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Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition
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Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 8524

Editor

Dr. Ju Kyong Lee

E-Mail Website
Guest Editor
Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
Interests: genetics; molecular breeding science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to invite you to contribute your original research, review articles, or short communications to our Special Issue, “Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition.”

As global agricultural systems face increasing demands for productivity, resilience, and sustainability, the integration of molecular markers into crop breeding has emerged as a powerful tool to accelerate the development of improved crop varieties. This Special Issue aims to bring together recent advances, methodologies, and applications of molecular marker-assisted selection (MAS), genome-wide association studies (GWAS), marker-assisted backcrossing, QTL mapping, and genomic selection in crop improvement programs.

Topics of interest include (but are not limited to) the following:

  • The development and application of molecular markers (SSR, SNP, AFLP, etc.);
  • Marker-assisted selection and backcrossing strategies;
  • Genomic tools for trait discovery and genetic diversity assessment;
  • High-throughput genotyping and phenotyping platforms;
  • Integration of MAS with traditional breeding approaches;
  • Case studies on the successful deployment of marker-assisted technologies in breeding programs;
  • Advances in bioinformatics and data analysis for MAS.

We believe your expertise in this field would make a valuable contribution to this issue. Submissions will undergo a rigorous peer-review process, and selected papers will be published in Plants, a leading journal in the field of plant sciences and crop genetics.

Dr. Ju Kyong Lee
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • crops
  • landrace accession
  • agroecological zone
  • SSR marker
  • genetic diversity
  • population structure
  • UPGMA dendrogram

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Related Special Issue

Published Papers (6 papers)

