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Applications of DNA Markers in Plant Science

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 30008

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Prof. Dr. Klaudija Carović-Stanko

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1. University of Zagreb Faculty of Agriculture, Department of Plant Biodiversity, 10000 Zagreb, Croatia
2. Center of Excellence for Biodiversity and Molecular Plant Breeding, 10000 Zagreb, Croatia
Interests: seed science and technology; DNA marker techniques for assessment of genetic diversity; plant genetic resources conservation; medicinal and aromatic plants
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Dear Colleagues,

The progress made in DNA marker technologies has been tremendous in the past few decades. It has found application in phylogenetics, biodiversity analysis, and molecular plant breeding, reshaping our knowledge of plant genetics. Different types of DNA marker systems (RFLPs, RAPDs, SSRs, AFLPs, SNPs) have been successfully applied in various plants. Although there are still substantial differences in the development of procedures across the plant species.

This Special Issue invites original research papers and reviews focusing on the application of DNA markers in plant science. Despite the astonishing amount of existing information, there are still challenges in this exciting field. Special focus will be given to novel approaches for plant population analysis, characterization of plant genetic resources, and molecular plant breeding, but other related research is also welcomed.

Prof. Klaudija Carović-Stanko
Guest Editor

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Keywords

Biodiversity
Genome-wide association studies (GWAS)
Genotyping platforms
Marker-assisted selection
Molecular ecology
Molecular plant breeding
Plant genetic resources conservation
Quantitative trait locus (QTL) analysis

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Published Papers (9 papers)

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20 pages, 2969 KiB

Open AccessArticle

Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification

by Rahul Jamdade, Maulik Upadhyay, Khawla Al Shaer, Eman Al Harthi, Mariam Al Sallani, Mariam Al Jasmi and Asma Al Ketbi

Plants 2021, 10(12), 2741; https://doi.org/10.3390/plants10122741 - 13 Dec 2021

Cited by 8 | Viewed by 3023

Abstract

Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers’ reliability. Our analysis suggests that from the unsupervised method, TaxonDNA’s All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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18 pages, 4901 KiB

Open AccessArticle

Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars

by Lidia S. Samarina, Valentina I. Malyarovskaya, Stefanie Reim, Lyudmila G. Yakushina, Natalia G. Koninskaya, Kristina V. Klemeshova, Ruset M. Shkhalakhova, Alexandra O. Matskiv, Ekaterina S. Shurkina, Tatiana Y. Gabueva, Natalia A. Slepchenko and Alexey V. Ryndin

Plants 2021, 10(7), 1302; https://doi.org/10.3390/plants10071302 - 27 Jun 2021

Cited by 14 | Viewed by 3294

Abstract

Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20–50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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23 pages, 51527 KiB

Open AccessArticle

Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

by Monika Vidak, Zlatko Šatović, Zlatko Liber, Martina Grdiša, Jerko Gunjača, Andrzej Kilian and Klaudija Carović-Stanko

Plants 2021, 10(4), 665; https://doi.org/10.3390/plants10040665 - 30 Mar 2021

Cited by 12 | Viewed by 3422

Abstract

Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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17 pages, 5430 KiB

Open AccessArticle

Development and Application of Gene-Specific Markers for Tomato Yellow Leaf Curl Virus Resistance in Both Field and Artificial Infections

by Jang Hee Lee, Dae Jun Chung, Je Min Lee and Inhwa Yeam

Plants 2021, 10(1), 9; https://doi.org/10.3390/plants10010009 - 23 Dec 2020

Cited by 10 | Viewed by 4242

Abstract

Tomato yellow leaf curl virus (TYLCV) is a disease that is damaging to tomato production worldwide. Resistance to TYLCV has been intensively investigated, and single resistance genes such as Ty-1 have been widely deployed in breeding programs. However, resistance-breaking incidences are frequently reported, and achieving durable resistance against TYLCV in the field is important. In this study, gene-specific markers for Ty-2 and ty-5, and closely-linked markers for Ty-4 were developed and applied to distinguish TYLCV resistance in various tomato genotypes. Quantitative infectivity assays using both natural infection in the field and artificial inoculation utilizing infectious TYLCV clones in a growth chamber were optimized and performed to investigate the individual and cumulative levels of resistance. We confirmed that Ty-2 could also be an effective source of resistance for TYLCV control, together with Ty-1. Improvement of resistance as a result of gene-pyramiding was speculated, and breeding lines including both Ty-1 and Ty-2 showed the strongest resistance in both field and artificial infections. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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14 pages, 2049 KiB

