Genetic Diversity In Animals Research Articles

GENETIC VARIATION IN TWO PHENOTYPES OF BALI CATTLE (Bos javanicus) INFERRED BY (AG)9C ISSR MARKER

<p class="Abstract"><strong>Background.</strong> Bali cattle (<em>Bos javanicus</em>) are Indonesian native cattle that are kept as beef cattle. Among Bali cattle, however, there are white Bali cattle, called Taro cattle which are found in small numbers of the population and used only for religious ceremony needs. <strong>Objective. </strong>To quantify the genetic variation in two phenotypes of Bali cattle (wildtype and white colors) with inter-simple sequence repeat (ISSR) primer of (AG)<sub>9</sub>C. <strong>Methodology. </strong>Forty Bali cattle, 20 wildtype bulls, and 20 white Bali cows were used. The blood samples were taken from the jugular vein of each animal using venoject vacutainer tube containing EDTA. The DNA extraction was performed using DNA extraction kit following the manufacturer’s protocol. Number of DNA fragments, number of effective alleles (n<sub>e</sub>), and polymorphic informative content (PIC) were calculated to describe the genetic diversity in animals under study. <strong>Result</strong><strong>s</strong>: Results showed that three haplotype (H) types were observed in the animals under this study based on the ISSR fragments. The polymorphic informative content (PIC) in the white animals was higher than in the wild-type animals (0.62 vs 0.18). According to (AG)<sub>9</sub>C ISSR marker, mostly white (50%) and wildtype (90%) animals were classified into H2 type. Therefore, a total of 25% of white and 10% of wild-type animals were classified into H3 type. While 25% of white animals were classified into H1 type. <strong>Implications. </strong>the information generated in this study can be used as early information to investigate the molecular genetics of Taro cattle. <strong>Conclusion</strong><strong>s</strong>: This study suggests that many white animals have a specific locus which is absent in wild-type animals. </p>

Genetic characteristics of the herd of KP "Rybkovskoe" by alleles of the EAB-locus of blood groups

The analysis of the genetic structure of the herd to the marker alleles of the EAB locus - blood groups was according. The EAB-allele G2Y2E/1Q/according to the results of the study with a high frequency of 11.9 – 15.7%, in the herd, whereas its frequency is 18% for the breed was found. In the period 2011-2015 sixteen main alleles of the EAB-locus of blood groups with a total frequency of 0.802 in the herd were found. In 2016-2020, the main EAB-alleles were 12 and the frequency of their occurrence was equal 0,752. The number of four main alleles of the Red-and-White Holstein breed Y1A/1, O2A/2J/2K/O/, I1Y2E/3G/G//, B1O1 decreased from 0,213 to 0,102. With the highest frequency, totaling 40.6% marker EAB - alleles G2T2Y2A/1B/D/G/I/Q/Y/B// (0.052), E/3G/G// (0,070), B1I1Q (0,053), O1I/Q/ (0,080), B2G2O1Y2D/E/2G// (0,056), b (0.095) in KP "Rybkovskoe" are found. In the breed, these alleles occur with a frequency of 29.8%. There are no significant differences between the breed and the herd in the frequency of EAB alleles. The difference did not exceed 2.4 – 2.7%. From a genetic standpoint, the animals of the herd and the breed are close. The index of genetic similarity between them is 0.95. The level of homozygosity was 6.2% in the herd in the period 2016-2020, but its increase over the past five years was 1,2%, indicating a decrease in the genetic diversity of animals. The number of producer sires used by the pedigree farm decreased to 14 and the total diversity of their alleles decreased to 15. Comparative analysis showed that the difference in productivity of the daughters of bulls with alternative EAB-alleles was from 7 to 710 kg of milk, 0.01 – 0.19% fat and 0.02 – 0.09% protein for the first lactation in favor of one or another marker allele from the producer. By the highest lactation, the differences in milk yield are 55 – 1034 kg of milk, in fat content – 0.01 – 0.22%, protein – 0.02 – 0.14%.

