scholarly journals Search of the new SSR-loci of DNA for development of effective technology for soybean genotyping

2021 ◽  
Vol 188 (4) ◽  
pp. 18-24
Author(s):  
S.A. Ramazanova ◽  
◽  
V.G. Savichenko ◽  
E.G. Ustarkhanova ◽  
E.D. Loginova ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Dna Amplification ◽  
Pcr Analysis ◽  
Major Protein ◽  
Soybean Cultivars ◽  
Literary Sources ◽  
Effective Technology ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Polymorphism Level

Soybean is the major protein-oil crop of a huge economic importance. Currently, to describe the new cultivars being applied for a patent there are used the modern methods based on an analysis of microsatellite (SSR) loci of DNA. The purposes of this work were a search of the new microsatellite markers to optimize the existing technology of soybean cultivars certification and identification as well as selection of conditions for PCR analysis and to test them on cultivars from the VIR’s collection. Seven microsatellite loci demonstrated the high polymorphism level on soybean cultivars and located in the different chromosomes were chosen in the literary sources and librarian data bases. The optimal temperatures for annealing were selected empirically for all the pairs of SSR-markers. The results of DNA amplification of 20 soybean genotypes showed all seven studied SSR-loci were polyallel. In general, we revealed 22 alleles that on average are 3.1 per a locus. The effective number of alleles Ne for the studied soybean genotypes varied from 1.69 to 2.27 and on average was equal to 2.01. An average meaning of an index of the polymorphic information content (PIC) was 0.50. All the investigated soybean samples have the unique sets of alleles by the studied loci. Seven approbated loci can be used in development of an effective technology for identification and certification of the soybean genotypes.

scholarly journals A linkage of gene of resistance to a broomrape race G with microsatellite loci of a sunflower linedonor RGP1 of VNIIMK’s breeding

2021 ◽  
Vol 186 (2) ◽  
pp. 3-9
Author(s):  
S.Z. Guchetl ◽  
◽  
D.L. Savichenko ◽  
Keyword(s):  
Microsatellite Loci ◽  
Physical Map ◽  
Pcr Analysis ◽  
Sources Of Resistance ◽  
Resistant Varieties ◽  
Literary Sources ◽  
Ssr Loci ◽  
Environmentally Safe ◽  
Yield Formation ◽  
Sunflower Genome

Broomrape (Orobanche cumana Wallr.) is one of the main biotic factors limiting high sunflower yield formation. The most effective and environmentally safe method of protection is cultivation of resistant varieties and hybrids of sunflower. Development of resistant sunflower genotypes includes search and usage of sources of resistance in breeding process as well as accurate and productive procedures of material assessment. The purpose of the research is to analyze a linkage of a gene Or7 with microsatellite loci of the line-donor of resistance to broomrape race G from the VNIIMK’s collection. The objects of the research are the line RGP1 – a donor of resistance to broomrape race G and a susceptible to this race line VR 678 from the VNIIMK’s collection. Sunflower plants were crossed in field to produce F1. Also we conducted self-pollination of F1 plants to obtain F2 progeny. Plants were tested in a greenhouse in soil infected with seeds of broomrape race G using a method of early diagnostic. Sunflower DNA was extracted from the top leaves of the young sprouts of the vegetative plants. For PCR-analysis we used three SSR-primers demonstrated polymorphism in parental lines: ORS 683, ORS 1040, and ORS 1112. We tested joint inheritance of the gene Or7 and these loci, and inheritance between SSR-loci. An independent inheritance of the gene Or7 with DNA-loci ORS 683, ORS 1040, and ORS 1112, as well as SSR-loci between ORS 1040 and ORS 1112, ORS 1040 and ORS 683 was showed. Loci ORS683 – ORS 1112 are linked with a frequency of recombination of 0.27 ± 0.41 (27 cM). As a result of our research location of the gene Or7 in the nearest area to microsatellite loci ORS 683, ORS 1040, and ORS 1112 was excluded. Basing on studied literary sources and a representative sunflower genome HanXRQr2.0-SUNRISE we made a partial physical map LG3 for determination of an area for the further search of a localization of the Or7 and DNAmarkers co-segregating with this gene.

