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Plant Breeding and Genetics: New Findings and Perspectives
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Plant Breeding and Genetics: New Findings and Perspectives

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 1390

Special Issue Editor

Dr. Andrés J. Cortés

E-Mail Website
Guest Editor
1. Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia
2. Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
Interests: plant genomics; plant breeding; genetics of adaptation; population genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

The Special Issue entitled “Plant Breeding and Genetics: New Findings and Perspectives” in the International Journal of Molecular Sciences focuses on exploring the latest advancements in the field of quantitative genetics for plant improvement. This Special Issue aims to bridge critical research gaps in the development and deployment of advanced breeding approaches to meet the growing global food security demands, while facing in a sustainable manner more extreme climate change events.

The scope of this Special Issue spans cutting-edge original research and systematic reviews that explore the theoretical and practical aspects of quantitative genetics and plant breeding. The issue seeks to provide a comprehensive overview of the latest methodologies, technologies, and innovations that are driving the field forward, enabling more rapid and precise selection schemes. Diverse disciplines that orbit the plant breeding spectrum are encourage to collide in this Special Issue, a much-needed modern synthesis between the basic and applied genetic arenas to boost the utilization of plant resources and the effectiveness of crop improvement schemes.

By integrating traditional and modern breeding techniques, this Special Issue aims highlighting strategies that can significantly enhance the efficiency and precision of plant breeding programs. This way, the current collection is expected to make significant contributions to the scientific community by providing conceptual frameworks and practical approaches capable to modernize and integrate in innovative manners the fields of plant breeding and quantitative genetics, ultimately supporting global efforts to secure food production, climate change adaptation, and sustainable agricultural practices.

Dr. Andrés J. Cortés
Guest Editor

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • quantitative genetics
  • classical plant breeding
  • marker-assisted selection
  • genomic selection
  • speed breeding
  • gene editing and biotechnology

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Published Papers (3 papers)

