scholarly journals SSR analysis of modern Russian potato varieties using DNA samples of nomenclatural standards

2021 ◽  
Vol 3 (4) ◽  
pp. 77-96
Author(s):  
O. Yu. Antonova ◽  
N. S. Klimenko ◽  
D. A. Rybakov ◽  
N. A. Fomina ◽  
V. V. Zheltova ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Potato Cultivars ◽  
Cultivated Plants ◽  
Pcr Analysis ◽  
Ssr Analysis ◽  
Ssr Loci ◽  
High Level ◽  
Modern Russian

The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) is developing new approaches to documentation of national cultivars, taking into account recommendations of the International Code of Nomenclature for Cultivated Plants in parallel with methods of genetic certification. The nomenclatural standard of a particular cultivar represented by a herbarium specimen can be used as a reference for verifying authenticity and uniformity of cultivar specimens obtained from various sources. The verification requires fast and reliable methods for cultivar genotyping. This paper presents protocols for modified methods of DNA extraction, PCR-analysis and SSR-genotyping, which allow potato cultivars identification without the use of expensive reagent kits. A set of ten chromosome-specific microsatellite markers was used to study polymorphisms in 66 modern Russian potato cultivars, as well as in 11 pre-cultivars and breeding clones, represented by nomenclatural standards and voucher specimens, respectively. This subset of 77 specimens has demonstrated a high level of polymorphism in ten studied microsatellite loci. The SSR analysis identified 73 alleles; 7.3 alleles per locus were observed on average, the number of which varied from 3 (STG0025 locus) to 11 (locus StI046). The PIC values varied from 0.544 (STG0025 locus) to 0.836 (StI046 locus). The alleles, unique for this subset, were found at six studied loci. The high level of polymorphism at the SSR loci made it possible to unambiguously identify almost every cultivar, with the exception of the expected coincidence of microsatellite profiles of two cultivars, which are somaclonal variants. Using an optimized set of eight microsatellite markers, the genetic relationships of modern Russian potato cultivars were studied.

scholarly journals Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

2014 ◽  
Vol 139 (5) ◽  
pp. 507-517 ◽  
Author(s):  
Xiaoying Li ◽  
Hongxia Xu ◽  
Jianjun Feng ◽  
Junwei Chen
Keyword(s):  
Large Scale ◽  
Trinucleotide Repeat ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Eriobotrya Japonica ◽  
Pcr Products ◽  
Ssr Loci ◽  
Trait Locus ◽  
High Level ◽  
Simple Sequence

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.

scholarly journals DNA Sequence Analysis of Microsatellite Markers Enhances Their Efficiency for Germplasm Management in an Italian Olive Collection

2006 ◽  
Vol 131 (3) ◽  
pp. 352-359 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Nicola Lombardo ◽  
Aldo Musacchio ◽  
Maria Elena Noce ◽  
Giuseppe Pellegrino ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Microsatellite Markers ◽  
Dna Sequence ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Electrophoretic Analysis ◽  
Dna Sequence Analysis ◽  
Germplasm Management ◽  
Olive Cultivars ◽  
High Level

Genetic diversity studies using microsatelite analysis were carried out in a set of 39 accessions of Olea europaea L., corresponding to the majority of the regional autochthon germplasm in Apulia. Samples of olive leaves were harvested from plants growing in the olive germplasm collection of the Consiglio per la Ricerca e Sperimentazione in Agricoltura (C.R.A.) - Istituto Sperimentale per l'Olivicoltura at Rende in Cosenza Italy. Herein, we evaluated the extent to which microsatellite analysis using electrophoresis was capable of identifying traditional olive cultivars. In addition, the DNA sequence of all amplicons was determined and the number of repeat units was established for each sample. Using five loci, electrophoretic analysis identified 24 genotype profiles, while DNA sequence analysis detected 28 different genotype profiles, identifying 54% of cultivars. The remaining 46% were composed of seven different accession groups containing genetically indistinguishable cultivars, which are presumably synonyms. This study demonstrates the utility of microsatellite markers for management of olive germplasm and points out the high level of polymorphisms in microsatellite repeats when coupled with DNA sequence analysis. The establishment of genetic relationships among cultivars in the Apulian germplasm collection allows for the construction of a molecular database that can be used to establish the genetic relationships between known and unknown cultivars.

scholarly journals Gene flow among wild and cultivated common walnut (Juglans regia) trees in the Qinling Mountains revealed by microsatellite markers

2020 ◽  
Author(s):  
Huijuan Zhou ◽  
Peng Zhao ◽  
Keith Woeste ◽  
Shuoxin Zhang
Keyword(s):  
Gene Flow ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Juglans Regia ◽  
Pollen Flow ◽  
Qinling Mountains ◽  
Female Partners ◽  
Genetic Pollution ◽  
High Level ◽  
Common Walnut

