scholarly journals The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

2020 ◽  
Vol 24 (7) ◽  
pp. 747-754
Author(s):  
V. R. Kharzinova ◽  
N. A. Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Genetic Material ◽  
Animal Husbandry ◽  
Molecular Genetic Analysis ◽  
Fixation Index ◽  
Large White ◽  
Black And White ◽  
The Republic

One of the main tasks of genetics and animal breeding is the assessment of genetic diversity and the study of genetic relationships between different breeds and populations using molecular genetic analysis methods. We analysed the polymorphism of microsatellites and the information on the state of genetic diversity and the population structure of local breeds in Russia: the Kemerovo, the Berkshire, the Liven, the Mangalitsa, and the Civilian; in the Republic of Belarus: the Large White and the Black-and-White; and in Ukraine: the White Steppe, as well as commercial breeds of imported origin of domestic reproduction: the Large White, the Landrace, and the Duroc. The materials used for this study were the tissue and DNA samples extracted from 1,194 pigs and DNA of the UNU “Genetic material bank of domestic and wild animal species and birds” of the L.K. Ernst Federal Research Center for Animal Husbandry. Polymorphisms of 10 microsatellites (S0155, S0355, S0386, SW24, SO005, SW72, SW951, S0101, SW240, and SW857) were determined according to the previously developed technique using DNA analyser ABI3130xl. To estimate the allele pool of each population, the average number of alleles (NA), the effective number of alleles (NE ) based on the locus, the rarified allelic richness (AR), the observed (HO ) and expected (HE ) heterozygosity, and the fixation index (FIS) were calculated. The degree of genetic differentiation of the breeds was assessed based on the pairwise values of FST and D. The analysis of the allelic and genetic diversity parameters of the local breeds showed that the maximum and minimum levels of polymorphism were observed in pigs of the Ukrainian White Steppe breed (NA = 6.500, NE = 3.709, and AR = 6.020) and in pigs of the Duroc breed (NA = 4.875, NE = 2.119, and AR = 3.821), respectively. The highest level of genetic diversity was found in the Large White breed of the Republic of Belarus (HO = 0.707 and NE = 0.702). The minimum level of genetic diversity was found in pigs of the imported breeds – the Landrace (HO = 0.459, HE = 0.400) and the Duroc (HO = 0.480, HE = 0.469) – indicating a high selection pressure in these breeds. Based on the results of phylogenetic analysis, the genetic origin of Large White pigs, the breeds, from which the Berkshire pigs originated, and the genetic detachment of the Landrace from the Mangalitsa breeds were revealed. The cluster analysis showed a genetic consolidation of the Black-and-White, the Berkshire, and the Mangalitsa pigs. Additionally, the imported breeds with clustering depending on the origin were characterised by a genetic structure different from that of the other breeds. The information obtained from these studies can serve as a guide for the management and breeding strategies of the pig breeds studied, to allow their better use and conservation.

scholarly journals Molecular Genetic Diversity Among 12 Clones of Lagerstroemia fauriei Revealed by AFLP and RAPD Markers

HortScience ◽  
2003 ◽  
Vol 38 (2) ◽  
pp. 256-259 ◽  
Author(s):  
Margaret R. Pooler
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Genetic Material ◽  
The United States ◽  
Aflp Markers ◽  
Economic Significance ◽  
Molecular Genetic Diversity ◽  
In The Wild ◽  
The U.S

Many popular crapemyrtle (Lagerstroemia L.) cultivars grown in the United States are interspecific hybrids between L. indica L. and L. fauriei Koehne. The 22 hybrid cultivars released from the U.S. National Arboretum contain primarily genetic material from L. fauriei PI 237884. Examining the genetic diversity ofL. fauriei specimens in the U.S. is valuable because of the historical and economic significance of the species, the increasing interest it is receiving as a source of new cultivars, and its threatened status in the wild. Our objectives were to examine molecular genetic diversity among L. fauriei accessions using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphisms (AFLP) markers. Our results indicate: 1) RAPD and AFLP markers are generally consistent in the genetic relationships that they suggest; 2) the L. fauriei germplasm we examined falls into at least three distinct clusters; and 3) the genetic base of cultivated Lagerstroemia could be broadened significantly by incorporating some of this more diverse L. fauriei germplasm into breeding programs.