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Research

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18 pages, 1099 KB  
Article
Genetic Diversity and Marker–Trait Associations in Commercial Cultivars and Weedy Perilla frutescens from South Korea and Japan Based on Morphological Traits and SSR Markers
by Da Hyeon Lee, Jungeun Cho, Hyeon Park, Tae Hyeon Heo and Ju Kyong Lee
Plants 2026, 15(8), 1273; https://doi.org/10.3390/plants15081273 - 21 Apr 2026
Viewed by 475
Abstract
Domestication has profoundly shaped the phenotypic differentiation and genetic architecture of Perilla. However, analyses of the morphological difference between its cultivated and weedy forms across its varieties remains incomplete. This study analyzed morphological variation, genetic diversity, population structure, and marker–trait associations of [...] Read more.
Domestication has profoundly shaped the phenotypic differentiation and genetic architecture of Perilla. However, analyses of the morphological difference between its cultivated and weedy forms across its varieties remains incomplete. This study analyzed morphological variation, genetic diversity, population structure, and marker–trait associations of 45 accessions representing the cultivated and weedy forms of two Perilla varieties (P. frutescens var. frutescens and var. crispa) collected from South Korea and Japan. Analyses of ten qualitative and quantitative agronomic traits revealed clear domestication-related differentiation. Cultivated var. frutescens showed larger and heavier seeds, whereas cultivated var. crispa and the weedy accessions were characterized by longer inflorescences and higher floret numbers but smaller seeds. Strong positive correlations were observed among seed-related traits, particularly between seed size and seed weight (r = 0.932), indicating coordinated selection of seed traits. Genetic diversity analysis using 70 SSR markers identified 330 alleles consistent with domestication bottlenecks in cultivated forms while higher diversity was generally retained in the weedy accessions. Population structure, UPGMA clustering, and principal coordinate analyses broadly differentiated the cultivated and weedy accessions, although partial admixture indicated shared ancestry and historical gene flow. Association mapping using Q-based GLM and Q + K MLM models identified 23 significant marker–trait associations involving 16 SSR markers consistently detected across both models. Several markers were associated with multiple traits, implying pleiotropy or tight genetic linkage. Notably, five SSR markers (KNUPF192, KNUPF202, KNUPF207, KNUPF230, and KNUPF238) may represent potential candidate loci for marker-assisted selection to improve seed-related traits in var. frutescens and leaf-related traits in var. crispa. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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25 pages, 3702 KB  
Article
Seed the Difference: QTL Mapping Reveals Several Major Loci for Seed Size in Cannabis sativa L.
by Stephen Eunice Manansala-Siazon, Paolo Miguel Siazon, Erwin Tandayu, Lennard Garcia-de Heer, Adam Burn, Qi Guo, Jos C. Mieog and Tobias Kretzschmar
Plants 2025, 14(24), 3853; https://doi.org/10.3390/plants14243853 - 17 Dec 2025
Viewed by 1723
Abstract
Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on [...] Read more.
Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on C. sativa cultivation and research throughout most of the 20th century has delayed crop improvement using modern breeding approaches. As a result, genetic loci contributing to key agronomic traits, including with respect to maximizing yield as a seed crop, remain largely unknown. In this study, a feminized segregating F2 mapping population, derived from a tall parent with spacious inflorescences and large seeds and a short-stature parent with compact inflorescences and small seeds, was phenotyped for key seed and agronomic traits related to yield. A mid-density Single Nucleotide Polymorphism (SNP) genotyping panel was used to generate a genetic linkage map of 291.5 cM with 455 SNPs. Quantitative Trait Locus (QTL) mapping identified major loci for hundred-seed weight—qHSW3, 26.59 percent variance explained (PVE), seed volume—qSV1, 33.24 PVE, and plant height—qPH9, 46.99 PVE. Our results provide novel target regions, associated molecular markers, and candidate genes for future breeding efforts to improve C. sativa. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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17 pages, 5052 KB  
Article
Genetic Analysis and Fingerprint Construction for Thick-Skinned Melon (Cucumis melo subsp. melo) Based on InDel Markers
by Dandan Ren, Jinglei Liao, Keyan Zhang, Jiaying Zhang, Jingtao Qu, Guobin Ma and Jufen Li
Plants 2025, 14(24), 3782; https://doi.org/10.3390/plants14243782 - 12 Dec 2025
Cited by 1 | Viewed by 798
Abstract
Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’ is an F1 hybrid derived from a cross between two [...] Read more.
Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’ is an F1 hybrid derived from a cross between two Hami melon inbred lines, ‘M06-1-3’ and ‘M15-3’. This study utilized resequencing data derived from the bi-parents of ‘Dongfangmi No.4’ to identify 557,878 insertion and deletion (InDel) variations across the entire genome. Thirty-nine highly polymorphic InDel markers were screened to conduct a genetic analysis of 40 representative cultivated varieties, with marker MS108 specifically distinguishing ‘Dongfangmi No.4’ from the other 39 cultivated varieties. Genetic analysis revealed a high level of genetic diversity within the population (average observed heterozygosity Ho = 0.313, Shannon index I = 0.528), and polymorphic information content (PIC) analysis indicated that 54% of the markers (21/39) were highly polymorphic. Principal component analysis (PCA) and clustering demonstrated significant genetic differentiation between cantaloupe and Hami melons, as well as between cantaloupe and honeydew. In contrast, the genetic boundaries between Hami melons and honeydew were obscured due to frequent germplasm exchange. Ultimately, seven core InDel markers were selected to construct the DNA fingerprinting map, successfully achieving complete differentiation of 40 varieties. This marker system provides an effective molecular tool for melon variety identification, intellectual property protection, and breeding. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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12 pages, 1833 KB  
Article
Elevated Soybean Seed Oil Phenotype Associated with a Single Nucleotide Polymorphism in GmNFR1α
by Sri Veda Patibandla, Militza Carrero-Colón, Qijian Song, Quilin Qin, Elizabeth Clevinger, Hongyan Zhu, M. A. Saghai Maroof and Karen Hudson
Plants 2025, 14(23), 3676; https://doi.org/10.3390/plants14233676 - 3 Dec 2025
Cited by 1 | Viewed by 960
Abstract
Soybean seed composition, particularly the oil and protein content of the seed, has been a longstanding focus of research due to the economic and nutritional importance of these components for both feed and industrial applications. Through forward genetic screening of a mutagenized population [...] Read more.
Soybean seed composition, particularly the oil and protein content of the seed, has been a longstanding focus of research due to the economic and nutritional importance of these components for both feed and industrial applications. Through forward genetic screening of a mutagenized population derived from the soybean cultivar Williams-82, a mutant line designated PID 17238 was identified for high seed oil content. This phenotype is associated with a decrease in levels of protein with respect to Williams-82. The phenotype was mapped to chromosome 2 to a region near Satt459. Fine mapping and whole-genome resequencing were used to identify the causative mutation. Analysis of the resequencing data within the candidate region uncovered 55 sequence variants. Glyma.02G270800 contained a single nucleotide polymorphism (SNP) within the coding sequence. Glyma.02G270800 encodes a lysin motif (LysM) receptor-like kinase previously reported in the literature as GmNFR1α. Importantly, this locus is allelic to the well-characterized rj1 locus, a recessive mutation known to cause a non-nodulating phenotype in soybean. Nodulation in soybeans, which enables nitrogen fixation, is crucial for protein synthesis in seeds, and the lack of nodulation may explain the lower protein content in PID 17238. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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12 pages, 1087 KB  
Article
Multi-Environment QTL Mapping of Rust Resistance in Faba Bean (Vicia faba L.) to Uromyces viciae-fabae
by Sergio G. Atienza, Amero A. Emeran, Ramadan A. Arafa, Fouad Maalouf, Josefina C. Sillero and Carmen M. Ávila
Plants 2025, 14(18), 2860; https://doi.org/10.3390/plants14182860 - 13 Sep 2025
Viewed by 1789
Abstract
Faba bean rust is one of the major threats to the cultivation of faba beans worldwide. Three genes for rust resistance (Uvf-1, Uvf-2 and Uvf-3) and fifteen marker-trait associations have been identified so far. This study examines the genetic basis [...] Read more.
Faba bean rust is one of the major threats to the cultivation of faba beans worldwide. Three genes for rust resistance (Uvf-1, Uvf-2 and Uvf-3) and fifteen marker-trait associations have been identified so far. This study examines the genetic basis of rust resistance derived from BPL-261, an accessions that exhibits low infection frequency and a long latency period. We constructed a genetic map based on a RIL6 population derived from the BPL-261/Vf-274 cross, which consists of 91 individuals. Subsequent generations were used to evaluate rust resistance in Lattakia (Syria), Kafr El-Sheikh (Egypt) and Córdoba (Spain). A total of six QTLs for resistance were detected on chromosomes II, III, IV and V. Comparative analyses suggest that the QTL located on chromosome V is likely to be associated with Uvf-3. The QTL on chromosome III is close to Uvf-2 but it seems to be a different QTL since the confidence intervals do not overlap. Finally, the other QTLs constitute additional sources of rust resistance in faba beans. Functional analysis of the candidate genes within the confidence intervals suggests the hypothetical involvement of various resistance mechanisms, with salicylic acid playing a significant role but it should be confirmed with further studies. Our results advance understanding of rust resistance in faba bean. Markers identified in this study should be used to develop kompetitive allele-specific PCR (KASP) assays, after their utility has been confirmed in different genetic backgrounds. This will contribute to the development of durable rust-resistant faba bean cultivars. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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Review