AbstractPatterns of gene flow and gene introgression can be used to assess the risk of genetic pollution of wild forest trees from widespread cultivated trees. A comprehensive understanding of the genetic relationships and levels of gene flow among wild and cultivated common walnut (Juglans regia) has become an urgent issue. Using twelve microsatellite markers, we investigated the genetic diversity and gene flow between cultivated and wild trees of J. regia in the Qinling Mountains, China. A high level of genetic variation was detected in both cultivated and wild trees. The mean number of alleles per locus was 17.5. Observed heterozygosity (HO) and expected heterozygosity (HE) were 0.777 and 0.800, respectively. Pollination of mother trees was not by nearest neighbors, and a paternity of 60.7% of offspring evaluated could not be assigned to a local, sampled tree. Pollen flow from cultivated trees to wild trees was infrequent (5.4%), and selfing rates ranged from zero to 25.0%. Male parents were located from 0 to 1005 m from their female partners, with an average pollination distance of 285.1 m. These results are discussed in light of the cultivated species' diversity, outlining the frequent spontaneous genetic contributions from the wild to the cultivated compartment. In addition, the pollen flow parameters provide useful information about the dynamics of pollen movement within J. regia populations.

scholarly journals Microsatellite Markers Developed from `Bluecrop' Reveal Polymorphisms in the Genus Vaccinium and Are Suitable for Cultivar Fingerprinting

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1122B-1122 ◽  
Author(s):  
Peter Boches ◽  
Lisa J. Rowland ◽  
Kim Hummer ◽  
Nahla V. Bassil
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Distance Measures ◽  
Hybrid Origin ◽  
Pedigree Information ◽  
Species Relationships ◽  
Ssr Loci

Microsatellite markers for blueberry (Vaccinium L.) were created from a preexisting blueberry expressed sequence tag (EST) library of 1305 sequences and a microsatellite-enriched genomic library of 136 clones. Microsatellite primers for 65 EST-containing simple sequence repeats (SSRs) and 29 genomic SSR were initially tested for amplification and polymorphism on agarose gels. Potential usefulness of these SSRs for estimating species relationships in the genus was assessed through cross-species transference of 45 SSR loci and cluster analysis using genetic distance values from five highly polymorphic EST-SSR loci. Cross-species amplification for 45 SSR loci ranged from 17% to 100%, and was 83% on average in nine sections. Cluster analysis of 59 Vaccinium species based on genetic distance measures obtained from 5 EST-SSR loci supported the concept of V. elliotii Chapm. as a genetically distinct diploid highbush species and indicated that V. ashei Reade is of hybrid origin. Twenty EST-SSR and 10 genomic microsatellite loci were used to determine genetic diversity in 72 tetraploid V. corymbosum L. accessions consisting mostly of common cultivars. Unique fingerprints were obtained for all accessions analyzed. Genetic relationships, based on microsatellites, corresponded well with known pedigree information. Most modern cultivars clustered closely together, but southern highbush and northern highbush cultivars were sufficiently differentiated to form distinct clusters. Future use of microsatellites in Vaccinium will help resolve species relationships in the genus, estimate genetic diversity in the National Clonal Germplasm Repository (NCGR) collection, and confirm the identity of clonal germplasm accessions.

scholarly journals Nomenclatural standards and genetic passports of potato cultivars bred in the A.G. Lorkh All-Russian Research Institute of Potato Farming

2020 ◽  
Author(s):  
D. А. Rybakov ◽  
O. Yu. Аntonova ◽  
I. G. Chukhina ◽  
N. А. Fomina ◽  
N. S. Klimenko ◽  
...  
Keyword(s):  
Plant Genetic Resources ◽  
Potato Cultivars ◽  
Cultivated Plants ◽  
Molecular Screening ◽  
Cyst Nematodes ◽  
Russian Scientific ◽  
Code Of Nomenclature ◽  
Russian Research Institute ◽  
Russian Scientific Research Institute ◽  
Research Institute