scholarly journals Evaluation of Clonal Uniformity in Six Superior Cacao Clones Based on SSR Marker

2018 ◽  
Vol 5 (3) ◽  
pp. 135
Author(s):  
Indah Sulistiyorini ◽  
Rubiyo Rubiyo ◽  
Sudarsono Sudarsono
Keyword(s):  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Germplasm Conservation ◽  
Plant Molecular Biology ◽  
Dna Amplification ◽  
Genetic Uniformity ◽  
Two Samples ◽  
Ssr Loci ◽  
Variant Alleles ◽  
Biology Laboratory

<p><em>Propagation of cacao plants is generally carried out vegetatively. Therefore, plants that are clonally propagated should be genetically uniform. Genetic uniformity in cacao clones is also very important information for germplasm conservation and in obtaining pure parental crosses. Evaluation of genetic uniformity can be seen through analysis using SSR markers. This study aimed to determine the genetic uniformity in six cacao clones using SSR markers. This experiment was conducted at IIBCRI Integrated Laboratory in Sukabumi and Plant Molecular Biology Laboratory, IPB Bogor, from September 2015 to December 2016.  Six cacao clones used (TSH 858, TSH 908, ICS 13, PA 300, GC 7 and UIT) are from Kalitelepak experimental station of  PTPN XII, Genteng District, Banyuwangi, East Java.  Ten samples were taken randomly to represent cacao clones. DNA amplification was carried out using 12 SSR markers. The result showed that 12 SSR markers generated 45 alleles with the number of alleles per locus was 3-4 alleles. The polymorphic information content (PIC) ranges from 0.37</em>–<em>0.67, which are identied as very informative molecular analysis </em><em>in identifying the genetical uniformity of the evaluated cacao population. Six SSR loci generated variant alleles within both the TSH 858 and UIT clones, indicating there are off-type plants in these two samples. Clonal uniformity were detected for samples of the GC 7, ICS 13, PA 300 and TSH 908 clones. On the other hand, 8.33% of evaluated samples within the TSH 858 and UIT clones were off-type plants.</em></p>

scholarly journals Polymorphisms in SSR-loci associated with E genes in soybean mutant lines offer perspective for breeding

2019 ◽  
Vol 6 (3) ◽  
pp. 45-55
Author(s):  
D. Zharikova ◽  
G. Chebotar ◽  
E. Aksyonova ◽  
I. Temchenko ◽  
S. Chebotar
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Vegetation Period ◽  
Vegetative Period ◽  
Soybean Cultivars ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Soybean Plants ◽  
Mutant Lines ◽  
And Control

