Search Results (32)

More than 5.9 million plant germplasm accessions currently conserved in over 850 national genebanks worldwide will accumulate deleterious mutations over long-term conservation. However, little is known about how mutations accumulate in germplasm under long-term conservation. An attempt was made using seed-based RNA-Seq analysis to identify and characterize deleterious genetic variants in 190 diverse soybean accessions that were conserved since 1972 and were regenerated up to 10 cycles. The analysis identified 588 deleterious variants, which were widely distributed across 20 soybean chromosomes, mostly present in 10 or fewer samples, associated with diverse biological processes, and largely predicted to be weakly and mildly detrimental. Significant differences in estimates of three mutation burdens (total, heterozygous, and homozygous) were found among the samples, including sample groups representing different countries of origin. Total and heterozygous mutation burden estimates were found to increase significantly with the number of conservation years since accession acquisition and the number of germplasm regenerations, but homozygous mutation burden estimates were not correlated with these two conservation-related accession features. Total mutation burden estimates were negatively correlated with expressed gene counts and RNA integrity numbers (RINs) and marginally positively associated with averaged gene expression levels. Correlations were also found among expressed gene count, averaged gene expression level, and RIN value. No significant differences were detected between seed-based and leaf-based estimates of total mutation burden, expressed gene count, averaged expression level, and RIN. These findings provide the first empirical evidence that total mutation burden increased primarily through the accumulation of heterozygous, rather than homozygous, deleterious mutations over successive soybean germplasm regenerations. This insight is useful for conducting informative assessments of deleterious mutation accumulation and enhancing the management and conservation of plant germplasm. Full article

Two germplasm collections, comprising 1026 peach accessions located in Italy, were analyzed with 12 simple sequence repeat (SSR) markers. SSR reactions were performed using the multiplex-ready PCR protocol, and 147 alleles were amplified with an average of 12 alleles per locus. BPPCT001 was the most informative marker displaying the highest discrimination power (0.734). The observed heterozygosity showed an average of 0.45 alleles per locus, lower than expected (0.61). The fixation index (F) values were positive in all loci, with an average of 0.27 alleles per locus, suggesting the presence of endogamy. The DNA fingerprinting data allowed the discrimination of 80.95% of the analyzed accessions. If we exclude known sport mutations, known synonymies, and cultivars with the same pedigree, 161 accessions are mislabeled, with an error rate of 16.56% within or between collections. Population structure analysis revealed three subpopulations: modern peach cultivars, modern nectarine cultivars, and a third group mainly comprising traditional peach cultivars. The results obtained in this work will be useful to efficiently manage Genebank, reducing unwanted redundancy, synonyms and homonyms, mislabeling, and spelling errors, as well as identifying parents in controlled crosses. Full article

The maintenance of plant germplasm and its genetic diversity is critical to preserving and making it available for food security, so this invaluable diversity is not permanently lost due to population growth and development, climate change, or changing needs from the growers and/or the marketplace. There are numerous genebanks worldwide that serve to preserve valuable plant germplasm for humankind’s future and to serve as a resource for research, breeding, and training. The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) and the Consultative Group for International Agricultural Research (CGIAR) both have a network of plant germplasm collections scattered across varying geographical locations preserving genetic resources for the future. Besides the USDA and CGIAR, there are germplasm collections established in many countries across the world that also aim to preserve crop and plant collections. Due to the advancement of technology, genotyping and sequencing whole genomes of plant germplasm collections is now feasible. Data from genotyping can help define genetic diversity within a collection, identify genetic gaps, reveal genetic redundancies and verify uniqueness, enable the comparison of collections of the same crop across genebanks (rationalization), and determine errors or mix-ups in genetic identity that may have occurred in a germplasm collection. Large-scale projects, such as genotyping germplasm collections, require strategic planning and the development of best practices. This article details strategies and best practices to consider when genotyping whole collections, considerations for the identity verification of germplasm and determining genetic replicates, quality management systems (QMS)/QC genotyping, and some use cases. Full article

