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Results for “Germplasm resources”

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PubMed2001

Putative quantitative trait locus affecting birth weight on bovine chromosome 2.

A genome scan for chromosomal regions influencing birth weight was performed using 151 progeny of a single Hereford x composite bull and 170 microsatellite markers spanning 2.497 morgans on 29 bovine autosomes. A QTL was identified at the telomeric end of bovine chromosome 2 (maximum effect at 114 cM) accounting for approximately 2.8 kg of birth weight or 0.64 residual standard deviations (after adjustment for sex of calf, age of dam, and breed of dam). No significant effect on growth from birth to weaning was detected in this region. The presence of this QTL within a resource herd composed of breeds common to the Northern Great Plains provides an opportunity to initiate marker-assisted selection to reduce birth weight with minimal effect on postnatal growth. Thus, potentially the amount and degree of dystocia can be reduced and the economic loss associated with calving difficulty lessened without compromise of subsequent growth performance. In addition, this finding indicates that significant genetic variation for birth weight (and presumably other production-related traits) exists within herds composed of commercially adapted Bos taurus germplasm.

Animals↗

PubMed2003

Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato.

Characterization of nearly 1,000 cultivated potato accessions with simple sequence repeats (SSRs; also referred to as microsatellites) has allowed the identification of a reference set of SSR markers for accurate and efficient genotyping. In addition, 31 SSRs are reported here for a potato genetic map, including new map locations for 24 of them. A first criterion for this proposed reference set was ubiquity of the SSRs in the eight landrace cultivar groups of the potato, Solanum tuberosum. All SSRs tested in the present study displayed the same allele phenotypes and allele size range in the diverse germplasm set as in the advanced potato cultivar germplasm in which they were originally discovered. Thirteen of 13 SSR products from all cultivar groups are shown to cross-hybridize with the corresponding SSR product of the source cultivar to ascertain sequence homology. Other important SSR selection criteria are quality of amplification products, locus complexity, polymorphic index content, and well-dispersed location on a potato genetic map. Screening of 156 SSRs allowed the identification of a highly informative and user-friendly set comprising 18 SSR markers for use in characterization of potato genetic resources. In addition, we have identified true- and pseudo-multiplexing SSRs for even greater efficiency.

Alleles↗

PubMedDate not supplied

[Using methods of plant biotechnology for conservation and study of the world flora biodiversity].

Ex situ germplasm bank of plant species of world flora has been created at the Institute of Cell Biology and Genetic Engineering of the National Academy of Sciences of Ukraine as a result of investigations in the fields of botany and plant biotechnology. At present the bank contains more than 4000 samples in seed bank and more than 2000 cell lines in in vitro bank. The germplasm bank which has been put on the List of scientific objects of national property of Ukraine is the basis of elaboration ofbiotechnological methods of plant biodiversity preservation and of plant material screening for biologically active substances.

Agriculture↗

PubMed2005

Use of AFLP markers in surveys of plant diversity.

The collection of the available range of genetic variation in a gene pool, usually made of the cultivated species and their undomesticated relatives, is referred to as a germplasm collection. Increasingly, discriminator data generated using molecular genetic markers are either complementing or completely replacing those from morphological characters (known as descriptors) in surveys of genetic diversity. In addition to highlighting the state of knowledge on the specific applications of amplified fragment length polymorphisms (AFLPs) in surveys of plant genetic diversity, an attempt at a brief description and comparison of the different marker systems in use has also been made in this chapter. We have also attempted a description of the AFLP marker technology, its strengths and weaknesses, methodologies for generating reliable AFLP data, available resources (hardware, software, consumables); the kinds of questions for which AFLP data provide valid answers; and data management options. This chapter also highlights salient considerations that would guide decisions on the adoption of molecular marker assays.

DNA, Complementary↗

PubMed2025

A single hybrid origin of cultivated peanut.

This study, the first in a three-part series, lays the foundation for understanding the origin of the peanut crop (Arachis hypogaea). Its subsequent evolution is explored in the two papers that follow. The evidence that A. hypogaea originated from a single hybridization event between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago was already very strong. Here, we extend this evidence using more than 1600 single-nucleotide polymorphisms to make an almost exhaustive comparison of wild Arachis section germplasm conserved ex situ with the A and B subgenomes of divergent, sequenced cultivated peanuts. The wild relatives of peanut are highly selfing and their geocarpy means they plant their own seeds, allowing them to persist as discrete populations for millennia. This unusual biology creates a rare opportunity for genetic archaeology: ancestral lineages can be identified with exceptional precision. Our results reaffirm a single origin for the cultigen, identifying A. duranensis from Río Seco and A. ipaënsis K 30076 as the closest known relatives of the A and B subgenomes of peanut. As a genomic resource, we generated a chromosome-scale assembly of the Río Seco A. duranensis K 30065 and confirmed that it is more closely related to the A subgenome of peanut than the current reference genome (V14167). Even if somewhat closer wild accessions were found through new field collections, they would still belong to the same ancestral lineage. With this level of evidence, the origin of peanut is now known in greater detail than that of any other ancient polyploid crop.