scholarly journals PSVII-29 Genetic differentiation of modern and historical samples of the Russian Large White pigs

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 466-466
Author(s):  
Olga V Kostyunina ◽  
Lyubov Getmantseva ◽  
Alexandra Abdelmanova ◽  
Lidia Petrikeeva ◽  
Natalia A Zinovieva
Keyword(s):  
Quality Control ◽  
Molecular Genetic ◽  
Research Result ◽  
Animal Husbandry ◽  
Fixation Index ◽  
Science Center ◽  
Large White ◽  
Bone Powder ◽  
Thermo Fisher Scientific ◽  
Historical Samples

Abstract Involvement in research of historical samples can help to clarify the demographic processes in livestock populations. In most cases, bone powder derived from teeth or skull bones are used for molecular genetic studies of historical samples. The aim of our study was to evaluate genetic differences between historical and modern samples of the Russian Large White pigs. Eight historical specimens of the Large White pigs dated by 60s of the 20th century which are maintained in the Craniological collection of the Livestock Museum named after E.F. Liskun were used for the study. The modern representatives of breed were presented by the samples from eight different farms (LW_New1 - LW_New8, n = 152). All works with historical DNA were carried out in the special facilities of the L.K. Ernst Federal Science Center for Animal Husbandry dedicated for work with ancient DNA. DNA was isolated using COrDIS “Extract” Decalcin kit (COrDIS, Russia) and Prep Filer™ BTA Forensic DNA Extraction Kit (Thermo Fisher Scientific, USA). The whole-genome genotyping was performed using Porcine GGP HD BeadChip chips (Illumina/Novogene, USA). The quality control was performed in PLINK 1.9 using the following settings: geno-0.2, mind-0.2, MAF-0.01, HWE-P< 8.27×10−7. The fixation index (Fst) was calculated using the ADMIXTURE software. The concentration of DNA isolated from the historical samples was varied from 0.550 to 600 ng/μl (A260/280 = 1.46–1.96). The genotypes’ call rates were 0.187–0.986. Six historical samples passed through the quality control were used for the further study. Calculation of Fst values showed, that the historical samples were closer to the LW_new1 and LW_new4 groups (Fst = 0.151 and 0.157, respectively), and the most divergent from the LW_new3 group (Fst = 0.304). Our research result will help to elucidate the genetic architecture of the Russian Large White pigs. This research was supported by the RSF (Project No. 19-16-00109).

scholarly journals New breeding and genetic methods in pig breeding in Belarus

2020 ◽  
Vol 64 (6) ◽  
pp. 757-768
Author(s):  
I. P. Sheyko ◽  
T. N. Timoshenko ◽  
N. V. Pristupa ◽  
E. A. Yanovich ◽  
V. N. Zayats ◽  
...  
Keyword(s):  
Technological Development ◽  
Animal Husbandry ◽  
National Academy Of Sciences ◽  
Large White ◽  
First Order ◽  
Black And White ◽  
Processing Plants ◽  
The Republic ◽  
Scientific Practical ◽  
Effective Development

Six pig breeds: Belarusian large white, Belarusian meat, Belarusian black and white, landrace, Yorkshire and Duroc are involved in breeding and hydridization of pig breeding in Belarus. More than 85 % of pigs supplied to meat processing plants of the Republic are provided by different combinations of interbreed hydridization.For the effective development of this branch in the Republic, the Scientific-Practical Center on Animal Husbandry of the National Academy of Sciences of Belarus organized the system of selection and breeding work in pig breeding directed to create new competitive breeds, types, and hydrides of pigs adapted to the industrial production conditions and not inferior to the productivity of the analogs of the world selection.The main link of this system is the first-order breeding plants (nucleus units) as new-type plants dealing with the selection and breeding of the best animals with the outstanding genetically conditioned breeding and productive qualities. The second link of this system is the first-order breeding breeders that are completed with high-valuable breeding pigs from the leading nucleus unit and are engaged in their reproduction to obtain grandparents (GP).Assessing the level of the technological development of pig breeding in Belarus during the period to the 2030 year, we predicted the indices for the all predictable years (2020–2030). The existing level of the technological development of the pig breeding branch is assessed as the mean one. During 2020–2021 the pig breeding level will be moderate-high, during 2022– 2023 – high, and since 2025–2030 – intensive.