LITERATURE REVIEW: APLIKASI PENANDA MOLEKULER UNTUK ANALISIS KEANEKARAGAMAN GENETIK HEWAN

Background: Molecular markers (DNA markers) are DNA sequences that are easily detected to characterize or detect certain genetic diversity, one of which is in animals. There are various marker systems used with their respective characteristics. Some of the molecular markers include RFLP, RAPD, ISSR, SSR, and SNP. The purpose of this study was to analyze genetic diversity in animals using molecular marker applications.Methods: The method used is literature review using reputable national and international journals.Results: Based on the results of a literature review, the genetic diversity of various species such as catfish, deer, tilapia, crabs, seahorses, ducks, cattle and buffaloes can be analyzed for genetic diversity using various molecular markers either by using PCR-RFLP, RAPD, ISSR, SSR, or SNPs.Conclusion: The application of molecular markers can be used to analyze animal genetic diversity.

Production of germline chimeric quails by transplantation of cryopreserved testicular cells into developing embryos

The germplasm is a resource and tool for the conservation of genetic diversity in animals, including birds. Securing germplasm is limited in most bird species due to difficulties in semen collection and germ cell isolation, lack of germ cell-specific markers, and in vitro culture systems. Here, we report the production of germline chimeric quails by transplant of cryopreserved testicular cells (TCs) into the developing embryo.The testicular germ cell properties were maintained after freeze-thaw, with no significant reduction in cell viability irrespective of storage length. Cryopreserved TCs were transferred into Hamburger Hamilton (HH) stage 14–17 quail embryos, and were demonstrated to migrate into the embryonic gonads with similar efficiency to freshly isolated TCs. Twenty of 81 recipient embryos yielded hatchlings from cryopreserved TCs and the germline transmission efficiency was similar to that of freshly isolated cells. In conclusion, cryopreserved adult quail TCs are capable of (de)differentiation into functional gametes in recipient quail gonads and can generate donor TCs-derived progenies. This system is feasible for the isolation of sufficient germplasm resources from various bird species for conservation purposes.

IN MEMORY OF LEONID VYSHNEVSKYI

On May 21, 2019, at the age of 59, a well-known scientist and statesman, head of the department of animal genetic resources of the Institute of Animal Breeding and Animal Genetics of Zubets NAAS, Director of State Enterprise "Main Scientific Production Breeding and Information Center in Animal Production of the Institute of Breeding and Genetics of Animals of NAAS" Candidate of Agricultural Sciences Leonid Vyshnevsky died.
 We have lost an outstanding person who has worked hard throughout his life to improve the breeding stock that meets current European requirements.
 Leonid Vyshnevskyi was born on May 1, 1960 in the village Listvyn of Ovruch district , Zhytomyr region in family of employees.
 After graduating with honors in 1982 from the Zootechnical Faculty of the Zhytomyr Agricultural Institute, he worked for some time as the chief zootechnician in the state farms of the Zhytomyr region. Since 1984 - Junior Research Fellow at the Research Institute of Agriculture of the Non-Black Zone of the USSR. Since September 1985 - postgraduate student of the Department of Breeding of Animals of the Ukrainian Agricultural Academy. After graduation from 1993 to 1998 he worked as a chief specialist of the department of breeding and breeding work of the association of state breeding factories of Ukraine "Ukrderzhplemzavody", carrying out work on the organization of breeding accounting in the farms and introduction of an automated system of management of the breeding process in dairy cattle breeding. From 1999 to 2000, Leonid Vyshnevskyi, being the chief specialist of the department of the Main State Breeding Inspection, was engaged in the formation of the basics of the legal framework on breeding work in animal husbandry and the organization of assessment of breeding animals. From 2000 to 2003 - Deputy Director General of the State Scientific Production Production Selection, and from September 2003 to August 2006 - First Deputy Director of the State Agency for the Identification and Registration of Animals. At this time, with his direct involvement, that a unified state system for the identification and registration of farm animals was introduced at the national level. His responsibilities for being General Director of the Selection concern included the organization of a breeding system in animal husbandry (attestation of the subjects of breeding business in animal husbandry, creation and maintenance of the State Breeding Register, preparation of normative-legal acts on conducting breeding records and evaluation breeding value of different species of farm animals).
 In 2008, Leonid Vyshnevskyi defended his PhD thesis on "Selection and genetic methods of Myrhorod pigs breed improvent productivity and crossbreeding use" in the specialty 06.02.01 - breeding and selection animals. The scientist carried out the results of his research, being first as a scientific scientist, then as a senior researcher, and since September 2010 - head of the laboratory of the beef breed gene pool of the Institute of Breeding and Animal Genetics of NAAS. Due to the creation of the Department of Animal Genetic Resources and Information Systems, whose work was closely linked to the previous activities of Leonid Vasilyevich, he was transferred to the post of Head of Department since June 2011.
 Researches of the scientist have established the possibility of using modern methods of DNA-typing of animals for optimization of the breeding process in animal husbandry. Leonid Vyshnevskyi scientific achievements include a patent for the utility model "Application of ISSR-typing method for optimization of breeding process in small breeds of pigs as a means of individual selection for increasing productivity and preserving the genetic diversity of animals of endangered populations". While working at the Institute of Animal Breeding and Genetics, he actively participated in the development of methodological bases for biodiversity conservation in animal husbandry in Ukraine and the introduction of centralized automated breeding records at the state level.
 The Leonid Vyshnevskyi life is an example of a worthy, responsible leader who was able to organize and rally around the best specialists of the industry. He was able to inspire his energy, find the right word, give the right direction to make the necessary changes.Leonid Vyshnevskyi will forever remain in our grateful memory and our hearts. Light memory, eternal memory….

