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Plants
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Bean Breeding
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Bean Breeding

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 3152

Special Issue Editors

Dr. Barbara Pipan

E-Mail Website
Guest Editor
Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
Interests: molecular biology of plants; population genetics; MAS and genomic selection; NGS-based applications, phenomics, plant breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Creola Brezeanu

E-Mail Website
Guest Editor
VRDS Bacău—Vegetable Research and Development Station, Calea Bârladului, 220, 600388 Bacău, Romania
Interests: grain legumes conservation; organic farming; sustainable agriculture; crop improvement; population genetics; phenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Plants journal’s Special Issue, titled “Bean Breeding”, within the Research on Plant Genomics and Breeding section highlights the integration of advanced genetic, genomic, and biotechnological tools to accelerate bean crop improvement. It presents recent breakthroughs in understanding the molecular basis of key agronomic traits such as yield, stress tolerance, and disease resistance. This Speical Issue emphasizes the use of high-throughput sequencing and advanced phenomics tools to develop superior bean cultivars.

A notable focus is on enhancing the nutritional quality of beans—an essential food crop rich in protein, iron, zinc, and amino acids with a decreased content of antinutritive compounds. Through functional genomics and metabolomics, researchers are identifying genes that influence nutrient content, aiming to combat malnutrition and improve dietary health.

This Special Issue also underscores the importance of key breeding parameters in sustainable agriculture, showcasing how improved bean varieties can adapt to climate stress while maintaining high nutritional and agronomic value. It highlights the synergy between traditional breeding knowledge and modern genomic data to build resilient, high-performing cultivars.

By combining fundamental research with applied breeding strategies, this Special Issue bridges the gap between laboratory discoveries and field-level applications, contributing to global goals in food security, health, and environmental sustainability.

Dr. Barbara Pipan
Dr. Creola Brezeanu
Guest Editors

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-blind 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

  • crop improvement
  • marker-assisted and genomic selection
  • key breeding parameters
  • nutritional enhancement
  • NGS-based applications
  • functional genomics
  • sustainable agriculture

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Published Papers (6 papers)