Global geographical, climatic, and ecological diversity has given rise to a wealth of domestic animals, which are essential for food security and agricultural sustainability. Since the 1960s, these critical genetic resources have declined significantly due to overdevelopment, ecological degradation, and climate change, posing a serious threat to global food security. In the face of these challenges, we emphasize the critical importance of promoting indigenous livestock and poultry germplasm resources in biodiversity conservation to enhance the adaptability and resilience of agricultural systems. To promote the sustainable management and conservation of genetic resources, a multistakeholder international cooperation framework is needed. Globally, many national and international institutions have initiated a variety of conservation measures, legislation, and technical strategies. In particular, genebanks play an indispensable role in the conservation of important livestock and poultry genetic resources. These banks not only aid in maintaining biodiversity but also provide valuable genetic material for future breeding programmes and scientific research. Through systematic collection, conservation and evaluation, genebanks ensure the long-term availability and sustainable use of genetic resources and provide an important foundation for addressing global environmental change and agricultural challenges. Full article

Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of Peribacillus frigoritolerans from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2’s genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the Peribacillus frigoritolerans strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1. Full article

Community seed banks are farmer-managed organizations that conserve and sustainably manage local crop and tree diversity. They are found in many countries of the Global South and increasingly in the Global North. Altogether, they maintain hundreds of crop and tree species and thousands of mostly local varieties and distribute tons of quality seed per year. Through their activities, they share and safeguard the world’s agrobiodiversity, contribute to seed security, and allow farming households in local communities to produce and consume more affordable, secure, diverse, and nutritious foods. However, community seed banks are knowledge-, resource-, and time-intensive organizations that operate through their members’ voluntary contributions. The purpose of this article is to analyze the sustainability challenge of community seed banks and identify strategies that address it. Focus group discussions and key informant interviews were used, complemented by secondary data analysis of research reports and other deliverables, resulting in five case study countries in Africa and Asia. Five promising sustainability strategies can support viable community seed bank development: value addition; nature-positive agriculture; enabling environment and national genebank partnership; networking and digitalization; and modern, low-cost seed quality technologies. Sustainable community seed banks can make important contributions to national seed sector development but they need stronger policy and legal support to maintain their sustainability. Full article

Long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide is a challenging mission. The extent of deleterious mutations present in conserved germplasm and the genetic risk associated with accumulative mutations are largely unknown. This study took advantage of published barley genomic data to predict sample-wise mutation burdens for 19,778 domesticated barley (Hordeum vulgare L.) accessions conserved ex situ. It was found that the conserved germplasm harbored 407 deleterious mutations and 337 (or 82%) identified deleterious alleles were present in 20 (or 0.1%) or fewer barley accessions. Analysis of the predicted mutation burdens revealed significant differences in mutation burden for several groups of barley germplasm (landrace > cultivar (or higher burden estimate in landrace than in cultivar); winter barley > spring barley; six-rowed barley > two-rowed barley; and 1000-accession core collection > non-core germplasm). Significant differences in burden estimate were also found among seven major geographical regions. The sample-wise predicted mutation burdens were positively correlated with the estimates of sample average pairwise genetic difference. These findings are significant for barley germplasm management and utilization and for a better understanding of the genetic risk in conserved plant germplasm. Full article

