PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Germplasm resources”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources
PubMed2005

Vitrification, a complementary cryopreservation method for Betula pendula Roth.

Cryopreservation--the storage of plant germplasm in liquid nitrogen--provides a modern tool for the conservation of forest genetic resources. It is especially applicable for species in which their micropropagation can be initiated from mature tree buds, e.g., silver birch (Betula pendula Roth), thus enabling the conservation of specific genotypes: endangered elite trees and trees expressing rare, valuable or interesting characteristics. The aim of the present study was to develop a vitrification protocol applicable for the cryostorage of silver birch that avoids the use of expensive sophisticated freezers. The average recovery of vitrified axillary silver birch buds was 71% using a protocol that started with four-week cold hardening of bud-bearing in vitro donor shoots on modified medium under short day conditions. After cold hardening, the excised axillary buds were precultivated on medium containing 0.7 M sucrose for 24 h under the same conditions as during the cold hardening period. Following preculture, the buds were treated with loading solution containing 2M glycerol and 0.4 M sucrose for 20 min at room temperature. Finally, the buds were dehydrated with PVS2 cryoprotectant for 120 min followed by direct immersion in liquid nitrogen. According to the morphology and the RAPD profiles of regenerated plants in the greenhouse, the genetic fidelity of the vitrified birch material seems to have remained unchanged.

Betula↗
PubMed2006

Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.).

BACKGROUND: The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium. RESULTS: A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations. CONCLUSION: A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.

Chromosome Mapping↗
PubMed2026

Comprehensive plastome variation and RNA editing in Mentha: insights into phylogenetic relationships and candidate DNA barcodes.

INTRODUCTION: Mentha is an economically and medicinally important genus in Lamiaceae, but its taxonomy and species delimitation remain challenging because of frequent hybridization, polyploidy, and marked morphological plasticity. METHODS: In this study, we comparatively analyzed 12 plastomes representing major Mentha species, hybrid taxa, and unresolved accessions, including four newly assembled genomes, to characterize plastome structure, repeat composition, sequence divergence, phylogenetic relationships, and plastid RNA editing. The M. arvensis plastome and RNA-seq datasets originated from independent Swiss and Indian accessions, respectively. RESULTS: The plastomes were highly conserved in overall organization, ranging from 151,824 to 152,154 bp and displaying the typical quadripartite structure. Gene content and order were largely stable across taxa, with only minor variation likely associated with annotation differences at IR/SC boundary regions. Codon usage analysis revealed a clear bias toward A/U-ending synonymous codons, and most shared protein-coding genes showed low Ka/Ks ratios, indicating predominant purifying selection. Repeat analyses showed that simple sequence repeats were mainly composed of A/T-rich mononucleotide motifs, whereas long repeats were concentrated in the 30-40 bp size class. Comparative analyses identified six hypervariable regions, namely ccsA-ndhD, ycf1, ndhD, rpl32-trnL-UAG, rbcL-accD, and petA-psbJ, which represent promising candidate plastid markers for species discrimination. Phylogenetic analysis based on complete plastomes provided strong support for relationships among the sampled taxa and recovered a close affinity among M. aquatica, M. arvensis, and M. canadensis. In addition, RNA-seq analysis of M. arvensis identified 17 candidate plastid RNA editing sites, most of which were C-to-U conversions and nonsynonymous events. DISCUSSION: Together, these results expand plastid genomic resources for Mentha and provide a useful framework for phylogenetic inference, species identification, and future germplasm utilization.

RNA editing↗
PubMedDate not supplied

Identification and genetic variation among Hibiscus species (Malvaceae) using RAPD markers.

Germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or cultivars identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and determination of genetic variation within the two species of Hibiscus and 16 varieties of Hibiscus rosa-sinensis L. through random amplified polymorphic (RAPD) markers. Primer screening was made by using the DNA of variety "Prolific". Genetic analysis was made by using ten selected decamer primers. A total of 79 distinct DNA fragments ranging from 0.3 to 2.5 kb were amplified by using ten selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 16 varieties and two species formed one cluster. The first major cluster consisted of three varieties and a second major cluster consisted of two species and 13 varieties. The genetic distance was very close within the varieties and also among the species. Thus, these RAPD markers have the potential for identification of species/varieties and characterization of genetic variation within the varieties. This is also helpful in Hibiscus breeding programs and provides a major input into conservation biology.

Base Sequence↗
PubMed2026

Development of a 10K breeder-friendly SNP chip for faba bean.

INTRODUCTION: Faba bean breeding and genomics have seen steady progress in recent years, supported by genome sequences and high-density genotyping platforms. These tools have been valuable for trait mapping, diversity assessment, and genomic research, but they have limited routine use in breeding programs due to their relatively high cost. Recent progress in establishing an optimized, cost-efficient genotyping-by-sequencing protocol tailored to the large and complex faba bean genome has created the foundation for a more accessible genotyping solution. METHODS: Using this approach, we explored the genetic diversity of faba bean germplasm from various panels, providing a comprehensive representation of the crop's genetic landscape. From this dataset, we identified and selected a high-quality set of informative SNP markers that are evenly distributed across the genome. Building on these resources, we designed a breeder-friendly 10K SNP chip. RESULTS: The 10K SNP chip delivers high accuracy, broad genomic coverage, and affordability. The chip was validated across diverse germplasm panels, demonstrating strong clustering performance, high reproducibility, and applicability to breeding-relevant germplasm. DISCUSSION: This platform offers a cost-effective alternative to higher-density arrays, enabling its integration into genomic selection, marker-assisted breeding, and diversity monitoring, ultimately supporting accelerated genetic gain and the delivery of improved varieties to farmers.

SNP chip↗
PubMed1995

Polymerase chain reaction-based assays for the characterisation of plant genetic resources.

Plant genetic resources are an important component of biodiversity and provide the basic genetic variability that allow new and improved cultivars to be developed. Numerous germplasm collections have been established and it is important to established that such collections are representative and accessible to breeders and biotechnologists. Molecular markers provide the best estimate of genetic diversity since they are independent of the confounding effects of environmental factors. Assays based on the polymerase chain reaction (PCR) are considered to meet both the technical and genetical requirements for the characterisation of plant and animal genetic resources. Two main approaches are described, based on anonymous and defined primers. The use of both randomly amplified polymorphic DNA (RAPD) and microsatellites or simple sequence repeats (SSR) for the characterisation of perennial tree species, and distribution of variability within gene pools is reported. The detection of interspecific gene introgression between coffee species with RAPD markers is described together with the use of microsatellites to genotype potato. The use of PCR-based assays will facilitate the evaluation and utilisation of plant genetic resources.

Base Sequence↗
PubMed2025

Harnessing Landscape Genomics to Evaluate Genomic Vulnerability and Future Climate Resilience in an East Asia Perennial.

In this era of rapid climate change, understanding the adaptive potential of organisms is imperative for buffering biodiversity loss. Genomic forecasting provides invaluable insights into population vulnerability and adaptive potential under diverse climatic conditions, thereby facilitating management interventions and bolstering shaping species-specific germplasm conservation strategies. We primarily employed landscape genomics approaches, leveraging single-nucleotide polymorphisms obtained through whole-genome resequencing of 201 individuals across 43 Rheum palmatum complex populations, to pinpoint adaptive variation and its significance in the context of future climates, delineate seed zones, and establish guidelines for ex situ germplasm conservation. The species complex exhibited strong signatures of local adaptation and differential genomic vulnerabilities across its distribution range, with eastern lineage populations facing significant maladaptation risks under future climate scenarios. Using diverse datasets of putatively adaptive loci and climate change scenarios, we delineated three distinct seed zones within the species' range, estimated varying sample sizes per zone to capture most adaptive diversity, and predicted shifts in seed zone centroids ranging from 48.3 to 359.3&#x2009;km from historical distributions to mitigate climate change impacts. Collectively, our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive trajectory of an East Asian perennial under anticipated climate changes, guide seed zone delineation for germplasm conservation and enhance population resilience. These results provide a blueprint for designing targeted conservation strategies and restoration plans in other imperilled species.

