SELECTION AND ASSESSMENT OF ISSR-MARKERS FOR ANALYSIS OF SEPARATE CATTLE POPULATIONS

The article covers molecular genetic analysis of intermicrosatellite DNA sequences of dairy cattle productivity. Molecular markers based on DNA polymorphism were used for this monitoring. Such markers make it possible to assess quickly the genetic polymorphism of taprin in the herd. Іnsofar as a large number of intermicrosatellite repeats is in the genome of cattle, that increases the probability of detecting polymorphic loci. The ISSR markers selected for the study are based on multiclocus synthesis in polymerase chain reaction (PCR) and allow an objective study of the breed and interbreed diversity. And it makes possible to assess quickly and accurately genetic diversity for the presence of genes associated with economically useful traits. The purpose of this work is the selection and evaluation of ISSR-markers for the analysis and study of genetic diversity of Ukrainian and imported breeds of dairy cattle. Samples of biological material from representatives of three herds of cattle (Ukrainian Red-and-White spotted dairy, Montbeliard breed and their crossbreeds) were selected for the study by the method of groups-analogues. For the analysis of this material the generally accepted zootechnical methods of studying of a selection material and methods of an estimation of animals on molecular – genetic markers are included. According to standard methods, DNA was isolated from peripheral blood lymphocytes using a set of reagents "DNA Sorb B". Amplification of total DNA with ISSR primers was performed on a thermal cycler "Tertsyk" ("DNA technology" of the Russian Federation). Electrophoretic separation of DNA fragments was performed in an agarose gel according to conventional methods. The size of the obtained PCR products was detected using a molecular weight marker SM1343. As a result of the study of the biological material of these animals, the obtained ISSR-PCR products were quite heterogeneous. The vast majority of polylocus spectra had clear discrete bands, but there were amplicons without clear discrete bands. Analyzing the results of the study of the genetic structure of animals of the Ukrainian Red-and-White dairy breed, using primers ISSR-1, ISSR-2, ISSR-3 and ISSR-4, the range of obtained PCR products ranges from 250 bp. up to 3000 bp. The range of amplification products in Montbeliard animals has a smaller range and ranges from 250 bp, respectively. up to 1500 bp.The obtained amplicons for the use of primers ISSR-1 and ISSR-2, ISSR-3 and ISSR-4 in the turf of Ukrainian Red-and-White dairy and Montbeliard breeds have sizes from 350 bp to 2000 bp. Having analyzed the information you can determine the distribution of the number and length of DNA fragments using 4 ISSR-markers. The total number of amplified DNA fragments varies depending on the primer from 21 to 106, and their size ranges from 250 BP up to 3000 bp. Based on the analysis of DNA plymorphism, it is possible to assess the heterogeneity of selected populations of cattle. Thus, as a result of studying the genetic structure of animals of two breeds of dairy cattle and their crossbreeds by intermicrosatellite DNA loci, their individual polymorphism was revealed. The amplification products have significant variations depending on the primer used. Primers ISSR-1 and ISSR-2 were the most informative for the analysis of cattle DNA polymorphism.

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DNA polymorphism, genetic originality and identification of sterlet populations and replacement broodstock (Acipenser ruthenus)

Вестник Пермского университета. Серия «Биология»=Bulletin of Perm University. Biology ◽

10.17072/1994-9952-2021-1-53-60 ◽

2021 ◽

pp. 53-60

Author(s):

L. V. Komarova ◽

◽

A. R. Peleeva ◽

N. V. Kostitsyna ◽

A. G. Melnikova ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Gene Pool ◽

Dna Polymorphism ◽

Molecular Genetic ◽

Natural Populations ◽

Federal District ◽

Acipenser Ruthenus ◽

Sterlet Acipenser Ruthenus

DNA polymorphism has been studied, indicators of genetic diversity and genetic originality have been de-termined for three natural populations and three replacement broodstocks of sterlet (Acipenser ruthenus Linnaeus, Acipenseridae) from the Volga Federal District. In the group of A. ruthenus replacement broodstock, 106 ISSR-PСR markers were identified, and in the group of natural populations, 103 ISSR-PСR markers. The indicators of genetic diversity and the coefficient of genetic originality (CGO) were slightly higher in the group of natural populations. Analysis of genetic structure of natural populations and groups of broodstock herds A. ruthenus showed that the coefficient of genetic differentiation are also slightly higher in the group of natural populations and equal 0,377. As a result of molecular genetic iden-tification, generic and species identification fragments of sterlet DNA were revealed, as well as combina-tions of polymorphic fragments for identification of the studied natural populations and stocks. The data obtained can be used to preserve the gene pool of populations, which is characteristic for a particular re-gion.