Open AccessArticle

Search for New Allergens in Lolium perenne Pollen Growing under Different Air Pollution Conditions by Comparative Transcriptome Study

by Jose Antonio Lucas, Enrique Gutierrez-Albanchez, Teresa Alfaya, Francisco Feo Brito and Francisco Javier Gutierrez-Mañero

Plants 2020, 9(11), 1507; https://doi.org/10.3390/plants9111507 - 6 Nov 2020

Cited by 3 | Viewed by 2408

Abstract

The relationship between air pollution and the allergenic capacity of pollen is widely accepted, with allergenicity being directly related to air pollution. To our knowledge, this is the first study comparing the differential expression of Lolium perenne pollen genes by RNAseq, in two wild populations with different levels of air pollution. The objective is to search for proteins that are expressed differentially in both situations and to establish a relationship with increased allergenic capacity. Two populations of L. perenne (Madrid and Ciudad Real) have been studied in two consecutive years, under the rationale that overexpressed genes in Madrid, with higher levels of NO₂ and SO₂, could be a cause for their greater allergenic capacity. Heat shock proteins (HSP), glycoside hydrolases, proteins with leucin-rich repeat motifs, and proteins with EF-HAND motifs were consistently overexpressed in Madrid pollen in the two years studied. Interestingly, some genes were overexpressed only in one of the years studied, such as pectinesterases in the first year, and lipid transfer proteins (LTPs) and thaumatin in the second. Despite the fact that the potential of all these proteins in relation to possible allergies has been reported, this is the first time they are cited as possible allergens of L. perenne. The results found can contribute decisively to the knowledge of the allergens of L. perenne and their relationship with atmospheric pollution, and to the development of much more effective vaccines. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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15 pages, 1606 KiB

Open AccessArticle

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

by Min Fan, Yike Gao, Zhiping Wu and Qixiang Zhang

Plants 2020, 9(10), 1342; https://doi.org/10.3390/plants9101342 - 11 Oct 2020

Cited by 9 | Viewed by 2672

Abstract

Chrysanthemums (Chrysanthemum morifolium Ramat.) are famous ornamental crops with high medicinal and industrial values. The inflorescence and leaf traits are key factors that affect the yield and quality of chrysanthemum. However, the genetic improvement of those traits is slow within chrysanthemum because of its hexaploidy, high heterozygosity and enormous genome. To study the genetic control of the important traits and facilitate marker-assisted selection (MAS) in chrysanthemum, it is desirable to populate the genetic maps with an abundance of transferrable markers such as microsatellites (SSRs). A genetic map was constructed with expressed sequence tag–simple sequence repeat (EST-SSR) markers in an F₁ progeny of 192 offspring. A total of 1000 alleles were generated from 223 EST-SSR primer pairs. The preliminary maternal and paternal maps consisted of 265 marker alleles arranged into 49 and 53 linkage groups (LGs), respectively. The recombined parental maps covered 906.3 and 970.1 cM of the genome, respectively. Finally, 264 polymorphic loci were allocated to nine LGs. The integrated map spanned 954.5 cM in length with an average genetic distance of 3.6 cM between two neighbouring loci. Quantitative trait loci (QTLs) analysis was performed using the integrated map for inflorescence diameter (ID), central disc flower diameter (CDFD), number of whorls of ray florets (NWRF), number of ray florets (NRF), number of disc florets (NDF), number of florets (NF), ray floret length (RFL), ray floret width (RFW), ray floret length/width (RFL/W), leaf length (LL), leaf width (LW) and leaf length/width (LL/W). Overall, 36 (21 major) QTLs were identified. The successful mapping of inflorescence and leaf traits QTL demonstrated the utility of the new integrated linkage map. This study is the first report of a genetic map based on EST-SSR markers in chrysanthemum. The EST-SSR markers, genetic map and QTLs reported here could be valuable resources in implementing MAS for chrysanthemums in breeding programs. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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21 pages, 3847 KiB