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Research

Jump to: Review

27 pages, 8853 KB  
Article
Uncovering Phenotypic Variation in Common Bean (Phaseolus vulgaris L.): Insights from the INCREASE Project
by Hourieh Tavakoli Hasanaklou, Lovro Sinkovič, Roberto Papa, Elena Bitocchi, Elisa Bellucci, Peter Dolničar and Barbara Pipan
Plants 2026, 15(8), 1249; https://doi.org/10.3390/plants15081249 (registering DOI) - 18 Apr 2026
Abstract
The common bean (Phaseolus vulgaris L.) is a major food legume and an important plant genetic resource for sustainable agriculture. Effective use of this diversity requires integrated evaluation of phenotypic variation and agronomic performance, with preliminary assessments of line performance across seasons. [...] Read more.
The common bean (Phaseolus vulgaris L.) is a major food legume and an important plant genetic resource for sustainable agriculture. Effective use of this diversity requires integrated evaluation of phenotypic variation and agronomic performance, with preliminary assessments of line performance across seasons. In this study, phenotypic diversity was evaluated in a subsample of the INCREASE R-core collection, a large and well-defined core set of common-bean SSD lines derived from heterogeneous germplasm lines. A total of 507 lines were characterized using 57 agro-morphological traits. Multivariate analyses revealed wide phenotypic diversity structured mainly by growth habit, phenology, and yield-related traits, with clear differentiation among lines. Mixed-data clustering identified cluster 4 as the main phenotypic group associated with higher seed- and yield-related performance and composed predominantly of indeterminate climbing landraces. Multi-trait selection indices generally ranked lines from this group highest, while early, small-seeded types tended to show lower overall performance. Evaluation of a selected subset of 19 lines across two growing seasons revealed marked year-to-year variation in yield performance, indicating contrasting responses among otherwise high-performing lines. The multi-trait genotype–ideotype distance index further distinguished lines with balanced performance across traits and years. Overall, this study shows that large-scale phenotypic characterization combined with multi-trait evaluation can provide a useful exploratory basis for identifying breeding-relevant ideotypes and promising lines for further validation for common-bean improvement. Full article
(This article belongs to the Special Issue Bean Breeding)
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20 pages, 3139 KB  
Article
Integrative Transcriptomic Analysis and Co-Expression Network Characterization of Soybean Developmental Tissues
by Dounya Knizia, Khalid Meksem and My Abdelmajid Kassem
Plants 2026, 15(7), 1002; https://doi.org/10.3390/plants15071002 - 25 Mar 2026
Viewed by 406
Abstract
Soybean (Glycine max (L.) Merr.) is a globally important legume crop valued as a major source of plant-based protein and edible oil. Understanding the transcriptional programs underlying tissue-specific development is essential for improving seed quality and agronomic performance. Here, we present an [...] Read more.
Soybean (Glycine max (L.) Merr.) is a globally important legume crop valued as a major source of plant-based protein and edible oil. Understanding the transcriptional programs underlying tissue-specific development is essential for improving seed quality and agronomic performance. Here, we present an integrative transcriptomic analysis of soybean based on 12 samples representing key seed developmental stages—including globular, heart, cotyledon, embryo, dry seed, mid-mature, and late-mature—and vegetative and reproductive tissues, including leaf, root, stem, flower bud, and seedling at 6 days after imbibition (6 DAI). Following data preprocessing and filtering, 54,880 genes were retained for downstream analysis. Principal component analysis revealed clear separation between seed and non-seed tissues, indicating that tissue identity is the dominant driver of transcriptomic variation. Analysis of the top 100 most variable genes further highlighted distinct expression modules associated with seed maturation and vegetative growth. Differential expression analysis identified 9785 genes exhibiting significant expression differences between seed and non-seed tissues, including 1139 upregulated and 8646 downregulated genes under relaxed statistical thresholds. Functional characterization of seed-upregulated genes revealed enrichment of biological processes related to storage metabolism, embryo development, and stress protection mechanisms associated with desiccation tolerance. In addition, co-expression network and correlation analyses demonstrated strong transcriptional coherence among seed tissues and distinct clustering of vegetative organs. Together, these results provide a comprehensive systems-level overview of transcriptional organization across soybean tissues and identify candidate gene sets relevant to seed biology, functional genomics, and crop improvement. Full article
(This article belongs to the Special Issue Bean Breeding)
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27 pages, 6066 KB  
Article
Integrating Prognostic Breeding Approach Through Phenotypic and Marker-Assisted Selection for Yield and BCMV Resistance in Common Bean Greek Landraces
by Eirini N. Demertzi, Lefkothea Karapetsi, Chrysanthi I. Pankou, Nefeli Vasileiou, Eleftheria Georgiadou, Anastasia Kargiotidou, Varvara I. Maliogka, Dimitrios Vlachostergios, Panagiotis Madesis and Athanasios G. Mavromatis
Plants 2026, 15(6), 963; https://doi.org/10.3390/plants15060963 - 20 Mar 2026
Viewed by 569
Abstract
Addressing principal challenges in common bean (Phaseolus vulgaris L.) breeding requires a holistic approach. A combined strategy was implemented to assess seven genotypes (landraces and commercial varieties) for yield potential, stability and resistance to bean common mosaic virus (BCMV) under Mediterranean low-input [...] Read more.
