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Seeds for Future: Conservation and Utilization of Germplasm Resources

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

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 12332

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Special Issue Editors

Prof. Dr. Klaudija Carović-Stanko

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Guest Editor

1. University of Zagreb Faculty of Agriculture, Department of Plant Biodiversity, 10000 Zagreb, Croatia
2. Center of Excellence for Biodiversity and Molecular Plant Breeding, 10000 Zagreb, Croatia
Interests: seed science and technology; DNA marker techniques for assessment of genetic diversity; plant genetic resources conservation; medicinal and aromatic plants
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Dr. Monika Vidak

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Guest Editor

1. University of Zagreb Faculty of Agriculture, Department of Plant Biodiversity, 10000 Zagreb, Croatia
2. Center of Excellence for Biodiversity and Molecular Plant Breeding, 10000 Zagreb, Croatia
Interests: legumes; medicinal and aromatic plants; plant biodiversity; seed science and technology; plant genetic resources conservation

Special Issue Information

Dear Colleagues,

The recognised dangers of environmental change and the genetic erosion of plant genetic resources have inspired numerous efforts toward conserving plant genetic resources worldwide. As many plant species and local plant populations are under threat of extinction due to various disasters and the displacement of local populations by new, high-yielding cultivars, plant genebanks have been established for the conservation and sustainable use of biodiversity.

Agroecosystems' productivity is determined by seeds, which are crucial to the existence and spread of plants. Plant diversity creates a natural resilience to challenges such as new strains of disease or climate change. Conservation of germplasm, therefore, supports global efforts to ensure future food security through natural and existing plant diversity and the development of new crops for agriculture. Important plant genetic resources include seeds of landraces, wild relatives, wild species and modern cultivars. In addition, biotechnological advances are helping to accurately characterise and conserve rare and endangered species. As our planet becomes increasingly unpredictable and dramatic events become more frequent, we must develop seeds and crops that can withstand them.

This Special Issue aims to examine the role of seed conservation and utilisation in terms of quality, seedling establishment, nutrient uptake, drought resistance and resistance to pests and diseases, exploring local germplasm and underutilised crop species.

Prof. Dr. Klaudija Carović-Stanko
Dr. Monika Vidak
Guest Editors

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Keywords

biodiversity
food security
landraces
modern cultivars
plant gene banks
plant genetic resources
seedbank
wild species
wild relatives

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Published Papers (8 papers)

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Research

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28 pages, 5492 KiB

Open AccessArticle

In Vitro Propagation of Endangered Vanda coerulea Griff. ex Lindl.: Asymbiotic Seed Germination, Genetic Homogeneity Assessment, and Micro-Morpho-Anatomical Analysis for Effective Conservation

by Leimapokpam Tikendra, Asem Robinson Singh, Wagner Aparecido Vendrame and Potshangbam Nongdam

Agronomy 2025, 15(5), 1195; https://doi.org/10.3390/agronomy15051195 - 15 May 2025

Viewed by 316

Abstract

In nature, orchid seed germination is extremely low, making in vitro asymbiotic seed germination essential for the propagation and conservation of endangered Vanda coerulea. This study optimized a micropropagation protocol and evaluated the genetic homogeneity of regenerated orchids. The synergistic effect of kinetin (KN) with auxins in the Mitra (M) medium best supported protocorm formation and seedling development. The highest shoot multiplication (5.62 ± 0.09) was achieved with 1.2 mg L⁻¹ KN and 0.6 mg L⁻¹ IBA (indole-3-butyric acid) in the medium. Enhanced leaf production (4.81 ± 0.37) was observed when 3.2 mg L⁻¹ KN was combined with 1.8 mg L⁻¹ IAA (indole-3-acetic acid), while root development was superior when 3.2 mg L⁻¹ KN together with 2.4 mg L⁻¹ IAA was incorporated in the medium. Anatomical sections confirmed well-developed leaf and root structures. Genetic fidelity assessment using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), inter-primer binding site (iPBS), and start codon targeted (SCoT) markers revealed 97.17% monomorphism (240/247 bands) and low Nei’s genetic distances (0.000–0.039), indicating high similarity among the regenerants. Dendrogram clustering was supported by a high cophenetic correlation coefficient (CCC = 0.806) and strong resolution in Principal Coordinate Analysis (PCoA) (44.03% and 67.36% variation on the first two axes). The Mantel test revealed a significant correlation between both ISSR and SCoT markers with the pooled marker data. Flow cytometry confirmed the genome stability among the in vitro-propagated orchids, with consistently low CV (FL2-A) values (4.37–4.94%). This study demonstrated the establishment of a reliable in vitro protocol for rapidly propagating genetically identical V. coerulea via asymbiotic seed germination. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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16 pages, 3189 KiB

