using the PCR method in silico from the ‘Shuchazao’ scaffold genome, the chromosome-level genome of ‘Longjing 43’, and the ancient tea DASZ chromosome-level genome, respectively. A total of 230 tea ILP markers were used to amplify six tea tree species. Among these, 213 pairs of primers successfully characterize products in all six species, with 112 primer pairs exhibiting polymorphism. The polymorphism rate of primer pairs increased with the improvement in reference genome assembly quality level. The cross-species transferability analysis of 35 primer pairs of tea ILP markers showed an average amplification rate of 85.17% through 11 species in 6 families, with high transferability in Camellia reticulata and tobacco. We also used 40 pairs of tea ILP primers to evaluate the genetic diversity and population structure of C. tetracocca with 176 plants from Puan County, Guizhou Province, China. These genome-wide markers will be a valuable resource for genetic diversity analysis, marker-assisted breeding, and variety identification in tea, providing important information for the tea industry. Full article
(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)
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