Addressing principal challenges in common bean (Phaseolus vulgaris L.) breeding requires a holistic approach. A combined strategy was implemented to assess seven genotypes (landraces and commercial varieties) for yield potential, stability and resistance to bean common mosaic virus (BCMV) under Mediterranean low-input conditions. Pure-line selection and prognostic breeding together with SSR and CAPS-SCAR marker-assisted selection (MAS) formed the core methodology. Significant variation was detected across 24 morpho-agronomic descriptors, while SSR revealed 48.57% polymorphic loci and private alleles in specific landraces. High genetic coefficients of variation and high heritability were recorded for yield-related traits. Phenotypical evaluation showed diverse responses to BCMV, with mild symptoms predominating (52.14%). Entries G1 (45%) and G5 (35%) exhibited the highest frequency of the symptomless resistant phenotype. Molecular screening at I and bc-3/eIF4E loci confirmed G5’s robust dominant I gene profile, while G1 included individuals carrying both the dominant I gene and recessive bc-3, offering a valuable source for pyramiding resistance. Additionally, G1 (LI = 2.35; 100%) performed strongly in productivity, whereas G2 (SI = 3.1; 100%) and G7 (SI = 2.8; 89.7%) exhibited exceptional stability. Overall, the mixed-model approach highlighted the complementary characteristics of the tested genotypes and identified G1, G2, G5 and G7 as promising candidates for future breeding programs targeting high yield, low-input adaptability and resistance to BCMV. Full article
(This article belongs to the Special Issue Bean Breeding)
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17 pages, 1803 KB  
Article
Fine Mapping of the Co-12 Anthracnose Resistance Gene in the Andean Common Bean Cultivar in Brazil
by Jaqueline Bezerra da Silva, Maria Celeste Gonçalves-Vidigal, Pedro Soares Vidigal Filho, Giselly Figueiredo Lacanallo, Mariana Vaz Bisneta, Giseli Valentini and Larissa Fernanda Sega Xavier
Plants 2026, 15(6), 931; https://doi.org/10.3390/plants15060931 - 18 Mar 2026
Viewed by 493
Abstract
The common bean (Phaseolus vulgaris L.) cultivar Jalo Vermelho carries the Co-12 gene, which confers resistance to both Andean and Mesoamerican races of Colletotrichum lindemuthianum. Despite its importance for breeding programs, the genomic location and candidate genes underlying this resistance remain [...] Read more.
The common bean (Phaseolus vulgaris L.) cultivar Jalo Vermelho carries the Co-12 gene, which confers resistance to both Andean and Mesoamerican races of Colletotrichum lindemuthianum. Despite its importance for breeding programs, the genomic location and candidate genes underlying this resistance remain poorly defined. The Co-12 locus was fine-mapped using a biparental population derived from the cross Jalo Vermelho × Crioulo 159. A total of 172 F2 plants were used to generate 172 F2:3 families, which were phenotyped after inoculation with race 1545 of C. lindemuthianum. Segregation analysis confirmed a 1:2:1 Mendelian ratio, consistent with a single dominant resistance gene. Genotyping of resistant and susceptible plants using the BARBean6K_3 Illumina BeadChip (5398 SNP markers) mapped Co-12 to chromosome Pv04, between 1695 bp (ss715649768) and 9,651,954 bp (ss715646644). Subsequent fine mapping with simple sequence repeat (SSR) markers delimited the locus to a 41 kb genomic interval flanked by BARCPVSSR04557 and BARCPVSSR04570. Within this region, three candidate genes were identified, including one encoding a gamma-glutamyl-GABA enzyme and two encoding lipid transfer proteins (LTP2). Lipid transfer proteins are widely recognized components of plant defense; however, their association with anthracnose resistance in the common bean has not been previously reported. The identification of LTP2 genes within the Co-12 interval suggests a previously unrecognized resistance mechanism and expands the current understanding of host defense pathways in Phaseolus vulgaris. The markers identified here provide valuable tools for marker-assisted selection and will facilitate efficient introgression of Co-12 into common bean cultivars. Full article
(This article belongs to the Special Issue Bean Breeding)
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18 pages, 5437 KB  
Article
Genome-Wide Analysis of Cellulose Synthase Superfamily and Roles of GmCESA1 in Regulating Drought Tolerance and Growth of Soybean
by Chunhua Wu, Jie Chen, Jiazhou He, Xiujie Zhang, Shanhui Zheng, Yongpeng Pan, Ting Jin and Yan Li
Plants 2026, 15(1), 34; https://doi.org/10.3390/plants15010034 - 22 Dec 2025
Viewed by 786
Abstract
The cellulose synthase (CS) superfamily, comprising the cellulose synthase (CESA) and cellulose synthase-like (CSL) families, plays crucial roles in plant response to abiotic stresses, growth and development. However, there are few reports on the biological functions of CSs in soybean. In this study, [...] Read more.
The cellulose synthase (CS) superfamily, comprising the cellulose synthase (CESA) and cellulose synthase-like (CSL) families, plays crucial roles in plant response to abiotic stresses, growth and development. However, there are few reports on the biological functions of CSs in soybean. In this study, 80 soybean CS members were identified and classified into seven subfamilies. Collinearity analyses revealed that the segmental duplication is likely the primary driver for the expansion of CS superfamily in soybean. The abundant stress-responsive and growth-related cis-acting elements in the promoter regions of soybean CS genes suggest their potential functions. Notably, GmCESA1 exhibited significantly higher expression levels in drought-tolerant soybean under drought stress. Soybean plants with lower GmCESA1 expression via virus-induced gene silencing (VIGS-GmCESA1) were less drought-tolerant than the control plants (VIGS-EV), showing reduced relative water content and dry weight than VIGS-EV under drought stress. Furthermore, VIGS-GmCESA1 soybean plants displayed reduced plant height under both well-watered and drought-stressed conditions. Our findings highlight that GmCESA1 has pleiotropic functions in regulating both drought tolerance and growth in soybean, contributing to our knowledge on CS and providing a valuable gene to breed drought-tolerant soybean in the future. Full article
(This article belongs to the Special Issue Bean Breeding)
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Review