scholarly journals The Population Structure and Selection Signal Analysis of Shenxian Pigs Based on Genome Resequencing Technology

2021 ◽  
Author(s):  
Diao Liu ◽  
Chunlian Lu ◽  
Shang Li ◽  
Mengyu Jia ◽  
Yutao Miao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Meat Quality ◽  
Genetic Relationships ◽  
Animal Husbandry ◽  
Hebei Province ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Large White ◽  
Bioinformatics Analyses ◽  
Pig Breeds

Abstract Shenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3). However, no genes related to meat quality traits were successfully screened.

scholarly journals Cytomic analysis: a modern universal tool for biomedical and ecological and hygienic research (literature review). Part 1

2021 ◽  
Vol 100 (10) ◽  
pp. 1151-1156
Author(s):  
Elena K. Krivtsova ◽  
Faina I. Ingel ◽  
Lyudmila V. Akhaltseva
Keyword(s):  
Medical Research ◽  
Genetic Instability ◽  
Cell Transformation ◽  
Molecular Genetic ◽  
Genetic Material ◽  
Peripheral Blood Lymphocytes ◽  
Molecular Genetic Analysis ◽  
Research Literature ◽  
Prognostic Indicators ◽  
Long Time

The understanding of the connection between malignant cell transformation and genetic instability has existed for a long time. Such markers of genetic instability as micronuclei (MN) and nuclear abnormalities - nucleoplasmic bridges (NPM) and nuclear buds are signs of malignant growth. However, they were seen only as a by-product of genetic instability, a convenient tool for its study for a long time. Only the studies of recent decades that used the latest methods of molecular genetic analysis (genome sequencing of an individual cell, long-term intravital microscopy and individual chromosomes labelling, hybridization in situ, etc.) have made it possible to establish that the rearrangements of the genetic material in cancer cells are much deeper and more massive than it thought to be. In addition, MN turned out to play an active role in maintaining the state of chromosomal instability in the cell population. This review outlines the current understanding of the processes leading to the emergence of unstable genomes - the phenomenon of «genomic chaos» and its particular case, chromothripsis. The molecular biological features of MN and their role in cellular life and the life of the whole organism are also considered. The significance of MN as diagnostic and prognostic indicators in oncological, neurodegenerative and many other diseases has been analyzed. Much attention is paid to the use of cytome analysis of peripheral blood lymphocytes and human epithelial cells in medical research. It has been suggested that, when used in medical research, cytome analysis can serve as a tool to identify individuals with higher cancer risk. We used the PubMed, Web of Science, ResearchGate, Scopus, eLibrary databases as the sources of literature.

Tracing the remnants of medieval raspberries using molecular markers

2015 ◽  
Vol 14 (2) ◽  
pp. 149-156
Author(s):  
Vesna Novak ◽  
Anton Ivancic ◽  
Andrej Susek ◽  
Metka Sisko
Keyword(s):  
Molecular Markers ◽  
Genetic Analysis ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Molecular Study ◽  
Molecular Genetic Analysis ◽  
Microsatellite Data ◽  
Clustering Method ◽  
Natural Conditions ◽  
Fruit Setting

Our investigation was based on a molecular study of the genetic relationships among raspberry genotypes collected around selected medieval castles, Carthusian monasteries and nearby villages. We assumed that the hypothetical medieval raspberry genotypes could be traced to isolated medieval settlements that used to be highly prosperous during the feudal era but were later abandoned. Some of these genotypes could have survived in natural conditions without seed multiplication for at least three centuries. The molecular genetic analysis was based on microsatellite data. A total of 155 alleles were detected at 18 microsatellite loci. The clustering method grouped the analysed genotypes into seven main clusters. The analyses indicated that the most probable medieval genotypes had been collected around the ruins of two abandoned Carthusian monasteries: Zice and Jurkloster. They were morphologically very similar, vigorous and primitive but obviously not wild genotypes. The plants could be more than 2.3 m high, the canes were medium waxy, the lower and upper parts of the canes were covered by sparse short spines, the mid part was more or less completely smooth, the fully developed leaves were 15–25 cm long and the inflorescences were loose. In addition, the flowers were relatively small, the fruit setting was poor and the fruits were small, ovoid to conical and more aromatic than those of modern cultivars.

