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Molecular Marker-Assisted Technologies for Crop Breeding
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Molecular Marker-Assisted Technologies for Crop Breeding

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 13008

Special Issue 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 Issue Information

Dear Colleagues,

Maize is among leading global cereals, encompassing all agroecological zones of South Sudan; however, farmers’ fields yield very low amounts, which can only be accredited to their dependency on undeveloped varieties. When it comes to maize, small-scale farmers in South Sudan practice subsistence agriculture. In the current study, the genetic diversity and population structure were investigated among 37 South Sudan landrace maize accessions collected from farmers’ fields using 27 SSR markers. A total of (200) alleles was revealed with an average of (3.0) alleles per locus, ranging from 7.4 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91, with an average of (0.35). High PIC values were identified with a mean of 0.69, which showed the informativeness of the chosen SSR loci. A genetic structure analysis revealed a moderate genetic differentiation of 0.16 within maize populations with a fixation index (Fst), while a very high genetic differentiation of 0.37 mean Fst was recorded among a group of populations in three regions. The analysis of the unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with a 43% genetic similarity. The clustering pattern of maize accessions was comparatively consistent with their collection areas. The findings of this study can provide maize breeders with a superior understanding of maize diversification, as well as the reservation of genetic resources to be used in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.

Dr. Ju Kyong Lee
Guest Editor

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Keywords

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

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Published Papers (7 papers)