In order to preserve the genetic diversity of cultivars, it is recommended to develop documentation approaches through the registration of cultivar nomenclatural standards in accordance with the International Code of Nomenclature for Cultivated Plants. The N.I Vavilov Institute of Plant Genetic Resources keeps developing this approach along with the DNA marker technologies: SSR genotyping and molecular screening with DNA markers of genes controlling valuable traits. In 2018, VIR, together with the leading national centre for potato breeding – the A.G. Lorkh All-Russian Scientific-Research Institute of Potato Farming (now the A.G. Lorkh Russian Potato Research Center), initiated the preparation of nomenclatural standards for potato cultivars bred both at the A.G. Lorkh institute and in co-authorship with other breeding institutions. This paper presents 30 nomenclatural standards which are maintained in the Nomenclature standard fund of the Herbarium of cultivated plants and their wild relatives and weeds (VIR Herbarium, WIR). Also, the paper presents genetic passports of the mentioned 30 cultivars, developed using DNA samples extracted from the plant material of nomenclatural standards. Genetic passports include information about the polymorphism of the 8 chromosome-specific microsatellites and data on the results of molecular screening with 15 markers of 11 genes conferring resistance to the most dangerous pathogens and pests: potato viruses Y and X, late blight and potato cyst nematodes. A comparison of SSR-profiles of nomenclatural standards with those of 66 cultivar samples obtained from various sources made it possible to verify authenticity and homogeneity of the latter.

scholarly journals Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

2016 ◽  
Vol 141 (5) ◽  
pp. 475-484 ◽  
Author(s):  
Narinder P.S. Dhillon ◽  
Supannika Sanguansil ◽  
Roland Schafleitner ◽  
Yen-Wei Wang ◽  
James D. McCreight
Keyword(s):  
Genetic Relationships ◽  
Geographic Origin ◽  
Bitter Gourd ◽  
Breeding Lines ◽  
Ssr Loci ◽  
Geographical Group ◽  
Dark Green ◽  
High Level ◽  
Simple Sequence

We report here the genetic characterization of bitter gourd (Momordica charantia) based on polymorphisms of 50 simple sequence repeat (SSR) loci in 114 accessions that included landraces, breeding lines, and commercial open-pollinated and F1 hybrid cultivars widely grown in Asia. Neighbor-joining tree analysis revealed a high level of genetic variability in the collection. The 114 accessions formed three subpopulations represented by five clusters. Distribution of accessions across the five clusters reflected their geographic origin to a large extent. South Asian accessions originating from India, Bangladesh, and Pakistan were more closely related to each other than to any other geographical group. Likewise, southeast Asian accessions that originated from Cambodia, Vietnam, Indonesia, and Philippines were grouped together. Accessions that originated from Taiwan were genetically distinct and grouped separately. A landrace from Laos was genetically close to the accessions from Thailand and genetically distinct from the rest of the accessions. White-fruited genotypes were genetically distinct from green- and dark green–fruited genotypes. Low- and medium-bitter accessions were more similar to each other than to the high-bitter genotypes. Accessions with cylindrical fruit were genetically distinct from those with spindle or elongated fruit. Commercial cultivars in each cluster were closely related, which indicated a narrowing of the bitter gourd genetic base in Asia in response to market demands for uniformity and yield. Use of diverse germplasm resources in bitter gourd breeding will help in sustainable breeding and production.

scholarly journals SSR analysis of pea (Pisum sativum L.) cultivars and lines

2020 ◽  
Author(s):  
K. P. Gainullina
Keyword(s):  
Genetic Diversity ◽  
Pisum Sativum ◽  
Molecular Genetic ◽  
Molecular Genetic Diversity ◽  
Ssr Analysis ◽  
Pisum Sativum L ◽  
Ssr Loci ◽  
High Level

The analysis of molecular genetic diversity of pea cultivars by microsatellites was conducted. A high level of polymorphism of SSR loci which allows using them for identification of the studied cultivars and lines was revealed.

scholarly journals Using SSR to Evaluate the Genetic Diversity of Potato Cultivars from Yunnan Province (SW China)

2014 ◽  
Vol 56 (1) ◽  
pp. 16-27 ◽  
Author(s):  
Hong Liao ◽  
Huachun Guo
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Yunnan Province ◽  
Genetic Relationships ◽  
Potato Cultivars ◽  
Good Resolution ◽  
Ssr Analysis ◽  
Low Genetic Diversity ◽  
Polymorphic Bands

Abstract The genetic diversity of potato cultivars collected from Yunnan Province was evaluated using 24 pairs of SSR markers. SSR analysis of 24 pairs of primers showed varying degrees of polymorphism among the 85 cultivars: 297 of the 304 bands were polymorphic. The primers yielded between 5 (STM2028) and 19 (StI029) bands (mean 12). The ratio of polymorphic bands ranged from 83.33% to 100% (mean 97.75%). Polymorphism information content (PIC) varied from 69.31% to 93.67% (mean 86.47%). Genetic similarity ranged from 0.5987 to 0.7632, indicating relatively low genetic diversity in the potato cultivars from Yunnan Province. Cluster analysis by UPGMA and PCA clearly delineated the genetic relationships of all cultivars; 83 of the 85 cultivars could be discriminated by only two pairs of primers, STM0030 and STM1104. The high polymorphism and good resolution of the primers used in this study make them good tools for discriminating potato cultivars.

