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Agronomy
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Application of Molecular Marker Technology in Crop Breeding—2nd Edition
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Application of Molecular Marker Technology in Crop Breeding—2nd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 15 December 2024 | Viewed by 7024

Special Issue Editor

Dr. Dilip R. Panthee

E-Mail Website
Guest Editor
Department of Horticultural Science, North Carolina State University, Raleigh, NC 27608, USA
Interests: breeding for fruit quality; differential gene expression analysis; genomic selection; GWAS; molecular breeding; plant breeding; QTL mapping; resistance breeding; stress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The application of molecular markers in crop improvement first started in the 1980s. Initially, it was in the form of hybridization-based molecular markers, which were relatively less popular. As soon as PCR-based molecular markers became available, however, they became widely and easily applicable in several crop plants. Since then, several plant breeding programs have optimized the use of molecular markers associated with various traits, including disease resistance, quality, and abiotic stress tolerance. Still, there are several traits that need to be optimized, and research on that front is ongoing in various parts of the world. With the availability of genome sequences and SNP markers developed from the use of those sequences, high-density molecular linkage maps can be developed, and molecular markers associated with the traits of interest can be identified more precisely. Furthermore, mapping and fine mapping of QTL can be achieved, and eventually, such research can help us to identify the genes associated with the traits of interest. In the proposed Special Issue of Agronomy, we encourage researchers from around the world to publish their groundbreaking work in these areas of QTL mapping and marker analysis in various plant systems in this Special Issue of Agronomy. Papers directly associated with crop plants of economic importance will be given more priority.

Dr. Dilip R. Panthee
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agronomy 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

  • GWAS
  • linkage analysis
  • molecular marker
  • QTL
  • RNA-seq analysis

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Related Special Issue

Published Papers (3 papers)