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14 pages, 939 KB  
Review
Advancements in Molecular Breeding Techniques for Soybeans
by Ivan Fetisov, Olga Eizikovich, Dominique Charles Diouf, Elena Romanova and Parfait Kezimana
Plants 2026, 15(1), 5; https://doi.org/10.3390/plants15010005 - 19 Dec 2025
Cited by 2 | Viewed by 2104
Abstract
Recent advances in molecular breeding techniques have greatly accelerated the development of improved soybean varieties with enhanced agronomic and nutritional traits. This review summarizes current research on innovative molecular approaches, including marker-assisted selection (MAS), genomic selection (GS), CRISPR/Cas9-mediated gene editing, and RNA interference [...] Read more.
Recent advances in molecular breeding techniques have greatly accelerated the development of improved soybean varieties with enhanced agronomic and nutritional traits. This review summarizes current research on innovative molecular approaches, including marker-assisted selection (MAS), genomic selection (GS), CRISPR/Cas9-mediated gene editing, and RNA interference (RNAi) for soybean improvement. Marker-assisted selection using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) has facilitated the efficient identification and incorporation of desired traits such as disease resistance, abiotic stress tolerance, and improved seed quality. Genomic selection has improved prediction accuracy for complex quantitative traits such as yield by integrating genome-wide molecular markers with phenotypic data. CRISPR/Cas9 technology has enabled precise genetic modification, resulting in soybeans with improved oil composition, increased isoflavone content and resistance to biotic stresses. RNA interference has successfully modulated gene expression to optimize nutritional properties and stress responses. These molecular breeding approaches overcome the limitations of traditional methods by shortening the breeding cycle and allowing for simultaneous improvement of multiple traits. The integration of these complementary techniques offers promising avenues for developing climate-resilient, high-yielding soybean varieties with improved nutritional profiles to address global food security challenges. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding—2nd Edition)
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