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Characterization of Natural Isolates of Bipolaris maydis Associated with Mating Types, Genetic Diversity, and Pathogenicity in Fujian Province, China

Plant Disease ◽

10.1094/pdis-03-19-0650-re ◽

2020 ◽

Vol 104 (2) ◽

pp. 323-329

Author(s):

Yuli Dai ◽

Lin Gan ◽

Hongchun Ruan ◽

Niuniu Shi ◽

Yixin Du ◽

...

Keyword(s):

Genetic Diversity ◽

Mating Type ◽

Dna Polymorphism ◽

Sweet Corn ◽

Issr Markers ◽

Bipolaris Maydis ◽

Fujian Province ◽

Field Isolates ◽

Rational Distribution

Due to the natural destructiveness and persistence of the southern corn leaf blight (SCLB) fungus Bipolaris maydis (Nisikado et Miyake) Shoem, the characterization of B. maydis field isolates is essential to guide the rational distribution of resistant materials in corn-growing regions. In the present study, 102 field isolates collected from seven locations covering the entire region of Fujian Province, China, were assessed for mating type distribution, genetic diversity, and pathogenicity toward local sweet corn cultivars. Mating type detection via polymerase chain reaction indicated that 36.3 and 63.7% of isolates were MAT1-1 and MAT1-2, respectively; more than 80% of these isolates were confirmed using cross assays with known mating type isolates. Thirteen intersimple sequence repeat (ISSR) markers within and among two mating type populations revealed a high level of DNA polymorphism for all combined isolates and between MAT1-1 and MAT1-2 populations. The MAT1-2 population was more diverse based on DNA polymorphism than the MAT1-1 population. The value of GST was 0.0070, ranging from 0.0399 to 0.3044 based on analysis of combined isolates and individual regional populations, respectively, suggesting the presence of genetic differentiation in the two mating type populations from different locations. Pathogenicity assays revealed that both MAT1-1 and MAT1-2 populations were pathogenic to all 11 local sweet corn cultivars tested in this study. The potential of sexual reproduction, existence of genetic diversity in the two mating type populations, and pathogenicity suggest that B. maydis populations have independently clonally adapted under natural field conditions during corn cultivation.

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Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Royal Society Open Science ◽

10.1098/rsos.140255 ◽

2015 ◽

Vol 2 (8) ◽

pp. 140255 ◽

Cited By ~ 7

Author(s):

Claire C. Keely ◽

Joshua M. Hale ◽

Geoffrey W. Heard ◽

Kirsten M. Parris ◽

Joanna Sumner ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Dna Sequences ◽

Nuclear Dna ◽

Urban Expansion ◽

Nuclear Gene ◽

Management Approach ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

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A simple molecular method for rapid identification of commercially used Amblyseius and Neoseiulus species (Acari: Phytoseiidae)

Zootaxa ◽

10.11646/zootaxa.4394.2.9 ◽

2018 ◽

Vol 4394 (2) ◽

pp. 270

Author(s):

M.Y. SYROMYATNIKOV ◽

A.V. KOKINA ◽

N.A. BELYAKOVA ◽

E.G. KOZLOVA ◽

V.N. POPOV

Keyword(s):

Molecular Genetic ◽

Mite Species ◽

Rapid Identification ◽

Internal Transcribed Spacers ◽

Dna Fragments ◽

Neoseiulus Cucumeris ◽

Accurate Identification ◽

Pcr Rflp ◽

Pcr Products ◽

Its1 And Its2

Predatory mites from the Amblyseius (Neoseiulus) genus (Family Phytoseiidae, Order Parasitiformes) are widely used for protecting plants against pests, especially thrips. The differentiation of Amblyseius and Neoseiulus species by their morphological features is problematic despite the fact that they are taxonomically different genera. The Phytoseiidae family includes a lot of species that are extremely difficult to distinguish from each other. The discovery of new molecular genetic markers might considerably facilitate the express identification of commercial mite species. Despite their high morphological similarity, the three common commercial Amblyseius and Neoseiulus mite species (Neoseiulus cucumeris, Amblyseius swirskii, and Neoseiulus barkeri) differed significantly in the nucleotide sequences of DNA fragments containing the ITS1 and ITS2 internal transcribed spacers. We found that when PCR products of the amplified DNA fragments from A. swirskii, N. cucumeris, and N. barkeri were treated with a combination of AccB1I, AspLEI, and SspI endonucleases and the resulting products were separated by electrophoresis in agarose gel, the obtained picture was sufficiently specific to provide accurate identification of the analyzed mite species. The lengths of the digestion products were different enough to allow their resolution in agarose gels. The PCR-RFLP method developed by us allows the rapid and accurate identification of commercially used Amblyseius and Neoseiulus species without DNA sequencing. The combination of the three endonucleases (AccB1I, AspLEI, and SspI) and FaeI can be used for the differentiation of all other but less frequently commercially used Phytoseiidae mites.