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Research

11 pages, 1650 KiB  
Article
A RUBY Reporter for Efficient Banana Transformation and Development of Betalain-Rich Musa Germplasm
by Weidi He, Huoqing Huang, Shuxian Wang, Dalin Wang, Yanling Xie and Chunhua Hu
Int. J. Mol. Sci. 2025, 26(16), 7805; https://doi.org/10.3390/ijms26167805 - 13 Aug 2025
Viewed by 187
Abstract
Bananas are economically important crops valued for both their nutritional and dietary uses. However, the global banana industry suffers from a narrow base dominated by a single variety. Developing novel varieties enriched in health-promoting compounds such as betalains can help diversify banana germplasm [...] Read more.
Bananas are economically important crops valued for both their nutritional and dietary uses. However, the global banana industry suffers from a narrow base dominated by a single variety. Developing novel varieties enriched in health-promoting compounds such as betalains can help diversify banana germplasm and meet evolving consumer demands. In this study, the RUBY reporter system was employed to produce betalain-rich bananas via stable and transient genetic transformations. Transient transformation by injecting 3 mL of Agrobacterium suspension into immature fruits produced vivid red-purple pulp containing up to 1.78 mg/g of betalains. For stable transformation, embryonic cell suspensions expressing RUBY exhibited a red-purple coloration after the first screening, reducing the selection period from 45 to 15 days. These findings demonstrate that RUBY is a reliable visual reporter for efficient screening and can be used to develop nutritionally enhanced bananas. Full article
(This article belongs to the Special Issue Plant Breeding and Genetics: New Findings and Perspectives)
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24 pages, 1508 KiB  
Article
Genomic Prediction of Adaptation in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Hybrids
by Felipe López-Hernández, Diego F. Villanueva-Mejía, Adriana Patricia Tofiño-Rivera and Andrés J. Cortés
Int. J. Mol. Sci. 2025, 26(15), 7370; https://doi.org/10.3390/ijms26157370 - 30 Jul 2025
Viewed by 418
Abstract
Climate change is jeopardizing global food security, with at least 713 million people facing hunger. To face this challenge, legumes as common beans could offer a nature-based solution, sourcing nutrients and dietary fiber, especially for rural communities in Latin America and Africa. However, [...] Read more.
Climate change is jeopardizing global food security, with at least 713 million people facing hunger. To face this challenge, legumes as common beans could offer a nature-based solution, sourcing nutrients and dietary fiber, especially for rural communities in Latin America and Africa. However, since common beans are generally heat and drought susceptible, it is imperative to speed up their molecular introgressive adaptive breeding so that they can be cultivated in regions affected by extreme weather. Therefore, this study aimed to couple an advanced panel of common bean (Phaseolus vulgaris L.) × tolerant Tepary bean (P. acutifolius A. Gray) interspecific lines with Bayesian regression algorithms to forecast adaptation to the humid and dry sub-regions at the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme heat waves. A total of 87 advanced lines with hybrid ancestries were successfully bred, surpassing the interspecific incompatibilities. This hybrid panel was genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Three yield components (yield per plant, and number of seeds and pods) and two biomass variables (vegetative and seed biomass) were recorded for each genotype and inputted in several Bayesian regression models to identify the top genotypes with the best genetic breeding values across three localities on the Colombian coast. We comparatively analyzed several regression approaches, and the model with the best performance for all traits and localities was BayesC. Also, we compared the utilization of all markers and only those determined as associated by a priori genome-wide association studies (GWAS) models. Better prediction ability with the complete SNP set was indicative of missing heritability as part of GWAS reconstructions. Furthermore, optimal SNP sets per trait and locality were determined as per the top 500 most explicative markers according to their β regression effects. These 500 SNPs, on average, overlapped in 5.24% across localities, which reinforced the locality-dependent nature of polygenic adaptation. Finally, we retrieved the genomic estimated breeding values (GEBVs) and selected the top 10 genotypes for each trait and locality as part of a recommendation scheme targeting narrow adaption in the Caribbean. After validation in field conditions and for screening stability, candidate genotypes and SNPs may be used in further introgressive breeding cycles for adaptation. Full article
(This article belongs to the Special Issue Plant Breeding and Genetics: New Findings and Perspectives)
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16 pages, 4033 KiB  
Article
Construction of SNP Fingerprinting and Genetic Diversity Analysis of Eggplant Based on KASP Technology
by Wuhong Wang, Hongtao Pang, Na Hu, Haijiao Hu, Tianhua Hu, Yaqin Yan, Jinglei Wang, Jiaqi Ai, Chonglai Bao and Qingzhen Wei
Int. J. Mol. Sci. 2025, 26(11), 5312; https://doi.org/10.3390/ijms26115312 - 31 May 2025
Viewed by 533
Abstract
Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects [...] Read more.
Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects remains relatively limited. Current germplasm identification using fingerprinting primarily relies on traditional SSR markers, which suffer from limited polymorphism and labor-intensive workflows. This study aimed to identify high-quality single nucleotide polymorphisms (SNPs), develop reliable Kompetitive Allele-Specific PCR (KASP) markers for eggplant genotyping, and then conduct fingerprint construction and genetic diversity analysis. The ultimate goals were to achieve a precise identification of eggplant varieties and deeply explore the genetic background and evolutionary patterns of eggplant germplasm. In this study, 49 representative eggplant accessions were re-sequenced. After data quality control, sequence alignment, and multiple rounds of screening, 224 high-quality SNPs were identified. Based on these SNPs, 96 SNPs were selected to develop KASP markers. These markers can provide abundant genetic markers for eggplant genetic research, which are used to deeply explore the genetic background and conduct genetic diversity analysis. After multiple rounds of rigorous verification, 32 core candidate markers were finally screened out. The average polymorphic information content (PIC) and gene diversity (GD) values were 0.36 and 0.46, respectively. Phylogenetic tree, population structure, and principal component analyses divided the 280 eggplant accessions into eight distinct groups. Through the analysis of minimal core markers and core germplasm, 23 core SNP markers and a subset of 56 core germplasm accessions were identified, leading to the establishment of a comprehensive fingerprinting system for all 280 accessions. Our findings provide a foundational genetic resource for eggplant germplasm identification and offer significant support for future breeding efforts. Full article
(This article belongs to the Special Issue Plant Breeding and Genetics: New Findings and Perspectives)
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