Aim. To analyse genetic diversity in 10 new soybean lines created by using the chemical mutagens D-6, DMSSO-11, DMSSO-12, DMSNPIR-11, DUDMS12, D12DMC-11B obtained from four cultivars Femida, Oksana, Podils’ka 416, Zolotysta. The microsatellite (MS) markers Satt100, Satt229, Satt319, Satt354, Satt365, Sat_038 were used. These markers are linked with genes, which determine sensitivity of soybean plants to photoperiod and time to maturation. Methods of DNA extraction, PCR, MS-analysis, fi eld trial, one-way analysis of variance (ANOVA) have been applied. Results. Parental cultivars, mutant lines and control genotypes were characterized by alleles of microsatellite loci, 25 alleles of 6 microsatellite loci were detected. Signifi cant differences between investigated lines were detected in three year fi eld trials for traits − days to maturation (DTM) and length of the vegetative period (LV). We have revealed effects of the factor «Alleles of MS-locus», so alleles of Satt100 locus affected all traits except DTF (days to fl owering); alleles of Satt319 and Satt354 affected DTM and LV; Sat_038 affected DTF and S-F (duration of the period shoots-fl owering). Lines with alleles 167 bp at Satt100 and 175 bp at Satt319 loci (that marks dominant E7) were shown to have a longer vegetation period and later maturity, than other. The lines with allele 247 bp at Sat_038 fl owered earlier, than lines with a 245 bp allele, and the lines with allele 232 bp at Satt354 reached maturity later, than lines with other alleles at this locus. Conclusions. We have found that applied mutagens induce changes in the soybean genome and by using these mutagens it is possible to effectively increase genetic diversity in loci associated with genes/loci that determine time of maturity and/or photoperiod sensitivity of soybean, enabling to obtain soybean cultivars with different terms of maturity and yield. The microsatellite markers, particularly Sat_038, Satt100, Satt319 and Satt354 that were applied in our study are considered to be useful tools for marker assisted breeding of soybean cultivars with programmed time of development. We did not observe signifi cant effects of «Alleles of MS-locus Satt229» that is known to be linked with E3 on the investigated agronomical traits. For soybean genotypes with the E7 allele the DTF was longer for 3-9 days and LV for 10-11 days. In lines with an allele of 175 bp at locus Satt319 the S-F period was 6-9 days shorter

scholarly journals Relationships among cultivated peas and their wild relatives: Molecular and morphological characterization

2019 ◽  
Vol 48 (4) ◽  
pp. 1011-1019
Author(s):  
Fatih Hanci ◽  
Esra Cebeci
Keyword(s):  
Molecular Study ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Local Varieties ◽  
Ssr Loci ◽  
Taxonomic Groups ◽  
Clustering Pattern ◽  
Polymorphism Level ◽  
Different Sources ◽  
Simple Sequence

This study was conducted to determine relationship between some wild pea accessions (Pisum fulvum L., P. abyssinicum L., P. sativum var. elatius), local varieties (P. sativum var. sativum L. and P. sativum var. arvense L.) and commercial varieties “Boogie” and “Rondo”. The genetic diversity was evaluated with 14 simple sequence repeat markers and 50 morphological characters. The results of morphology indicated that, genotypes showed a clustering pattern based on the taxonomic groups when considering only flower characters and all morphological characters. During the molecular study, a total of 48 alleles were obtained. Used all primers showed polymorphism in accessions. The number of alleles varied between 2 - 6 among 14 SSR loci revealing the polymorphism level of markers. Similarity coefficient (Dice’s) ranged from 0.100 to 0.800 with an average of 0.378. A dendrogram grouped the 15 genotypes into two main clusters. This information can be utilized for genetic analysis, genotype identification from different sources and development of improved germplasm.

scholarly journals Genotyping oil flax varieties using the microsatellite DNA marker system

2020 ◽  
Vol 21 (5) ◽  
pp. 531-539
Author(s):  
S. Z. Guchetl ◽  
T. A. Tchelyustnikova
Keyword(s):  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Biotic And Abiotic Stresses ◽  
Crop Acreage ◽  
Marker System ◽  
Average Value ◽  
Ssr Loci ◽  
New Varieties ◽  
Microsatellite Dna Marker

The tendency to increase crop acreage of oil flax requires the development of new varieties with high indicators of ecological plasticity, productivity and resistance to biotic and abiotic stresses. The application of modern biotechnolog ical approaches based on the use of molecular markers can accelerate the assessment of genetic differences and the dete rmination of potential of the source material for breeding. The research was aimed at assessment of the genotyping parameters of some oil flax varieties of VNIIMK breeding using the system of microsatellite markers. Seventeen variety samples of flax were used as the material for the research. DNA was isolated using CTAB buffer. Eleven SSR loci were used for the identification of varieties. Ten polymorphic loci were identified during the research. The total number of counted alleles is 32. The size of alleles varied in the range of 111-210 bps. The number of alleles per locus ranged from 2 to 6 with an average value of 3.20. The value of the index of polymorphic information content (PIC) was from 0.29 to 0.75 with an average parameter value of 0.51. The effective number of alleles for different loci is determined in the range of 1.40-3.94 with an average value of 2.28. The level of information content of the marker system (PIC 0.51) corresponds to that for identifying sets of genotypes from collections with a limitation in geographical origin. There were established differences in the frequency of occurrence of alleles. The discriminatory potential of the used marker system allowed to identify 15 variety samples. Two genotypes with common origin were identical. The degree of genetic relatedness of the studied flax genotypes has been evaluated. The obtained results will serve as the basis for the subsequent construction of genetic passports of oil flax varieties of VNIIMK breeding.