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Research

11 pages, 1201 KiB  
Communication
Peanut Genotypes with Reduced Content of Immunogenic Proteins by Breeding, Biotechnology, and Management: Prospects and Challenges
by Tariq Alam and Sachin Rustgi
Plants 2025, 14(4), 626; https://doi.org/10.3390/plants14040626 - 19 Feb 2025
Viewed by 852
Abstract
Peanut allergies affect millions of people worldwide, often causing life-threatening reactions and necessitating strict avoidance. Recent advancements in oral immunotherapy, such as Palforzia™, and IgE-mediated treatments (e.g., Xolair), have improved care options; however, their high costs limit accessibility and widespread utility. To address [...] Read more.
Peanut allergies affect millions of people worldwide, often causing life-threatening reactions and necessitating strict avoidance. Recent advancements in oral immunotherapy, such as Palforzia™, and IgE-mediated treatments (e.g., Xolair), have improved care options; however, their high costs limit accessibility and widespread utility. To address these challenges, researchers are employing conventional breeding and advanced molecular tools, such as CRISPR editing, to develop peanut lines with reduced levels of major allergenic proteins (Ara h1, Ara h2, Ara h3, and Ara h6). These reduced-immunogenicity genotypes retain their agronomic viability, flavor, and nutritional quality to some extent, offering the potential for cost-effective oral immunotherapy and safe food options for use in public spaces by non-allergic individuals. Rigorous evaluation, including immunological assays and human feeding trials, is essential to confirm their effectiveness in reducing allergic reactions. Adoption will depend on the establishment of clear regulatory guidelines, stakeholder education, and transparent communication of the benefits and risks. With sustained research, public trust, and supportive policies, reduced-immunogenicity peanuts could substantially lower the global burden of peanut allergies. This communication examined the impact of peanut allergies worldwide and explored strategies to develop peanut genotypes with reduced allergen content, including conventional breeding and advanced genetic engineering. It also addressed the challenges associated with these approaches, such as policy and regulatory hurdles, and outlined key requirements for their successful adoption by farmers and consumers. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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12 pages, 1688 KiB  
Article
Development and Validation of Multiplex-PCR Assay for β-Carotene hydroxylase and γ-Tocopherol methyl transferase Genes Governing Enhanced Multivitamins in Maize for Its Application in Genomics-Assisted Breeding
by Munegowda Manoj Gowda, Vignesh Muthusamy, Rashmi Chhabra, Hriipulou Duo, Saikat Pal, Nisrita Gain, Ashvinkumar Katral, Ravindra K. Kasana, Rajkumar U. Zunjare and Firoz Hossain
Plants 2025, 14(1), 142; https://doi.org/10.3390/plants14010142 - 6 Jan 2025
Viewed by 893
Abstract
Traditional maize possesses low concentrations of provitamin-A and vitamin-E, leading to various health concerns. Mutant alleles of crtRB1 and vte4 that enhance β-carotene (provitamin-A) and α-tocopherol (vitamin-E), respectively, in maize kernels have been explored in several biofortification programs. For genetic improvement of these [...] Read more.
Traditional maize possesses low concentrations of provitamin-A and vitamin-E, leading to various health concerns. Mutant alleles of crtRB1 and vte4 that enhance β-carotene (provitamin-A) and α-tocopherol (vitamin-E), respectively, in maize kernels have been explored in several biofortification programs. For genetic improvement of these target nutrients, uniplex-PCR assays are routinely used in marker-assisted selection. However, due to back-to-back breeding seasons, the time required for genotyping individually for each target gene in large backcross populations becomes a constraint for advancing the generations. Additionally, multiple PCR assays for various genes increase the required costs and resources. Here, we aimed to develop a multiplex-PCR assay to simultaneously identify different allelic forms of crtRB1 and vte4 genes and validate them in a backcross-based segregating population. The PCR assay was carried out using newly developed primers for crtRB1 and a gene-specific primer for vte4. The uniplex-PCR assay was standardized for selected primer pairs in the BC1F1 population segregating for crtRB1 and vte4 genes. Subsequently, a multiplex-PCR assay for crtRB1 and vte4 genes was developed and employed for genotyping in the BC1F1 population. The assay differentiated among four possible genotypic classes, namely crtRB1+crtRB1/vte4+vte4, crtRB1crtRB1/vte4+vte4, crtRB1+crtRB1/vte4+vte4+, and crtRB1crtRB1/vte4+vte4+. This newly developed multiplex-PCR assay saved 41.7% of the cost and 35.6% of the time compared to two individual uniplex-PCR assays. The developed assay could accelerate maize nutritional quality breeding programs through rapid and cost-effective genotyping for the target genes. This is the first report of a multiplex-PCR assay specific to crtRB1 and vte4 genes for its use in genomics-assisted breeding in maize. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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14 pages, 1994 KiB  
Article
Quantifying Genetic Parameters for Blackleg Resistance in Rapeseed: A Comparative Study
by Jan Bocianowski, Ewa Starosta, Tomasz Jamruszka, Justyna Szwarc, Małgorzata Jędryczka, Magdalena Grynia and Janetta Niemann
Plants 2024, 13(19), 2710; https://doi.org/10.3390/plants13192710 - 27 Sep 2024
Viewed by 1033
Abstract
Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better [...] Read more.
Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better adaptation of crops to environmental challenges. Genetic parameters related to gene additivity and epistasis play a key role and can influence decisions on the suitability of breeding material. In this study, 188 rapeseed doubled haploid lines were assessed in field conditions for resistance to Leptosphaeria spp. Through next-generation sequencing, a total of 133,764 molecular markers (96,121 SilicoDArT and 37,643 SNP) were obtained. The similarity of the DH lines at the phenotypic and genetic levels was calculated. The results indicate that the similarity at the phenotypic level was markedly different from the similarity at the genetic level. Genetic parameters related to additive gene action effects and epistasis (double and triple) were calculated using two methods: based on phenotypic observations only and using molecular marker observations. All evaluated genetic parameters (additive, additive-additive and additive-additive-additive) were statistically significant for both estimation methods. The parameters associated with the interaction (double and triple) had opposite signs depending on the estimation method. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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19 pages, 4026 KiB  