Open AccessArticle

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

by Kai Jiang, Li-Yuan Miao, Zheng-Wei Wang, Zi-Yi Ni, Chao Hu, Xin-Hua Zeng and Wei-Chang Huang

Plants 2020, 9(10), 1332; https://doi.org/10.3390/plants9101332 - 9 Oct 2020

Cited by 9 | Viewed by 2841

Abstract

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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19 pages, 6074 KiB

Open AccessArticle

The Influence of a Seedling Recruitment Strategy and a Clonal Architecture on a Spatial Genetic Structure of a Salvia brachyodon (Lamiaceae) Population

by Ivan Radosavljević, Oleg Antonić, Dario Hruševar, Josip Križan, Zlatko Satovic, Doroteja Turković and Zlatko Liber

Plants 2020, 9(7), 828; https://doi.org/10.3390/plants9070828 - 30 Jun 2020

Cited by 6 | Viewed by 3517

Abstract

By performing a high-resolution spatial-genetic analysis of a partially clonal Salvia brachyodon population, we elucidated its clonal architecture and seedling recruitment strategy. The sampling of the entire population was based on a 1 × 1 m grid and each sampled individual was genotyped. Population-genetic statistics were combined with geospatial analyses. On the population level, the presence of both sexual and clonal reproduction and repeated seedling recruitment as the prevailing strategy of new genets establishment were confirmed. On the patch level, a phalanx clonal architecture was detected. A significant negative correlation between patches’ sizes and genotypic richness was observed as young plants were not identified within existing patches of large genets but almost exclusively in surrounding areas. The erosion of the genetic variability of older patches is likely caused by the inter-genet competition and resulting selection or by a random die-off of individual genets accompanied by the absence of new seedlings establishment. This study contributes to our understanding of how clonal architecture and seedling recruitment strategies can shape the spatial-genetic structure of a partially clonal population and lays the foundation for the future research of the influence of the population’s clonal organization on its sexual reproduction. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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22 pages, 1524 KiB

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Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat

by Min Tu and Yin Li

Plants 2020, 9(12), 1631; https://doi.org/10.3390/plants9121631 - 24 Nov 2020

Cited by 19 | Viewed by 2810

Abstract

Kernel hardness is one of the most important single traits of wheat seed. It classifies wheat cultivars, determines milling quality and affects many end-use qualities. Starch granule surfaces, polar lipids, storage protein matrices and Puroindolines potentially form a four-way interaction that controls wheat kernel hardness. As a genetic factor, Puroindoline polymorphism explains over 60% of the variation in kernel hardness. However, genetic factors other than Puroindolines remain to be exploited. Over the past two decades, efforts using population genetics have been increasing, and numerous kernel hardness-associated quantitative trait loci (QTLs) have been identified on almost every chromosome in wheat. Here, we summarize the state of the art for mapping kernel hardness. We emphasize that these steps in progress have benefitted from (1) the standardized methods for measuring kernel hardness, (2) the use of the appropriate germplasm and mapping population, and (3) the improvements in genotyping methods. Recently, abundant genomic resources have become available in wheat and related Triticeae species, including the high-quality reference genomes and advanced genotyping technologies. Finally, we provide perspectives on future research directions that will enhance our understanding of kernel hardness through the identification of multiple QTLs and will address challenges involved in fine-tuning kernel hardness and, consequently, food properties. Full article

(This article belongs to the Special Issue Applications of DNA Markers in Plant Science)

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