Open AccessArticle

Microsatellite Markers Determine the Genetic Structure and Diversity of Landraces of Quinoa from Ayacucho, Peru

by Germán De la Cruz, Carla L. Saldaña, Francisco Menéndez, Edgar Neyra and Carlos I. Arbizu

Agronomy 2025, 15(3), 611; https://doi.org/10.3390/agronomy15030611 - 28 Feb 2025

Viewed by 837

Abstract

Quinoa (Chenopodium quinoa, Amaranthaceae) is a pseudocereal native to the Andes of South America that contains high protein content and adequate nutrient levels. Peru possesses an abundant morphological diversity of quinoas and is among the top producers and exporters worldwide of this precious crop. However, knowledge about the genetic and population components of quinoa from the Peruvian Andes is still limited. Here, we used 13 microsatellite markers to determine the genetic diversity and population structure of 105 landraces of quinoa cultivated in 11 provinces of Ayacucho, the southern Peruvian Andes. A total of 285 bands were manually scored, generating a 105 × 285 presence/absence data set. Principal coordinate analysis, similar to a dendrogram using the UPGMA clustering algorithm, showed that quinoa from Ayacucho is grouped into three clusters without a clear geographic component. Estimation of the genetic diversity indices was conducted considering the three populations (C1: south 1, C2: south 2, C3: north) determined by STRUCTURE analysis, showing mean expected heterozygosity was 0.08, which may be attributed to high rates of inbreeding and genetic drift, as Ayacucho suffered decades of sociopolitical violence, promoting the migration of farmers. The highest population divergence (F_ST) was exhibited for C2 and C3 (0.03), whereas the lowest was for C1 and C3 (0.02). Analysis of molecular variance revealed the greatest variation within populations (80.07%) and indicated that variability between populations is 19.93%. Microsatellite markers were effective; however, more studies of the genetic components of quinoa from other Peruvian Andean localities are still needed. We expect that this work will help pave the way towards the development of modern breeding programs of quinoa in Peru, with accurate strategies for the conservation of this nutritious crop. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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13 pages, 904 KiB

Open AccessArticle

Diversity of Sweet Basil Accessions from Croatian National Plant Gene Bank Based on Amplified Fragment Length Polymorphism Markers

by Filip Varga, Monika Vidak, Zlatko Liber, Klaudija Carović-Stanko and Zlatko Šatović

Agronomy 2024, 14(12), 3073; https://doi.org/10.3390/agronomy14123073 - 23 Dec 2024

Viewed by 945

Abstract

This study investigates genetic diversity among five morphotypes and five chemotypes of Ocimum basilicum L. (sweet basil) using amplified fragment length polymorphism (AFLP) markers. Conducted on 80 basil accessions from the Collection of Medicinal and Aromatic Plants of the National Plant Gene Bank of the Republic of Croatia, this research aims to enhance the conservation and utilization of sweet basil’s genetic resources. AFLP analysis using extracted genomic DNA revealed high levels of polymorphism, particularly within the True basil morphotype, which displayed 95.6% polymorphic markers. The results showed genetic differentiation between the morphotypes, particularly between the ’green’ and ’purple’ groups, and within certain chemotypes, such as the High-linalool chemotype (Chemotype A). Principal coordinate analysis (PCoA) and Bayesian clustering further highlighted the genetic structures, with some admixture observed, particularly in the Purple basil B morphotype. Analysis of molecular variance (AMOVA) indicated that most of the genetic diversity was between accessions, emphasizing the value of individual variability. These findings underscore the genetic potential within sweet basil accessions, offering valuable insights for future breeding programs aimed at selecting basil cultivars with tailored biochemical and morphological traits suited for pharmaceutical, culinary, and ornamental applications. The study provides an important basis for the conservation and improvement of basil genetic resources. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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16 pages, 3386 KiB