Climate Change↗
PubMed2001

Cryopreservation of swine embryos: a chilly past with a vitrifying future.

Since the development of embryo freezing technologies for cattle in the 1980s, advances in cryobiology, cell biology and embryology of domestic animals have enabled the development of embryo preservation methodology for the pig, notorious for extreme sensitivity to cooling. This review outlines recent efforts to understand the biology of pig embryos as related to their extreme sensitivity to cooling. Cellular analyses and molecular approaches are discussed that have enabled pig embryos to survive cryopreservation and after transfer develop into live offspring with normal fecundity at maturity. In the near future, use of preserved embryos will be a routine breeding alternative for swine producers, providing: preservation methods for maternal germplasm; global genetic transport; increased selection pressure within herds; breeding line regeneration or proliferation; and methodology for genetic resource rescue. It took almost 50 years after the first successful embryo transfer to develop embryo preservation in the pig. Nonetheless, by applying novel methods described herein, rapid progress has been achieved.

Animals↗
PubMed2001

Large scale molecular analysis of traditional European maize populations. Relationships with morphological variation.

A representative sample of 130 European traditional maize populations was analysed for both their morphological and molecular variation. The morphological analysis of 19 variables revealed a significant variability. Correlation analysis allowed us to distinguish between traits affected by earliness (plant and ear height) and structural traits (plant architecture, grain structure). Two main morphological types could be distinguished. Molecular analyses were performed for 29 RFLP loci on DNA bulks. The number of alleles detected was high when compared to previous studies (9.59 alleles per locus). Genetic diversity was also high (0.55), with a strong differentiation between populations (GST value of 35.6%). A clear relationship between the genetic diversity of the populations and their agronomic performances was highlighted. Morphological and molecular distances showed a tendency towards a triangular relationship. We therefore considered a two-phase process to be the most efficient approach for the classification of genetic resources: firstly, a molecular study to define groups of genetically close populations, and secondly a morphological description of populations from each group. In our European collection, this approach allowed us to separate the populations from Northern and Southern Europe and to define six groups of genetically close populations, comparable to European races. This study opens new prospects concerning the molecular analysis of very large collections of genetic resources, hitherto limited by the necessity of individual analyses, and proposes a first molecular classification of European maize germplasm.

Alleles↗
PubMed2026

Genome-Wide Identification of SSR and InDel Markers and Experimental Validation of SSR Markers for Distinguishing Cold-Tolerant and Cold-Sensitive Lily Cultivars.

In this study, whole-genome resequencing was performed on the cold-tolerant variety ND-6 and the cold-sensitive variety 'Sorbonne'. After evaluation, the Lilium davidii var. unicolor reference genome was selected to analyze SSR distribution characteristics. Whole-genome InDel identification and comparative analysis were conducted for the two varieties, yielding 34,812,909 and 24,497,857 InDels, respectively. Short InDels were predominant, with deletions slightly outnumbering insertions, mostly located in intergenic regions. Twenty pairs of SSR primers were screened and synthesized. Among them, 10 pairs amplified clearly, with a polymorphism rate of 82.6%, effectively distinguishing the two cultivars examined in this study. This study provides systematic data and a reliable marker resource for the analysis of lily genomic variation, laying a foundation for the identification of cold-tolerant germplasm; validation across additional cultivars and individuals will be required to extend their utility to broader germplasm.

cold resistant lilies↗
PubMed1997

Rice genetic resources: history, conservation, investigative characterization and use in Japan.