scholarly journals ASSESSMENT OF THE INTEGRATED CHITINASE GENE STABILITY IN WHEAT LINES AFTER BIOBALLISTIC TRANSFORMATION

REPORTS ◽  
2020 ◽  
Vol 6 (334) ◽  
pp. 5-13
Author(s):  
N.P. Malakhova ◽  
◽  
Y.A. Skiba ◽  
E.R. Maltseva ◽  
G.A. Iskakova ◽  
...  
Keyword(s):  
Plant Immunity ◽  
Dna Amplification ◽  
Chitinase Gene ◽  
Fungal Diseases ◽  
Pr Proteins ◽  
Pcr Analysis ◽  
Soil Conditions ◽  
Wheat Lines ◽  
Resistance To Fungal Diseases ◽  
Regenerant Plants

The synthesis of PR-proteins (pathogenesis related proteins), the most studied of which are chitinases and β-1,3-glucanases, occurs in response to infection with pathogens in plants. Information about the exact role of individual PR proteins within plant immunity makes it possible to use certain specific antifungal proteins for the development of transgenic plants with increased resistance to fungal diseases. At the same time, it is important not only to obtain a plant with the desired trait, but also to fix in it the stable expression of the transferred gene and the inheritance of the acquired trait in generations. Herein we have studied the stability of the chitinase gene insertion in T1, T2 and T3 generations of transformed wheat lines obtained by the method of cis-gene transfer. Primary transformed regenerant plants were obtained as a result of bioballistic transformation of the chitinase gene into immature wheat germ of Saratovskaya 29 and Kazakhstanskaya 19 varieties. Following screening of regenerant plants by PCR for the presence of the target gene made it possible to select 6 lines presumably carrying the insert based on variety Saratovskaya 29 and 2 lines based on variety Kazakhstanskaya 19. The seed material of the selected regenerant plants was cultivated in soil conditions and the seeds of the T1 generation were obtained. DNA amplification of 8 selected lines St-29№25, St -29№43, St-29№44, St-29№33, St-29№26, St-29№35, Кz-19№1, Кz-19№2 with specific primers revealed insert-carrying lines, partially cleaved lines and lines with a high degree of insert instability. According to the results of the T2 and T3 generations PCR analysis, a complete absence of insertion in the St-29№35 and St-29№33 lines was revealed, a partial cleavage of the trait in the St-29№43 and Kz-19№2 lines was revealed, and the stable inheritance of the chitinase gene in four lines St-29№25, St-29№44, St-29№26 and Kz-19№1.was confirmed. These lines were selected as promising for in-depth study of their resistance to fungal diseases and further replication.

scholarly journals Use of "EP"(Peroxidase) allele in soybean varietal characterization

2014 ◽  
Vol 36 (4) ◽  
pp. 465-470
Author(s):  
Bárbara Panoff Valário ◽  
Cláudio Cavariani ◽  
José de Barros França-Neto ◽  
Elisa Serra Negra Vieira ◽  
Juliana Pereira Bravo ◽  
...  
Keyword(s):  
Plant Production ◽  
Pcr Analysis ◽  
Agarose Gel Electrophoresis ◽  
Conventional Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Molecular Biology Technique ◽  
Soybean Cultivars ◽  
Colorimetric Test