scholarly journals Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1424
Author(s):  
Julian David Trochez-Solarte ◽  
Ximena Ruiz-Erazo ◽  
Martha Almanza-Pinzon ◽  
Giselle Zambrano-Gonzalez
Keyword(s):  
Bombyx Mori ◽  
Genetic Relationships ◽  
Low Frequency ◽  
Gene Location ◽  
High Association ◽  
Preliminary Identification ◽  
Body Development ◽  
Ssr Loci ◽  
Technological Developments ◽  
High Level

In the genome of Bombyx mori Linnaeus (1758), the microsatellites, or simple sequence repeats (SSR), feature among their particular characteristics a high adenine and thymine (A/T) content, low number of repeats, low frequency, and a grouping in "families" with similar flanking regions. Such characteristics may be the result of a complex interaction between factors that limit the size and dispersion of SSR loci—such as their high association with transposons—and mean that microsatellites within this taxon suitable as molecular markers are relatively rare. The determination of genetic profiles in populations and cell lines has not been affected owing to the high level of polymorphism, nor has the analysis of diversity, structure and genetic relationships. However, the scarcity of suitable microsatellites has restricted their application in genetic mapping, limiting them to preliminary identification of gene location of genes or quantitative trait loci (QTLs) related to thermotolerance, resistance to viruses, pigmentation patterns, body development and the weight of the cocoon, the cortex, the pupa and the filament. The review confirms that, as markers, microsatellites are versatile and perform well. They could thus be useful both to advance research in emerging countries with few resources seeking to promote sericulture in their territories, and to advance in the genetic and molecular knowledge of characteristics of productive and biological interest, given the latest technological developments in terms of the sequencing, identification, isolation and genotyping of SSR loci.

scholarly journals Nomenclatural standards and genetic passports of potato cultivars bred at the Leningrad Research Institute for Agriculture “Belogorka”

2021 ◽  
Vol 3 (3) ◽  
pp. 18-54
Author(s):  
N. S. Klimenko ◽  
T. A. Gavrilenko ◽  
I. G. Chukhina ◽  
N. M. Gadzhiev ◽  
Z. Z. Evdokimova ◽  
...  
Keyword(s):  
Plant Material ◽  
Plant Genetic Resources ◽  
Morphological Characters ◽  
Potato Cultivars ◽  
Cultivated Plants ◽  
Herbarium Specimens ◽  
Joint Research ◽  
Code Of Nomenclature ◽  
Organelle Genomes ◽  
Research Institute

In the present paper, the potato cultivars bred at the Leningrad Research Institute for Agriculture “Belogorka”, were taken as an example for demonstrating the results of elaboration of methodological approaches that are currently developed at the N.I. Vavilov Institute of Plant Genetic Resources (VIR) for the preparing of nomenclatural standards and their genotyping. In 2018, joint research of VIR scientists and breeders from the Leningrad Research Institute for Agriculture “Belogorka” began in the field of preparing nomenclatural standards for potato cultivars bred at this institute. Nomenclatural standards were prepared according to the ‘International Code of Nomenclature for Cultivated Plants’. Plant material for herbarium specimens was collected in the experimental field of the “Belogorka” Institute in 2018 by cultivar authors and handed over to the VIR Herbarium of cultivated plants, their wild relatives and weeds (WIR). The plant material included stems with inflorescences and later - tubers of 21 cultivars which were bred at the “Belogorka” Institute. Two precultivars undergoing State variety testing and three breeding clones were also included in this study. Just before herbarium preparation, the obtained plant material was photographed, plant morphological characters described, and the results compared with the description given in such official documents as the “Cultivar Questionnaireˮ and “Description of selection achievementˮ. The nomenclatural standards of 21 cultivars registered in the VIR Herbarium Database and transferred for conservation to the VIR herbarium, are published in this paper. Before herbarium preparation, the plant material was sampled for DNA extraction and subsequent genotyping and molecular screening. The genetic passports include information about the polymorphism of 10 chromosome-specific microsatellite loci, as well as the data on the presence/absence of diagnostic fragments of 12 markers of the 11 R-genes conferring resistance to diseases and pests, and for some cultivars – the information about their cytoplasm type. These genetic passports are valuable not only because different types of DNA markers were used in their preparing (SSR, SCAR and CAPS markers of the R genes; markers specific to different loci of the nuclear and organelle genomes), but first of all because of the material itself, as the DNA samples were isolated from the plants with the assigned status of nomenclatural standard for each particular cultivar. Based on the genetic passports data, trueness to type of the “Belogorka” cultivar samples obtained from various sources was verified.

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