Article
Genome-Wide Analysis of Fruit Color and Carotenoid Content in Capsicum Core Collection
by Nayoung Ro, Hyeonseok Oh, Ho-Cheol Ko, Jungyoon Yi, Young-Wang Na and Mesfin Haile
Plants 2024, 13(18), 2562; https://doi.org/10.3390/plants13182562 - 12 Sep 2024
Cited by 2 | Viewed by 1413
Abstract
This study investigated carotenoid content and fruit color variation in 306 pepper accessions from diverse Capsicum species. Red-fruited accessions were predominant (245 accessions), followed by orange (35) and yellow (20). Carotenoid profiles varied significantly across accessions, with capsanthin showing the highest mean concentration [...] Read more.
This study investigated carotenoid content and fruit color variation in 306 pepper accessions from diverse Capsicum species. Red-fruited accessions were predominant (245 accessions), followed by orange (35) and yellow (20). Carotenoid profiles varied significantly across accessions, with capsanthin showing the highest mean concentration (239.12 μg/g), followed by β-cryptoxanthin (63.70 μg/g) and zeaxanthin (63.25 μg/g). Total carotenoid content ranged from 7.09 to 2566.67 μg/g, emphasizing the diversity within the dataset. Correlation analysis revealed complex relationships between carotenoids, with strong positive correlations observed between total carotenoids and capsanthin (r = 0.94 ***), β-cryptoxanthin (r = 0.87 ***), and zeaxanthin (r = 0.84 ***). Principal component analysis (PCA) identified two distinct carotenoid groups, accounting for 67.6% of the total variance. A genome-wide association study (GWAS) identified 91 significant single nucleotide polymorphisms (SNPs) associated with fruit color (15 SNPs) and carotenoid content (76 SNPs). These SNPs were distributed across all chromosomes, with varying numbers on each. Among individual carotenoids, α-carotene was associated with 28 SNPs, while other carotenoids showed different numbers of associated SNPs. Candidate genes encoding diverse proteins were identified near significant SNPs, potentially contributing to fruit color variation and carotenoid accumulation. These included pentatricopeptide repeat-containing proteins, mitochondrial proton/calcium exchangers, E3 ubiquitin-protein ligase SINAT2, histone–lysine N-methyltransferase, sucrose synthase, and various enzymes involved in metabolic processes. Seven SNPs exhibited pleiotropic effects on multiple carotenoids, particularly β-cryptoxanthin and capsanthin. The findings of this study provide insights into the genetic architecture of carotenoid biosynthesis and fruit color in peppers, offering valuable resources for targeted breeding programs aimed at enhancing the nutritional and sensory attributes of pepper varieties. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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16 pages, 1628 KiB  
Article
Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers
by Kyu Jin Sa, Hyeon Park, So Jung Jang and Ju Kyong Lee
Plants 2023, 12(2), 239; https://doi.org/10.3390/plants12020239 - 4 Jan 2023
Cited by 6 | Viewed by 2878
Abstract
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence [...] Read more.
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses—Q + K and PCA + K mixed linear models (MLMs)—and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker–trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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15 pages, 1114 KiB  
Article
Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea
by Zhen Yu Fu, Kyu Jin Sa, Hyeon Park, So Jung Jang, Yeon Joon Kim and Ju Kyong Lee
Plants 2022, 11(21), 2974; https://doi.org/10.3390/plants11212974 - 3 Nov 2022
Cited by 10 | Viewed by 2033
Abstract
The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop [...] Read more.
The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop (CWTPC) from South Korea. In this study, 30 PSPSs were newly developed based on transcriptome contigs in P. frutescens, and 17 of these PSPSs were used to study the genetic diversity, phylogenetic relationships and structure population among 90 accessions of the CWTPC collected from South Korea. A total of 100 alleles were detected from selected 17 PSPSs, with an average of 5.9 alleles per locus. The gene diversity (GD) ranged from 0.164 to 0.831, with an average of 0.549. The average GD values from the cultivated var. frutescens, weedy var. frutescens, and weedy var. crispa, were 0.331, 0.588, and 0.389 respectively. In addition, most variance shown by Perilla SSR markers was within a population (73%). An analysis of the population structure and phylogenetic relationships showed that the genetic relationship among accessions of the weedy var. frutescens and weedy var. crispa is closer than that for the accessions of the cultivated var. frutescens. Based on association analysis between 17 PSPSs and three seed traits in 90 Perilla accessions, we detected 11 PSPSs that together were associated with the seed size and seed hardness traits. Therefore, the newly developed PSPSs will be useful for analyzing genetic variation among accessions of the CWTPC, association mapping, and selection of important morphological traits in Perilla crop breeding programs. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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13 pages, 1946 KiB  
Article
Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers
by Emmanuel Andrea Mathiang, Kyu Jin Sa, Hyeon Park, Yeon Joon Kim and Ju Kyong Lee
Plants 2022, 11(20), 2787; https://doi.org/10.3390/plants11202787 - 20 Oct 2022
Cited by 19 | Viewed by 2668
Abstract
Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the [...] Read more.
Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers’ fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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