Open AccessArticle

Evaluation of the Effect of Low-Temperature Plasma Treatment on Seed Germination of Long-Term Stored Genetic Resources

by Martin Matějovič, Eva Jozová, Michael Rost, Vladislav Čurn, František Hnilička, Zora Kotíková and Petra Hlásná Čepková

Agronomy 2024, 14(9), 1918; https://doi.org/10.3390/agronomy14091918 - 27 Aug 2024

Viewed by 1290

Abstract

Low-temperature plasma (LTP) is currently one of the non-invasive and environmentally friendly methods of seed treatment and is massively tested on various types of crops. For the needs of gene banks, the use of LTP technology represents the treatment of seeds before sowing to improve the germination and emergence of long-term stored seed samples. Seeds of four genotypes of wheat, oats, flax, and rapeseed stored in the gene bank for 1, 10, and 20 years were plasma treated for 20, 25, and 30 min. Standard germination parameters (SG3, SG7, GR, MGT, and GI), as well as predictive models, were used to evaluate the effect of plasma treatment on seeds, and the effect on seed metabolism was assessed by superoxide dismutase (SOD) activity. The plasma treatment had different effects on germination and on the enzymatic activity of the tested species, and the result was influenced by both the duration of the treatment and the crop species/genotype. The plasma treatment has a positive effect on germination parameters in flax and rapeseed; in some variants, as in wheat, oats generally reacted negatively. SOD activity was variable in wheat, while higher activity with increasing treatment time was found in other crops. The results of this first study focused on long-term stored seeds and showed the potential of plasma treatment of seeds of plant genetic resources, the possibility of stimulating the germination of stored PGRs, and the need to optimize treatment conditions for individual genotypes. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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21 pages, 2480 KiB

Open AccessEditor’s ChoiceArticle

Hidden Secrets of Mangrove Swamp Rice Stored Seeds in Guinea-Bissau: Assessment of Fungal Communities and Implications for Food Security

by Sofia Conde, Amidu Barai, Sílvia Catarino, Gonçalo J. Costa, Sónia Ferreira, Idília Tavares, Maria Rosa Ferreira, Marina Padrão Temudo and Filipa Monteiro

Agronomy 2024, 14(8), 1870; https://doi.org/10.3390/agronomy14081870 - 22 Aug 2024

Cited by 3 | Viewed by 1529

Abstract

Rice cultivation is one of the most important agro-economic activities in many countries, and the correct seed storage between production cycles is essential for crop success. In Guinea-Bissau, mangrove swamp rice (MSR) is a highly productive rice cropping system, thus providing surplus for sale. Depending on storage conditions, rice grains may present moisture, insects, or the development of fungi that might affect crop productivity. Considering different rice varieties and storage conditions, samples were collected from 30 farmers within 13 villages across the main MSR-producing regions. Stored rice was used to isolate and identify seed-borne fungi through DNA barcoding, to test aflatoxin content, and to evaluate seed germination rates. Polyethylene bags (the container), raised wooden platforms, and storage rooms (the structures) are the most used facilities. Hermetic containers were recorded mainly in Oio. A total fungal richness of 18 genera was found, and 16 different species were identified. The most represented fungal genera are Aspergillus, Curvularia, and Bipolaris. Despite the presence of aflatoxin-producing fungal samples, they did not present concerning levels for human consumption, and the germination rate was not affected regardless of storage structures. These results provide a baseline on fungi occurrence in stored MSR seeds from traditional facilities in Guinea-Bissau. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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18 pages, 3301 KiB

Open AccessArticle

Diversity of Common Bean (Phaseolus vulgaris L.) and Runner Bean (Phaseolus coccineus L.) Landraces in Rural Communities in the Andes Highlands of Cotacachi—Ecuador

by María José Romero-Astudillo, César Tapia, Joaquín Giménez de Azcárate and Diego Montalvo

Agronomy 2024, 14(8), 1666; https://doi.org/10.3390/agronomy14081666 - 29 Jul 2024