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks. Full article

Genebanks are crucial for safeguarding global crop diversity but are themselves exposed to several risks. However, a scientific basis for identifying, assessing, and managing risks is still lacking. Addressing these research gaps, this study provides risk analysis for three key risk groups: natural hazards, political risks, and financial risks, carried out on a sample of 80 important national and international genebanks, comprising at least 4.78 million accessions or roughly 65% of the reported total of ex situ conserved accessions worldwide. The assessment tool of Munich Re “Natural Hazards Edition” allowed a location-specific comparison of the natural hazard exposure. Results showed that genebanks in the Asia-Pacific region are most exposed to natural hazards, while institutions in African and some Asian countries are rather vulnerable to political risks. Financing is a major problem for national genebanks in developing countries, whereas the Global Crop Diversity Trust achieved considerable financial security for international genebanks. Large differences in the risk exposure of genebanks exist, making a location- and institution-specific risk assessment indispensable. Moreover, there is significant room for improvement with respect to quality and risk management at genebanks. Transferring risks of genebanks to third parties is underdeveloped and should be used more widely. Full article

In this study, we used genotyping to determine the genetic structure and molecular identities of apple landraces from six species of Malus Mill. in China, based on the fingerprints revealed by microsatellite markers with tailed primer M13. A total of 46 apple landraces of Malus Mill. selected from the National Apple and Pear Germplasm Repository in Xingcheng, China were genotyped with 14 SSR markers. The primers differentiated all the accessions. At least three SSR primers, CH04h02, CH01f07a and CH04g07, with a higher heterozygosity and Shannon’s information index than other combinations can distinguish all the accessions. All the alleles for these three primers were arranged in descending order, and they were assigned values beginning with 01. Character strings were constituted by combining all the codes of the three primers for every accession. By such means, separate and special molecular identities were obtained for every apple landrace, which could be expressed in the form of a bar code. Using such bar codes, trees can be labeled and scanned, which aids in the identification and tracking of genebank collections. The eight-step method for establishing the molecular identities of apple landraces reported here may serve as a reference when determining the molecular identities establishment of other apple germplasms of Malus Mill. This method might also be used for the establishment of a molecular database to aid the preservation of Malus Mill., which is in imminent danger in China. It may also be used to improve the gene bank management of Malus Mill. Full article

Assessing genetic distinctness and redundancy is an important part of plant germplasm characterization. Over the last decade, such assessment has become more feasible and informative, thanks to the advances in genomic analysis. An attempt was made here to search for genebank germplasm with published genomic data and to assess their genetic distinctness and redundancy based on average pairwise dissimilarity (APD). The effort acquired 12 published genomic data sets from CIMMYT, IPK, USDA-ARS, IRRI, and ICRISAT genebanks. The characterized collections consisted of 661 to 55,879 accessions with up to 2.4 million genome-wide SNPs. The assessment generated an APD estimate for each sample. As a higher or lower APD is indicative of more genetic distinctness or redundance for an accession, respectively, these APD estimates helped to identify the most genetically distinct and redundant groups of 100 accessions each and a genetic outlier group with APD estimates larger than five standard deviations in each data set. An APD-based grouping of the conserved germplasm in each data set revealed among-group variances ranging from 1.5 to 53.4% across all data sets. Additional analyses showed that these APD estimations were more sensitive to SNP number, minor allele frequency, and missing data. Generally, 5000 to 10,000 genome-wide SNPs were required for an effective APD analysis. These findings together are encouraging and useful for germplasm management, utilization, and conservation, particularly in the genetic categorization of conserved germplasm. Full article

Seed longevity is the most important trait in the genebank management system. No seed can remain infinitely viable. There are 1241 accessions of Capsicum annuum L. available at the German Federal ex situ genebank at IPK Gatersleben. C. annuum (Capsicum) is the most economically important species of the genus Capsicum. So far, there is no report that has addressed the genetic basis of seed longevity in Capsicum. Here, we convened a total of 1152 Capsicum accessions that were deposited in Gatersleben over forty years (from 1976 to 2017) and assessed their longevity by analyzing the standard germination percentage after 5–40 years of storage at −15/−18 °C. These data were used to determine the genetic causes of seed longevity, along with 23,462 single nucleotide polymorphism (SNP) markers covering all of the 12 Capsicum chromosomes. Using the association-mapping approach, we identified a total of 224 marker trait associations (MTAs) (34, 25, 31, 35, 39, 7, 21 and 32 MTAs after 5-, 10-, 15-, 20-, 25-, 30-, 35- and 40-year storage intervals) on all the Capsicum chromosomes. Several candidate genes were identified using the blast analysis of SNPs, and these candidate genes are discussed. Full article