The aim of this work was to evaluate the use of the molecular biology technique of PCR (Polimerase Chain Reaction) in the characterization of soybean cultivars. The study was performed at the Department of Plant Production, Faculty of Agricultural Sciences/ UNESP and Institute of Bioscience, Botucatu-SP. Fourteen commercial soybean cultivars were used, of which six were selected as positive reaction to peroxidase (BRS 320, BRS 284, BRS 232, BRS 7860RR, BRSMG 760SRR, BRS295RR), four as negative reaction (BRS 326, BRS 8160RR, BRSMG 800A (NutriSoy), BRS Valiosa RR) and four as double reaction (BRSGO 8060, BRS 270RR, FTS Campo Mourão and BRS 239). Thus, the results attained by the traditional biochemical colorimetric test for the 14 cultivars were compared with the conventional PCR assay. For PCR analysis, DNA was extracted from whole seeds and the primers were tested, and subsequently PCR and agarose gel electrophoresis were performed. The combination of primers prx9 + prx10 confirmed the use of the PCR reaction to characterize soybean cultivars considered doubtful by conventional colorimetric text.

scholarly journals Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Man Liu ◽  
Xin Hu ◽  
Xu Wang ◽  
Jingjing Zhang ◽  
Xubing Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Medicinal Plant ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Sampling Strategy ◽  
Market Demand ◽  
Conservation Assessment ◽  
Information Index ◽  
Ssr Loci ◽  
Metabolic Data

Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon’s information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.

scholarly journals Unique Posttranslational Modifications of Chitin-Binding Lectins of Entamoeba invadens Cyst Walls

2006 ◽  
Vol 5 (5) ◽  
pp. 836-848 ◽  
Author(s):  
Katrina L. Van Dellen ◽  
Anirban Chatterjee ◽  
Daniel M. Ratner ◽  
Paula E. Magnelli ◽  
John F. Cipollo ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Cyst Wall ◽  
Low Complexity ◽  
Pcr Analysis ◽  
Major Protein ◽  
Chitin Binding Domain ◽  
Binding Domains ◽  
Reverse Transcription Pcr ◽  
Entamoeba Invadens

ABSTRACT Entamoeba histolytica, which causes amebic dysentery and liver abscesses, is spread via chitin-walled cysts. The most abundant protein in the cyst wall of Entamoeba invadens, a model for amebic encystation, is a lectin called EiJacob1. EiJacob1 has five tandemly arrayed, six-Cys chitin-binding domains separated by low-complexity Ser- and Thr-rich spacers. E. histolytica also has numerous predicted Jessie lectins and chitinases, which contain a single, N-terminal eight-Cys chitin-binding domain. We hypothesized that E. invadens cyst walls are composed entirely of proteins with six-Cys or eight-Cys chitin-binding domains and that some of these proteins contain sugars. E. invadens genomic sequences predicted seven Jacob lectins, five Jessie lectins, and three chitinases. Reverse transcription-PCR analysis showed that mRNAs encoding Jacobs, Jessies, and chitinases are increased during E. invadens encystation, while mass spectrometry showed that the cyst wall is composed of an ∼30:70 mix of Jacob lectins (cross-linking proteins) and Jessie and chitinase lectins (possible enzymes). Three Jacob lectins were cleaved prior to Lys at conserved sites (e.g., TPSVDK) in the Ser- and Thr-rich spacers between chitin-binding domains. A model peptide was cleaved at the same site by papain and E. invadens Cys proteases, suggesting that the latter cleave Jacob lectins in vivo. Some Jacob lectins had O-phosphodiester-linked carbohydrates, which were one to seven hexoses long and had deoxysugars at reducing ends. We concluded that the major protein components of the E. invadens cyst wall all contain chitin-binding domains (chitinases, Jessie lectins, and Jacob lectins) and that the Jacob lectins are differentially modified by site-specific Cys proteases and O-phosphodiester-linked glycans.

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.

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