Cited by 1 | Viewed by 2005

Abstract

Phaseolus species are cultivated worldwide as a primary food source for human consumption. Common bean (Phaseolus vulgaris L.) and runner bean (Phaseolus coccineus L.) landraces are often cultivated together. The purpose was to document the traditional knowledge held by farmers regarding bean landraces, to describe the diversity through seed morphological descriptors (five quantitative and five qualitative traits), to understand the geographic distribution using Moran’s I statistic, and to analyze the diversity through the Shannon–Wiener Diversity–Equity (H′) index and the Shannon J’ homogeneity index at the community level to better understand the richness of this geographic area. A total of 361 common and runner bean accessions were collected in 10 Andean rural communities of Cotacachi, North Ecuador. We identified 47 landraces, predominantly kept by indigenous female farmers, with limited access to formal education, highlighting the role of this disadvantaged population in agrobiodiversity conservation. The cluster analysis revealed three groups (cophenetic correlation coefficient = 0.6). In the principal component (PC) analysis, 94% of the variation was explained by PC1 and PC2. A positive spatial autocorrelation (Moran’s I: 0.24; z-score: 2.20; p-value: 0.03) was identified, confirming a spatial structure. The Morochos community showed the highest diversity (H′ = 1.55). The information of the diversity and distribution of common and runner bean variability provided in this study is a contribution to further research focused on conservation. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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Review

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15 pages, 3979 KiB

Open AccessEditor’s ChoiceReview

Cowpea (Vigna unguiculata) Cultivation and Breeding in the Republic of Korea: Advances and Future Perspectives

by Dong-Kwan Kim, Kanivalan Iwar, Kingsley Ochar, Sin-Young Park, Eun-Byul Go, Kyung-Dong Lee and Seong-Hoon Kim

Agronomy 2024, 14(11), 2679; https://doi.org/10.3390/agronomy14112679 - 14 Nov 2024

Viewed by 1409

Abstract

The cowpea is one of the most important legume species globally, with both the grains and fresh pods widely consumed for the rich nutritional content. In the Republic of Korea, the cultivation and breeding progress of cowpeas is relatively low but gradually receiving interest due to its potential contribution to nutrition and sustainable agriculture. Given the changing pattern of global climatic conditions, any effort in cowpea breeding in Korea may focus on important traits such as improving yield, stress resistance, and adaptability to local climate. This review provides a discussion on the current status of the cultivation and breeding of cowpeas in the Republic of Korea, with the aim of improving crop performance, agricultural sustainability, and food security. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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14 pages, 3263 KiB

Open AccessReview

The Role of Crop Wild Relatives and Landraces of Forage Legumes in Pre-Breeding as a Response to Climate Change

by Katarina Perić, Tihomir Čupić, Goran Krizmanić, Branimir Tokić, Luka Andrić, Marija Ravlić, Vladimir Meglič and Marijana Tucak

Agronomy 2024, 14(7), 1385; https://doi.org/10.3390/agronomy14071385 - 27 Jun 2024

Cited by 2 | Viewed by 2721

Abstract

Climate change and the variable extreme weather conditions that today’s agricultural producers are dealing with represent some of the most important issues in food production. Nowadays, weather patterns are increasingly unpredictable, characterized by frequent fluctuations in temperature, precipitation, and extreme weather events. As a result, there is an increasing demand for scientists to develop more resilient and tolerant crop cultivars. Plant breeders must become creative and utilize all available resources to create modern high-yielding and widely adapted cultivars to help agriculture grow and thrive amidst the emerging changes. Forage legumes, due to their beneficial characteristics, are among the crops that can contribute to mitigating the consequences of climate change. Furthermore, what certainly does not contribute to weather conditions is the erosion of plant genetic material, which has been caused by the modernization of agriculture and the selection of the best cultivars with desirable traits over many years. Crop wild relatives (CWRs) and landraces represent plant genetic materials rich in novel gene variants that contain traits for resistance and tolerance to different climatic conditions. To expand the genetic base of cultivars and mitigate the consequences of climate change, breeders are increasingly utilizing pre-breeding methods. These methods include all the activities connected to the identification of desirable genes and traits from un-adapted materials, such as CWRs, and the transformation of these traits to an intermediate set of materials that can be used for creating new cultivars. This review paper will cover the pre-breeding process, including its components, and the resistance and/or tolerance of the CWRs and landraces of forage legumes to different extreme environmental conditions. Full article

(This article belongs to the Special Issue Seeds for Future: Conservation and Utilization of Germplasm Resources)

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