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Research

18 pages, 1726 KiB  
Article
Genetic Diversity and Genome-Wide Association in Cowpeas (Vigna unguiculata L. Walp)
by Xingbo Wu, Vincent N. Michael, Felipe López-Hernández, Andrés J. Cortés, John B. Morris, Mingli Wang, Shyam Tallury, Max C. Miller II and Matthew W. Blair
Agronomy 2024, 14(5), 961; https://doi.org/10.3390/agronomy14050961 - 2 May 2024
Viewed by 2069
Abstract
Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and [...] Read more.
Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and genome-wide association study (GWAS) results for part of the cowpea core collection of the United States Department of Agriculture (USDA) along with breeding line controls. Included in the analysis were a total of 373 accessions analyzed with 6880 Single Nucleotide Polymorphism (SNP) markers from Genotyping by Sequencing (GBS). Population structure differentiated accessions into two groups irrespective of geographical origin and formed three clusters based on taxa upon phylogenetic analysis. A total of 56 SNPs were significantly associated to nine traits including pod length (25 Quantitative Trait Nucleotides, QTNs), seed anti-oxidant content (7 QTNs), dry pod color (7 QTNs), plant maturity (5 QTNs), flower color (5 QTNs), seed weight (4 QTNs), tolerance to low phosphate (1 QTN), growth habit (1 QTN), and response to rock phosphate (1 QTN) using Bayesian-information, Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Fixed and random model Circulating Probability Unification (FarmCPU) association models. Key genes related to all significant SNPs were identified based on annotations of the cowpea reference genome, including a flavonoid gene controlling flower color (Vigun08g040200.1), a root nodulation regulator for tolerance to low phosphate (Vigun11g168000.1), and numerous genes involved in signaling, biosynthesis, metabolite transport, and abiotic stress. Our results highlight the importance of maintaining public phenotyping databases at USDA and strengthening collaborations for data collection in cowpea to maximize research impacts. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding—2nd Edition)
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17 pages, 4667 KiB  
Article
Selection of Durum Wheat and SSR Markers for Organic Farming in Central Italy Using AMMI Analysis
by Ieva Urbanavičiūtė, Luca Bonfiglioli and Mario A. Pagnotta
Agronomy 2024, 14(3), 458; https://doi.org/10.3390/agronomy14030458 - 26 Feb 2024
Cited by 1 | Viewed by 2340
Abstract
Durum wheat is one of the main crops in the Mediterranean region, which is characterized as the hotspot of climate change, with large year-to-year weather fluctuations. Although chemical input reduction in agriculture is strongly demanded, as well as healthy food, there is still [...] Read more.
Durum wheat is one of the main crops in the Mediterranean region, which is characterized as the hotspot of climate change, with large year-to-year weather fluctuations. Although chemical input reduction in agriculture is strongly demanded, as well as healthy food, there is still a lack of stable and high-yielding crop varieties specifically adapted for organic conditions. This study evaluates the performance of fifteen durum wheat varieties in terms of suitability for organic farming in central Italy and assesses the impact of the genotype–environment interaction (GEI) on productive and quality traits. Variety performance was evaluated in field experiments over four successive seasons. In addition, a genotypic diversity analysis of 38 microsatellites associated with traits important for organic farming was performed. The AMMI (additive main effects and multiplicative interaction) stability analysis revealed that the best and most stable genotype regarding quality traits, such as thousand-kernel weight, protein content, and test weight was the ancient variety, Senatore Cappelli. The most stable and high yield was determined for the Fuego, Iride, and Mv-Pelsodur genotypes. Moreover, SSR markers that could be used for plant breeding, targeting organic farming systems based on molecular markers and GEI results, were identified. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding—2nd Edition)
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14 pages, 1754 KiB  
Article
Microsatellite-Based Genetic Diversity Analysis and Population Structure of Proso Millet (Panicum miliaceum L.) in Kazakhstan
by Meisam Zargar, Elmira Dyussibayeva, Aidyn Orazov, Aiym Zeinullina, Irina Zhirnova, Gulzat Yessenbekova and Aiman Rysbekova
Agronomy 2023, 13(10), 2514; https://doi.org/10.3390/agronomy13102514 - 29 Sep 2023
Cited by 6 | Viewed by 1935
Abstract
Proso millet is an important allotetraploid cereal crop; however, it is the least studied species of the Poaceae family, as it is an under-utilized crop. Genomic resources for proso millet are very limited compared to major crops. An understanding of the genetic relationships [...] Read more.
Proso millet is an important allotetraploid cereal crop; however, it is the least studied species of the Poaceae family, as it is an under-utilized crop. Genomic resources for proso millet are very limited compared to major crops. An understanding of the genetic relationships among germplasm resources is important for future breeding endeavors. In the present study, simplesequence repeat (SSR) markers were employed to assess the polymorphism and genetic diversity of 100 millet accessions from different countries, which were tested in the dry steppe zone conditions of the Akmola region from 2020 to 2022. The use of 20 SSR markers detected a total of 47 alleles, with an average allele number of 2.35 per locus among these proso accessions. Nine of them were polymorphic among the genotypes, which suggests that these SSR markers can be used for genetic studies. The results showed a moderate level of polymorphism information content (PIC) that averaged at 0.424, ranging from 0.125 to 0.795. The markers SSR-67, SSR-82, SSR-85 and SSR-109 showed high PIC values of 0.536, 0.756, 0.795 and 0.758, respectively. Markers SSR 85 and SSR 86 significantly correlated to agronomic traits, such as productive tillering (PT) and grain yield (GY). The genetic structure, UPGMA cluster and PCoA assay indicated that the accessions that originated from Central Asia had higher genetic diversity. Based on structure (K = 3), all the accessions were divided into three groups, where the gene pool that originated from Central Asia wasdetected in all three clusters. Based on a principal component analysis (PCA), the accessions of Central Asian origin were genetically closer to the North Asian group. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding—2nd Edition)
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