Arachis↗

PubMed2003

Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight.

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating potato disease in the world. Control of late blight in the United States and other developed countries relies extensively on fungicide application. We previously demonstrated that the wild diploid potato species Solanum bulbocastanum is highly resistant to all known races of P. infestans. Potato germplasm derived from S. bulbocastanum has shown durable and effective resistance in the field. Here we report the cloning of the major resistance gene RB in S. bulbocastanum by using a map-based approach in combination with a long-range (LR)-PCR strategy. A cluster of four resistance genes of the CC-NBS-LRR (coiled coil-nucleotide binding site-Leu-rich repeat) class was found within the genetically mapped RB region. Transgenic plants containing a LR-PCR product of one of these four genes displayed broad spectrum late blight resistance. The cloned RB gene provides a new resource for developing late blight-resistant potato varieties. Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system.

Amino Acid Sequence↗

PubMed2001

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system.

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.

Alleles↗

PubMed2004

Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

The selection of an appropriate sampling strategy and a clustering method is important in the construction of core collections based on predicted genotypic values in order to retain the greatest degree of genetic diversity of the initial collection. In this study, methods of developing rice core collections were evaluated based on the predicted genotypic values for 992 rice varieties with 13 quantitative traits. The genotypic values of the traits were predicted by the adjusted unbiased prediction (AUP) method. Based on the predicted genotypic values, Mahalanobis distances were calculated and employed to measure the genetic similarities among the rice varieties. Six hierarchical clustering methods, including the single linkage, median linkage, centroid, unweighted pair-group average, weighted pair-group average and flexible-beta methods, were combined with random, preferred and deviation sampling to develop 18 core collections of rice germplasm. The results show that the deviation sampling strategy in combination with the unweighted pair-group average method of hierarchical clustering retains the greatest degree of genetic diversities of the initial collection. The core collections sampled using predicted genotypic values had more genetic diversity than those based on phenotypic values.

Cluster Analysis↗

PubMed2026

De novo haplotype-resolved genome assembly of the endemic kiwifruit Actinidia hubeiensis.

The genus Actinidia, which encompasses the widely cultivated kiwifruit, is characterized by its rich species diversity. Wild Actinidia species serve as invaluable germplasm reservoirs for crop improvement. As an important kiwifruit species, Actinidia hubeiensis represents a unique taxonomic group endemic to Hubei Province, contributing valuable genetic diversity to the genus Actinidia. Here, we present a haplotype-resolved genome assembly for A. hubeiensis. The two haplotype assemblies (Hap1 and Hap2) spanned 658.03 Mb (N50 = 23.16 Mb) and 597.19 Mb (N50 = 20.89 Mb), encoding 35,741 and 36,647 high-confidence protein-coding genes, respectively. Based on comprehensive assessments, both haplotypes demonstrated high completeness (BUSCO completeness > 99%), excellent continuity (LAI up to 21.67), low base-error rates (QV > 40), and nearly complete read mapping rates (> 98%). This genome assembly provides crucial genomic resources for the genus, enriching our understanding of kiwifruit biodiversity and offering new insights into the genetic background and evolutionary characteristics of this distinctive species.

Actinidia↗

PubMed2026

Natural variation in BRN1 enhances nitrogen sensitivity to improve rice nitrogen use efficiency.

Green Revolution rice varieties deliver high yields but require excessive nitrogen (N) fertilizer and show diminished N responsiveness, severely reducing nitrogen-use efficiency (NUE). To dissect the molecular basis of low N sensitivity in modern cultivars, we conducted a genome-wide association study (GWAS) for biomass response to N (BRN), a trait tightly linked to N sensitivity, using a diverse rice germplasm panel. We identified BRN1 as a key regulator of N-dependent biomass accumulation that regulates NLP3, a master transcription factor governing nitrate signaling. Under elevated N supply, the strigolactone signaling repressor D53 accumulates substantially and interacts with BRN1 to repress NLP3 transcription, thereby reducing rice N response. Notably, the high-response BRN1H allele encodes a more stable protein that alleviates D53-mediated suppression. Introgression of this allele into modern cultivars significantly enhanced N sensitivity and grain yield under both low and high N conditions. Our findings establish a D53-BRN1-NLP3 regulatory module controlling rice NUE, providing a target for rice breeding to sustain high productivity with improved resource sustainability.