Rice has been grown in Japan for about 3000 years. Although both japonica and indica varieties have been grown in Japan, now japonica rices are grown. Japanese rice breeding has used an ecological breeding approach. While emphasis in rice breeding in the 1940's and 1950's focussed on yield in recent decades quality has been of major importance. Consumer preference and name recognition of high quality varieties, such as Koshihikari, has resulted in slow acceptance of new varieties. Rice germplasm was systematically collected throughout Japan between 1962 and 1963. Subsequent acquisition and collecting, in Japan and other countries, has resulted in 28,000 accessions being conserved in the National Genebank, based at the National institute of Agrobiological Resources (NIAR). Research on genetic diversity of rice using a range of techniques, for example esterase isozymes, has revealed clinal variation in rice radiating from the center of diversity of rice in and around southwest China. Newly found genes in traditional rice germplasm, such as genes for non-elongating mesocotyl, are now routinely identified on the rice genome. Pioneering studies on eco-genetic differentiation of species in the genus Oryza in Japan has revealed much about the complex genepool for which rice evolved. Pest and disease resistance sources, particularly to blast, bacterial blight and brown plant hopper, from many countries have been incorporated into Japanese varieties. Cold tolerance at the booting stage was found in the Indonesian variety Silewah. In the future in characterisation of rice germplasm and interaction between rice germplasm specialists and rice molecular scientists, both in Japan and internationally, will be corner stones to securing rice genetic diversity and rice improvement in the next century.

Conservation of Natural Resources↗
PubMed2004

Expression of terpenoid indole alkaloid biosynthetic pathway genes corresponds to accumulation of related alkaloids in Catharanthus roseus (L.) G. Don.

Madagascar periwinkle, Catharanthus roseus (L.) G. Don, a medicinally important plant, produces anticancer dimeric alkaloids, vinblastine and vincristine, in the leaves and accumulates antihypertensive alkaloids, ajmalicine and serpentine, in the roots. This plant grows wild in distant tropical and sub-tropical geographical locations with different agro-climates and shows wide variations in morphological and alkaloid yield-related traits. In order to understand the correlation between the expression of terpenoid indole alkaloid (TIA) pathway genes and accumulation of related alkaloids, six different genetic resources of C. roseus, including the medicinal cultivars Nirmal, Prabal, Dhawal, the mutants gsr-3 and gsr-6, and one horticultural variety, Pacifica blush, were studied. The expression profiles of one early and two late TIA biosynthetic pathway genes, namely, strictosidine synthase, desacetoxyvindoline 4-hydroxylase and deacetyl vindoline 4-O-acetyl transferase were analyzed in these plants. A positive correlation between transcript abundance and accumulation of related alkaloids was observed in the different genetic resources. The potential of these TIA biosynthetic pathway genes for use in screening of high-yielding C. roseus germplasm has been discussed.

Acetyltransferases↗
PubMed2005

Microsatellite variation within and among populations of Oryza officinalis (Poaceae), an endangered wild rice from China.

Oryza officinalis Wall. ex Watt. is an agriculturally important but seriously endangered species of wild rice. To obtain more accurate estimates of population structure for improved conservation planning of the species, genetic variability at 14 microsatellite DNA loci was examined in population samples covering most of the species' range in China. Considerable genetic variability (overall Na = 1.886, P = 62%, HO = 0.056, HE = 0.216, and HS = 0.277) was detected at the 14 loci in 442 individuals of the 18 natural populations. The evaluation of partitioning of genetic variability (FST = 0.442) suggested high genetic differentiation among the Chinese O. officinalis populations. An overall value of Nm = 0.316 suggested limited gene flow occurred among the sampled populations. Most of the populations showed heterozygote deficits in tests of Hardy-Weinberg equilibrium and significantly positive FIS values. This could be due to some inbreeding occurring in this predominantly outcrossing species. For effective in situ conservation and restoration genetics, maintenance of significant historical processes is particularly important, including high outbreeding, considerable gene flow, and large population effective sizes. The high FST values detected among populations in this study are instructive for adopting a conservation plan that includes representative populations with the greatest genetic variation for either in situ conservation management or germplasm collection expeditions.