Persistence of remnant patches and genetic loss at the distribution periphery in island and mainland populations of the quokka

Understanding the spatial structure of populations is important in developing effective management options for threatened species, and for managing habitat connectivity for metapopulation function, and for demographic and genetic heterogeneity. We used genetic information to investigate the structure of populations of the quokka, Setonix brachyurus, in south-west Western Australia. We hypothesised that movement between known populations would be relatively rare and result in significant genetic structuring. Genetic analyses from 412 adult individuals at 14 nuclear markers (microsatellite) from 33 sampling locations identified structure, diversity and spatial separation of quokkas across their mainland distribution and on two islands. We identified nine inferred (K = 9) populations of quokka that would be otherwise difficult to define with standard ecological techniques. The highest genetic diversity was evident in a large central population of quokka in the southern forest area and genetic diversity was lower at the peripheries of the distribution. The Rottnest Island population contained 70% of the genetic diversity of the mainland populations but the genetic diversity of animals on Bald Island was markedly lower. Populations of quokka in the northern jarrah forest were the only ones to show evidence of recent or long-term population bottlenecking. Of particular interest was the recently identified population at the Muddy Lakes area (the only remaining locality on the Swan Coastal Plain), which was identified as being genetically associated with the southern forest population. Overall, spatial and population cluster analysis showed small insular populations in the northern jarrah forest area, but in the southern forests there appears to be a large panmictic population.

FEATURES OF INHERITANCE OF GENOTYPES OF BLOOD GROUPS ON SYSTEM EAB EMBRYOS CATTLE BREED UKRAINIAN WHITEHEADED

FEATURES OF INHERITANCE OF GENOTYPES OF BLOOD GROUPS ON SYSTEM EAB EMBRYOS CATTLE BREED UKRAINIAN WHITEHEADED

Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication

BackgroundGene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels’ unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods.ResultsIn the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions.ConclusionsSyntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.

Analysis of microsatellite DNA in rodents from Eastern Urals Radioactive Trace zone and contiguous territories

The variability of four microsatellite loci of rodents, caught from the head part of Eastern Urals Radioactive Trace (EURT), along with the rodents inhabiting contiguous zone with background radiation level and distant-reference territory, was analyzed forthe first time. Differences in the parameters of genetic diversity between northern red-backed voles from the EURT zone and from the reference population were detected. An increase in some indices of genetic diversity in animals from a contiguous to the EURT zone was found; this is probably associated with animal migration and configuration of the area of pollution. A transfer of radiation-induced effects to the contiguous territories and a decrease in the possibility of fixation of adaptations in a series of generations of mobile rodent species in the area of local radioactive pollution are consequences of migrations. The results of the study make it possible to recommend microsatellite markers for the analysis of radiation-induced effects in rodents as model objects of radioecological monitoring.