Oryza↗

PubMed2004

An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum.

Over the past 10 years, resources have been established for the genetic analysis of pearl millet, Pennisetum glaucum (L.) R. Br., an important staple crop of the semi-arid regions of India and Africa. Among these resources are detailed genetic maps containing both homologous and heterologous restriction fragment length polymorphism (RFLP) markers, and simple sequence repeats (SSRs). Genetic maps produced in four different crosses have been integrated to develop a consensus map of 353 RFLP and 65 SSR markers. Some 85% of the markers are clustered and occupy less than a third of the total map length. This phenomenon is independent of the cross. Our data suggest that extreme localization of recombination toward the chromosome ends, resulting in gaps on the genetic map of 30 cM or more in the distal regions, is typical for pearl millet. The unequal distribution of recombination has consequences for the transfer of genes controlling important agronomic traits from donor to elite pearl millet germplasm. The paper also describes the generation of 44 SSR markers from a (CA)n-enriched small-insert genomic library. Previously, pearl millet SSRs had been generated from BAC clones, and the relative merits of both methodologies are discussed.

Africa↗

PubMed2026

Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressed Coffea arabica accessions.

Chromosome 4 introgression in Timor hybrid-derived Coffea arabica is established, but the robustness of accession prioritization and the relative strength of cultivated-introgressed differentiation across the canephora-derived (sgC) and eugenioides-derived (sgE) subgenomes remained unclear under explicit subgenome filtering. We reanalyzed public genomic resources from 44 coffee accessions using strict contig-level subgenome filtering, Arabica-only population-structure analysis, SNP-panel sensitivity testing, genome-wide differentiation scans, permutation testing, and direct sequence alignment. Population structure and accession rankings were stable across marker densities and random seeds, and the same six introgressed references were retained throughout. Chromosome 4 ranked first in both subgenomes, with a strong sgC signal and a markedly weaker sgE signal; independent baseline-panel permutation tests supported both chromosome 4-associated signals. Direct alignment supported correspondence to the expected chromosome 4 pseudomolecules while showing incomplete source coverage and unresolved exact boundaries. Alignment-supported blocks contained 88 sgC and 62 sgE provisional defense-, signaling-, and regulatory-associated annotations. These results provide a genome-wide, quantitatively validated framework for prioritizing introgressed germplasm and candidate chromosome 4 regions for phenotype-linked coffee research without implying equivalent introgression, exact liftover, or causal resistance genes.

Coffea arabica↗

PubMed2005

ISSR markers show differentiation among Italian populations of Asparagus acutifolius L.

BACKGROUND: Asparagus acutifolius L. is a dioecious and native plant species, widely distributed in the Mediterranean Basin. It is known for its fine flavour and could represent an important resource for cultivation programs in desert areas. Few molecular studies have been performed on this species. In the present paper, the ISSR technique was employed to study genetic diversity in Italian A. acutifolius. RESULTS: Twenty-three primers produced a total of 228 polymorphic fragments used to evaluate genetic variation. FST (0.4561) and Theta B (0.4776) values indicate a wide genetic variation among the samples examined. The distance UPGMA tree grouped together the genotypes strictly according to their geographical origin, showing that each sample is genetically structured and can be considered a distinct population. AMOVA analysis further confirmed genetic structuring of the populations. Population-specific fragments were also detected. CONCLUSION: The results suggest that ISSR markers are useful in distinguishing the populations of A. acutifolius according to geographical origin, and confirm the importance of genetic studies for designing germplasm conservation strategies.

Asparagus Plant↗

PubMed2003

Encapsulation of nodal cuttings and shoot tips for storage and exchange of cassava germplasm.

We report the encapsulation of in vitro-derived nodal cuttings or shoot tips of cassava in 3% calcium alginate for storage and germplasm exchange purposes. Shoot regrowth was not significantly affected by the concentration of sucrose in the alginate matrix while root formation was. In contrast, increasing the sucrose concentration in the calcium chloride polymerisation medium significantly reduced regrowth from encapsulated nodal cuttings of accession TME 60444. Supplementing the alginate matrix with increased concentrations of 6-benzylaminopurine and alpha-naphthaleneacetic acid enhanced complete plant regrowth within 2 weeks. Furthermore, plant regrowth by encapsulated nodal cuttings and shoot tips was significantly affected by the duration of the storage period as shoot recovery decreased from almost 100% to 73.3% for encapsulated nodal cuttings and 94.4% to 60% for shoot tips after 28 days of storage. The high frequency of plant regrowth from alginate-coated micropropagules coupled with high viability percentage after 28 days of storage is highly encouraging for the exchange of cassava genetic resources. Such encapsulated micropropagules could be used as an alternative to synthetic seeds derived from somatic embryos.