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First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽

10.12688/f1000research.3567.1 ◽

2014 ◽

Vol 3 ◽

pp. 66 ◽

Cited By ~ 3

Author(s):

Javier Monzón

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Genetic Structure ◽

Dna Sequences ◽

Canis Latrans ◽

Regional Analysis ◽

Model Organism ◽

Nucleotide Polymorphisms ◽

Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

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Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

Research Society and Development ◽

10.33448/rsd-v10i16.23025 ◽

2021 ◽

Vol 10 (16) ◽

pp. e187101623025

Author(s):

Daniele Paula Maltezo ◽

Julliane Dutra Medeiros ◽

Ana Aparecida Bandini Rossi

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Variability ◽

Polymorphic Information Content ◽

Issr Markers ◽

Group Method ◽

Mato Grosso ◽

Copaifera Langsdorffii ◽

Genetic Structure And Diversity ◽

Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81. The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

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ISSR analysis of two founding plant species on the volcanic island Surtsey, Iceland: grass versus shrub

Surtsey research ◽

10.33112/surtsey.13.2 ◽

2015 ◽

Vol 13 ◽

pp. 17-30 ◽

Cited By ~ 2

Author(s):

Agnieszka Sutkowska ◽

Kesara Anamthawat-Jónsson ◽

Borgthór Magnússon ◽

Wojciech Bąba ◽

Józef R. Mitka

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Diversity Indices ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Plant Colonization ◽

Common Source ◽

High Genetic Diversity ◽

Early Arrival

Prior to the present study there was limited knowledge about the genetic basis of plant colonization on the 50-year-old island of Surtsey, South Iceland. The aim here was to compare genetic structure of two contrasting species, Festuca rubra (arctic fescue) and Empetrum nigrum (crowberry), which have colonized Surtsey since 1973 and 1993, respectively. Inter-simple sequence repeat (ISSR) markers were used to assess genetic diversity and population structure. Two census periods were compared: 1996-1997 and 2005-2006. Using six ISSR primers, we obtained 103 and 139 discernible DNA fragments from F. rubra and E. nigrum respectively. Although the two species displayed similarly high genetic diversity indices (h = 0.238 and 0.235; I = 0.384 and 0.380, respectively), they differed significantly in their genetic profiles. Festuca was genetically structured at the subpopulation level (FST = 0.034, p = 0.007), whereas Empetrum showed a lack of genetic differentiation. A Bayesian STRUCTURE computation further revealed temporal and spatial genetic structure of the species. The early arrival grass F. rubra has expanded from a local genepool. The population was however initially established from different sources, forming a genetic melting pot on Surtsey. On the other hand, the late arrival shrub E. nigrum probably derived from a common source of immigrants.

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Different Habitats Show Similar Genetic Structure of Bunias orientalis L. (Brassicaceae)in Lithuania

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4129186 ◽

2013 ◽

Vol 41 (2) ◽

pp. 396 ◽

Cited By ~ 5

Author(s):

Jolanta PATAMSYTĖ ◽

Tatjana ČĖSNIENĖ ◽

Donatas NAUGŽEMYS ◽

Violeta KLEIZAITĖ ◽

Virginija TUNAITIENĖ ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Genetic Difference ◽

Habitat Type ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Baltic Countries ◽

Bunias Orientalis ◽

The Impact

We studied genetic diversity within and among populations of warty cabbage (Bunias orientalis L.), which is an alien species in Lithuania and other Baltic countries. In Lithuania, this weed colonises two main types of habitats: railway/roadsides and meadows on riversides. The aim of this study was to assess the genetic structure of invasive populations of B. orientalis in Lithuania and consider the impact of diverse habitats on the partitioning of genetic diversity using inter-simple sequence repeat (ISSR) markers. An analysis of molecular variance (AMOVA) carried out on the basis of ISSR showed that there is high genetic differentiation (46%) among populations of B. orientalis, which is probably caused by the founder effect and limited gene flow. However, we observed no impact of habitat on the genetic difference among populations. Similar levels of ISSR polymorphic loci were observed in riverside (P = 31.67%) and railway/roadsides (P = 30.51%) populations. UPGMA cluster analysis and principal coordinate analysis (PCoA) also did not show grouping of studied populations according to habitat type. High genetic differentiation among populations, as indicated by ISSR markers, confirm multiple independent introductions of this species in Lithuania.

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