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 108-114 ◽  
Author(s):  
José Miguel Soriano ◽  
Carlos Romero ◽  
Santiago Vilanova ◽  
Gerardo Llácer ◽  
María Luisa Badenes
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Malus Domestica ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Mean Value ◽  
Eriobotrya Japonica ◽  
Fixation Index ◽  
Group Method ◽  
Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

scholarly journals Reindeer Population as an Indicator of Sustainable Development of the Arctic Territory

2021 ◽  
Vol 9 (4) ◽  
pp. 21-28
Author(s):  
Natalia V. Karmanovskaya
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Genetic Relationships ◽  
Animal Husbandry ◽  
Komi Republic ◽  
Genetic Distances ◽  
The Arctic ◽  
Murmansk Oblast ◽  
The Matrix ◽  
Breeding Programmes

The objectives of this study are to carry out genetic monitoring of domestic reindeer of Nenets breed raised on the territory of Taimyr; establishment of the genetic bank of domestic reindeer of Nenets breed; as well as a comparative analysis with populations of the Nenets breed from other breeding regions (Nenets and Yamalo-Nenets Autonomous Okrug, Murmansk Oblast and the Komi Republic) using DNA markers. The microsatellites were used in the studies as DNA markers of genetic diversity. Genotyping was carried out by the methods of the Laboratory of molecular selection basis of L.K. Ernst Federal Research Center for Animal Husbandry. Statistical data processing was performed using the GenAlEx 6.5, SplitsTree 4.14.5 software, as well as the software packages “diveRsity”, “pophelper”, and “adegenet” for the R computing environment. As a result of the study, it was found that the population of reindeer of Taimyr breed in the village of Tukhard is characterised by the minimum level of polymorphism and genetic diversity, as indicated by the minimum values of all population genetic indicators. The authors assume that the patterns that have been identified are primarily the result of breeding programmes on the samples presented in this study (such studies have not been conducted before). The results of the PCA analysis and the phylogenetic dendrogram of genetic relationships, built on the basis of the matrix of Jost's D pairwise genetic distances using the NeighborNet, revealed a similar genetic structure of Taimyr populations, which, most likely, could be due to the close geographical localisation of the studied individuals. The authors come to the conclusion that a low level of both allelic and genetic diversity in the future may negatively affect the adaptation of animals to environmental conditions.

scholarly journals MONITORING OF Aegilops L. LOCAL SPECIES GENETIC DIVERSITY OF KAZAKHSTAN’S FLORA

2018 ◽  
Vol 22 (4) ◽  
pp. 484-490 ◽  
Author(s):  
R. Urazaliev ◽  
M. Yessimbekova ◽  
K. Mukin ◽  
A. Chirkin ◽  
G. Ismagulova
Keyword(s):  
Genetic Diversity ◽  
Global Climate ◽  
Molecular Genetic ◽  
Crop Wild Relatives ◽  
Molecular Genetic Analysis ◽  
Ex Situ ◽  
Marker Allele ◽  
New Genes ◽  
Local Species ◽  
Allelic Variations

Cereal Crop Wild Relatives (CWR) are a very  important gene pool for cereal/wheat improvement. New genes for resistance to diseases and pests are urgently needed to avoid using pesticides and to raise adaptivity to the environmental stresses caused by global climate change. In this regard, the study is aimed at ex situ conservation of Aegilops L. genus local ecotypes’ genetic diversity, which is very relevant and promising for breeding. In order to establish breeding utility and form an ex situ collection reflecting the intra- and inter-specific diversity, the phenotypic screening of Kazakhstan’s local populations of Aegilops L. genus (Ae. cylindrica, Ae. tauschii, Ae. triuncialis and Ae. crassa) was conducted on the basis of multiple indicators. For the first time molecular-genetic analysis of 50 representatives of Aegilops L. genus from Kazakhstan’s flora was performed. The microsatellite analysis with the use of 11 EST-SSR markers revealed eight of them to be most effective. For each marker, allele frequency and average heterozygosity was calculated. For the most informative markers the presence of 5 and 6 respective allelic variations was found. A bank of genomic DNA was created and kept in ex situ storage (–70 °С, long-term) in the IMBB of the MES of RK.

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