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26 pages, 25452 KB  
Review
Polyploidy and Mutagenic Germplasm Innovation in Minor Legumes: Paradigm Shift and Challenges from Model Crops to Mung Bean
by Feixiang Guo, Chao Ma, Yuan Liu, Lixia Wang and Chunxia Li
Plants 2026, 15(7), 1051; https://doi.org/10.3390/plants15071051 - 29 Mar 2026
Viewed by 369
Abstract
Minor legume crops, including mung bean (Vigna radiata), cowpea, and adzuki bean, are crucial for global food security and sustainable agriculture, yet their genetic improvement has been hindered by narrow germplasm resources and lagging breeding technologies. This article systematically reviews the [...] Read more.
Minor legume crops, including mung bean (Vigna radiata), cowpea, and adzuki bean, are crucial for global food security and sustainable agriculture, yet their genetic improvement has been hindered by narrow germplasm resources and lagging breeding technologies. This article systematically reviews the strategy of integrating polyploid breeding with mutagenic breeding as an innovative pathway to overcome the genetic bottlenecks of minor legumes. It focuses on insights gained from model plants and major legume crops like soybean and alfalfa regarding polyploid advantages and efficient mutagenesis techniques. Furthermore, it provides an in-depth analysis of the unique challenges and adaptation barriers encountered when transferring these paradigms to minor crops. Using mung bean as a representative case study, this review highlights specific challenges, including the creation of stable polyploid germplasm, the elucidation of complex regulatory mechanisms in polyploid genomes, and the technical bottlenecks in gene mapping and functional validation. The review also outlines future directions involving the integration of cutting-edge technologies—such as multi-omics, high-throughput phenomics, and gene editing—to establish a holistic research framework of “germplasm innovation-gene mapping-designer breeding”. This integrated approach aims to advance the breeding practices of minor legumes into a new era of precision design. Full article
(This article belongs to the Special Issue Bean Breeding)
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