Citrus is among the most economically important fruit crops. Its vast species diversity and global production was observed by N.I. Vavilov during his international plant explorations from the early to mid-1900s. Currently, ex situ citrus collections located around the world conserve and protect citrus genetic resources, as revealed in a survey conducted in 2021. Responses were received from 43 collections in 27 countries, of which 35 provided data regarding collection composition, management practices, and security, as well as other information. The six largest citrus collections have between 1000 and 1735 accessions. The largest accession holdings are mandarins and sweet oranges, although all citrus fruit types are maintained: mandarin, sweet orange, lemon, pummelo, grapefruit, hybrids, lime, sour orange, citron, kumquat, papeda, finger lime, and crop wild relatives. Diseases pose significant threats to collections, though some collections are maintained in a clean-plant state as a result of intensive sanitation efforts. National and regional quarantine regulations often limit the export and import of citrus plants or propagative materials, thus limiting the availability of materials at an international level. Resources, both financial and human, are necessary to ensure the long-term safety and security of citrus collections on a global scale. Future efforts to develop citrus genebanking communities will provide opportunities for improved conservation, as well as collaborations and training. Full article

Beta patula Aiton is a crop wild relative (CWR) which belongs to the Gene Pool 1b and is considered a Critically Endangered species, and is present in very specific environments, such as the Desembarcadouro islet (DI) in Ponta de São Lourenço or Chão islet (CI) in the Desertas Islands. The ISOPlexis Center (University of Madeira) has been providing continuous support for its in situ conservation by keeping a management plan of wild populations and an ex situ conservation strategy through the storage of accessions in the ISOPlexis GeneBank. The present work intends to present the spatial distribution of genetic variability and diversity in these B. patula populations using eight polymorphic Simple Sequence Repeat (SSR) markers. The overall results lead to the identification of three spots with a high genetic diversity. CI with a small cluster of individuals shows a genetic footprint different from DI, having unique alleles present in its population. DI has two distinct areas: the western area, with a higher individual density but with a lower genetic diversity and higher allele fixation; and the central area, with a lower individual count but with a higher genetic diversity and with the presence of unique alleles. Despite some genetic differences, the comparison of the two islets’ DI and CI populations shows that they have more similarities than differences. Analysis of the Molecular Variance, based on the hierarchical cluster, showed a 9% diversity between populations, 68% among individuals, and 23% within individuals. This data will be used for the establishment of a protocol to monitor and manage B. patula genetic diversity under a genetic reserve, subsequently contributing to the European Genetic Reserve network implementation and the protection of this important CWR. Full article

Seed traits are essential quantitative variables to assess seed quality and are also indicators of crop success. The World Vegetable Center Genebank in Arusha, Tanzania, has an important legume collection; however, there is limited information on seed traits per genotype, i.e., 1000-seed weight, the number of seeds per gram, germination percentage (GP), and mean germination time (MGT). In this study, 8 cowpea, 54 mungbean, and 15 soybean accessions were evaluated for the abovementioned parameters. A significant difference was observed among the genotypes of the selected legumes with respect to all the measured parameters. An intraspecific variation was also observed for the measured seed traits. The 1000-seed weight decreased with an increase in the number of seeds per gram. Unlike cowpea, the GP of mungbean and soybean accessions was significantly and negatively influenced by the number of seeds per 1 g. Hence, the smaller-sized seeds (with many seeds in 1 g) exhibited lower GP. It is concluded that the seed traits and initial quality among the selected legumes are strongly influenced by their genetic makeup. These results are useful to inform seed management, exchange, utilization, and have a high potential in breeding programs, and require further research attention. Full article