China↗
PubMedDate not supplied

Implementation of garlic cryopreservation techniques in the national plant germplasm system.

The USDA-ARS National Plant Germplasm System (NPGS) maintains more than 200 Allium sativum (garlic) accessions at the Western Regional Plant Introduction Station in Pullman, WA. All accessions must be grown out in the field annually since garlic plants from these accessions do not reliably produce seeds and bulbs do not store well. Shoot tips excised from garlic cloves can be successfully cryopreserved using either Plant Vitrification Solution 2 (PVS2; 15 percent v/v DMSO, 15 percent v/v ethylene glycol, 30 percent v/w glycerol, 0.4 M sucrose) or Plant Vitrification Solution 3 (PVS3; 50 percent v/w sucrose, 50 percent v/w glycerol). We compared regrowth of shoot tips representing diverse garlic germplasm after exposure to either PVS2 or PVS3 during the cryopreservation procedure. At the USDA-ARS National Center for Genetic Resources Preservation, a component of the NPGS, we consider accessions successfully preserved if a minimum of 40 percent of explants exhibit regrowth after liquid nitrogen exposure and at least 60 viable shoot tips remain in long-term storage. Ten of twelve diverse garlic accessions were successfully cryopreserved using either PVS2 or PVS3 as cryoprotectants. Five genotypes had the best post liquid nitrogen regrowth after exposure to PVS2, four genotypes had the best regrowth after exposure to PVS3, and three genotypes performed equally well using either cryoprotectant solution. This project is part of an ongoing program to cryopreserve accessions of NPGS clonal crop collections.

Cryopreservation↗
PubMed2000

Plant genome databases: from references to inference tools.

Plant genome databases play an important role in the archiving and dissemination of data arising from the international genome projects. Recent developments in bioinformatics, such as new software tools, programming languages and standards, have produced better access across the Internet to the data held within them. An increasing emphasis is placed on data analysis and indeed many resources now provide tools allied to the databases, to aid in the analysis and interpretation of the data. However, a considerable wealth of information lies untapped by considering the databases as single entities and will only be exploited by linking them with a wide range of data sources. Data from research programs such as comparative mapping and germplasm studies may be used as tools, to gain additional knowledge but without additional experimentation. To date, the current plant genome databases are not yet linked comprehensively with each other or with these additional resources, although they are clearly moving toward this. Here, the current wealth of public plant genome databases is reviewed, together with an overview of initiatives underway to bind them to form a single plant genome infrastructure.

Computational Biology↗
PubMed2005

How can we use genomics to improve cereals with rice as a reference genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.

Chromosome Mapping↗
PubMed2001

Bioinformatics for rice resources.

The distinguishing feature of the 'new biology' is that it is information intensive. Not only does it demand access to and assimilation of vast data sets accumulated by engineered laboratory processes, but it also demands a previously unimaginable level of data integration across data types and sources. There are various information resources available for rice. In addition, there are various information resources that are not focused on rice but that contain rice data. The challenge for rice researchers and breeders is to access this wealth of data meaningfully. This challenge will grow significantly as international efforts aimed at sequencing the entire rice genome come into full swing. Only through concerted efforts in bioinformatics will the power of these public data be brought to bear on the needs of rice researchers and breeders worldwide. These efforts will need to focus on two large but distinct areas: (1) development of an effective bioinformatics infrastructure (hardware systems, software systems, and software engineers and support staff) and (2) computational biology research in visualization and analysis of very large, complex data sets, such as those that will be developed using high-throughput expression technologies, large-scale insertional mutagenesis, and biochemical profiling of various types. In the midst of the large flow of high-throughput data that the international rice genome sequencing efforts will produce, it is also imperative that integration of those data with unique germplasm data held in trust by the CGIAR be a part of the informatics infrastructure. This paper will focus on the state of rice information resources, the needs of the rice community, and some proposed bioinformatics activities to support these needs.

Algorithms↗