Adenine↗

PubMed2001

Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.).

The progress of genome sequencing projects of model plants like barley, combined with the recent advances of high throughput assays, has provided a wealth of sequence information. This information is being employed to develop a high density transcript map of barley (Hordeum vulgare L.). To achieve this goal, the available EST database is being used as a resource for the development of novel microsatellite (SSR) and single nucleotide polymorphism (SNP) markers. So far, a total of 692 microsatellites representing different di-, tri- and tetra-nucleotide repeats were identified from a set of 19,000 EST sequences. Non-redundant SSRs have been used for mapping and so far 76 microsatellite loci were mapped. In addition to the 180 SNP primer pairs, which were designed to target specific ESTs, 72 were polymorphic among the seven genotypes examined here. Of these, 60 SNPs have been mapped applying a denaturing HPLC approach. To examine the potential of the EST-derived markers for pedigree studies, EST-derived SSRs (75 loci) and SNPs (72 loci) were used to fingerprint a set of seven genotypes. The results show that although both marker types yielded similar groupings, a larger data set of both SSRs and SNPs is necessary to obtain stable clusters in unrelated germplasm.

Chromatography, High Pressure Liquid↗

PubMed2005

Genetic fingerprinting of germplasm accessions as an aid for species conservation: a case study with Borderea chouardii (Dioscoreaceae), one of the most critically endangered Iberian plants.

BACKGROUND AND AIMS: Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. METHODS: Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. KEY RESULTS: The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). CONCLUSIONS: The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.

Alleles↗

PubMedDate not supplied

Cryopreservation of shoot tips of blackberry and raspberry by encapsulation-dehydration and vitrification.

Encapsulation-dehydration and PVS2-vitrification cryopreservation protocols were evaluated for the long-term conservation of a diverse group of Rubus germplasm. Cold acclimation for a 4-week period prior to cryopreservation was necessary for regrowth of shoot apices from blackberry and raspberry genotypes. For the encapsulation-dehydration protocol, encapsulated apices were pretreated in 0.75 M sucrose for 20 h, desiccated 6-h under laminar flow to c. 20 percent moisture content, then plunged in liquid nitrogen (LN) and rapidly warmed. The PVS2-vitrification protocol included pretreating shoot tips on 5 percent dimethyl sulfoxide (DMSO) medium for 48 h, exposure to loading solution (LS) and PVS2 for 20 min each at 25 degree C , followed by immersion in LN and rapid warming. Shoot tips of 25 genotypes in 9 Rubus species and 9 Rubus hybrids were successfully cryopreserved with recovery of 60 to 100 percent using the encapsulation-dehydration protocol. Four genotypes of 3 species were tested using the vitrification protocol with 71 percent average regrowth. The present results indicate that both of these improved cryopreservation protocols can be applied to a diverse range of Rubus genetic resources.

Cryopreservation↗

PubMed2000

Hygienic aspects of storage and use of semen for artificial insemination.

The artificial insemination (AI) industry has developed over the last 50 years to the extent that it is used in almost every country in the world. One of the main factors contributing to its success is the confidence of the farmers that germplasm is not associated with pathogens, so that AI can be performed without risks. This has been achieved as a result of a considerable amount of research based on sound scientific data that has identified the major risk pathogens. A summary of these studies, given in this section, shows that despite the large number of agents that could be transmitted via the semen, there are cost-effective means to prevent such hazards. One of the basic rules is that the males should be housed in strictly protected semen collection centres (SCCs). Such centres should be approved by the veterinary authorities based upon specific criteria, which include special housing and operating specifications. This also includes specific means of monitoring the health of individual males through regular clinical examinations, assessment of semen and testings for various diseases. Two new challenges can now be identified, one relevant to so-called emerging diseases the impact of which on the status of the semen donors should always be assessed, and the second, relates to endangered genetic resources which may become extinct without active conservation programmes. The experience gained by the AI industry over the last 50 years should help to solve those problems. Currently, the use of semen derived from approved SCCs warrants their disease-free status.

Animal Diseases↗