Population structure and genetic diversity of the black-footed rock-wallaby (Petrogale lateralis MacDonnell Ranges race)

Genetic diversity is a critical determinant of the persistence of populations because it enables animals to evolve and adapt to environmental change. Black-footed rock-wallabies (Petrogale lateralis MacDonnell Ranges race), or warru, once occupied virtually all suitable habitat within the arid zone of central Australia. However, only two metapopulations now remain in the southern portion of this race’s range (South Australia) and a recovery program has involved both in- and ex-situ conservation initiatives. To establish whether genetic factors such as inbreeding may be inhibiting population recovery, the current study examined the population structure and genetic diversity of animals in the three largest-known extant colonies using six polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed substantial population structuring (pairwise FST values 0.122–0.278), congruent with geographically distinct colonies. There was some evidence of dispersal, with two migrants identified across two colonies, but little evidence for extensive interbreeding among colonies. Population substructure was evidenced by high values of FIS in one colony. All populations possessed relatively high levels of genetic diversity (allelic richness: 5.1–7.5, heterozygosity: 0.70–0.72). On the basis of a genetic analysis of parentage, approximately half of all males and females in the known metapopulations produced offspring. This has likely contributed to the retention of genetic diversity across colonies. These findings have implications for the management of both the in- and ex-situ warru populations.

Genome-Wide Copy Number Variations Inferred from SNP Genotyping Arrays Using a Large White and Minzhu Intercross Population

Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.

Elevated genetic diversity of mitochondrial genes in asexual populations of Bark Lice (‘Psocoptera’: Echmepteryx hageni)

Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: 'Psocoptera') is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H=0.98), whereas the sexual forms had significantly lower haplotypic diversity (H=0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π=0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: (i) larger effective population size, (ii) greater mutation rate or (iii) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.

Multiplex PCR panels of novel microsatellites for the ark shell Scapharca broughtonii (Pteriomorphia, Arcoida)

A pivotal role of conservation genetics is to establish an appropriate strategy to maintain the genetic diversity of animals with dwindling natural resources. Tackling this issue requires polymorphic genetic markers such as microsatellites. We developed 11 microsatellite markers for a marine bivalve, the ark shell (Scapharca broughtonii), whose natural resources have considerably declined in recent years. We applied the novel markers coupled with a previously reported one to multiplex polymerase chain reaction trials, successfully allocating them into four multiplex panels. Of the 11 markers, nine met Hardy–Weinberg equilibrium (P > 0.05) with a certain degree of polymorphisms in a natural population, suggesting the potential of the markers in its application to the conservation genetics for the ark shell.

Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"

Bazin et al. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.

Mitochondrial DNA and Population Size

In their Report “Population size does not influence mitochondrial genetic diversity in animals” (28 Apr., p. [570][1]), E. Bazin et al. present compelling evidence that selective sweeps occur in animal mitochondrial DNA (mtDNA) and reduce genetic diversity below the level expected at mutation-

The genetic response to Snowball Earth: role of HSP90 in the Cambrian explosion

ABSTRACTThe events that shaped the Cambrian explosion from 545 to 530 Ma, when multicellular animals suddenly appeared in the fossil record, are not fully understood. It is likely that the evolution of new transcription factors and other signal transduction proteins that regulated developmental networks was important in the emergence of diverse animal phyla seen in the Cambrian. I propose that one or both extensive glaciations that ended about 670 and 635 Ma were important in the evolution of signal transduction proteins in small animals in the Neoproterozoic/Proterozoic. These glaciations have been called Snowball Earth. One consequence of these glaciations is that they increased the expression of genetic diversity in animals due to the effect of extreme climatic stress on heat‐shock protein 90 (HSP90). Climatic stress diverted HSP90 from chaperoning the folding and proper intracellular localization of many signal transduction proteins that regulate development in animals. As a result, pre‐existing mutant signal transduction proteins and developmental pathways were expressed in animals. Selectively advantageous mutations were fixed in stem group animals and later were a source for the expansion of animal phyla during the Cambrian.