scholarly journals Population structure and phylogenetic analysis of laboratory rabbits in Taiwan based on microsatellite markers

2018 ◽  
Vol 26 (1) ◽  
pp. 57 ◽  
Author(s):  
Fang-Yu Lai ◽  
Shih-Torng Ding ◽  
Po-An Tu ◽  
R.S. Chen ◽  
Der-Yuh Lin ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Animal Health ◽  
Principal Component ◽  
Fixation Index ◽  
Genetic Characteristics ◽  
Software Analysis ◽  
New Genes ◽  
Unrooted Phylogenetic Tree ◽  
Research Institute

Laboratory rabbits used in Taiwan are primarily supplied by the Livestock Research Institute (LRI) and the Animal Drugs Inspection Branch (ADIB) of the Animal Health Research Institute. An analysis of the genetic characteristics and structure of these populations would thus be a fundamental step in building a long-term management programme for maintaining stable animal quality and preserving the genetic variation among the populations. In this study, DNA samples were isolated from founders of 5 populations: New Zealand White rabbits (NZW) and Japanese White rabbits (JPN) from the ADIB, NZW and Rex rabbits (REX) from the LRI, and NZW from a private rabbit breeding farm in Ban Ciao (BC). A set of microsatellite markers, 18 in total, was designed for genetic analysis. The average values for the allele number (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (H<sub>E</sub>), and Wright’s fixation index (F<sub>IS</sub>) were 5.50, 2.437, 0.442, 0.568 and 0.232, respectively. These results revealed that this set of microsatellite markers has high diversity and that the major local populations have a tendency toward inbreeding. At the same time, analysis of molecular variance results showed that the laboratory rabbits used in Taiwan have maintained a high level of within-population genetic differentiation (83%). The genetic differentiation among clusters was moderate (F<sub>ST</sub>=0.18), and Bayesian cluster analysis showed that the most likely number of groups was 4 (K=4). Principal component analysis (PCA) also showed 4 divergent clusters. The LRI and BC NZW populations were not separated when K=4 was used in a Structure software analysis and were also hard to split until principal component 3 in PCA. The individual unrooted phylogenetic tree showed that the 5 populations were separated, except that some individuals from the LRI NZW population overlapped with the ADIB NZW and BC NZW populations. As such, in order to counteract the reduced F<sub>IS</sub> (0.232) and maximise heterozygosity, the 3 NZW populations could be interbred or have new genes introduced into them. The set of microsatellite markers used herein was useful for studying the relationships and genetic diversities among these rabbit populations of Taiwan. Based on the resulting data, rabbit farms in Taiwan could select parental stocks for planned mating in the future as part of strategies to preserve and restore the rational breeding of laboratory rabbits.

scholarly journals Monitoring of genetically close Tsaiya duck populations using novel microsatellite markers with high polymorphism

2020 ◽  
Vol 33 (6) ◽  
pp. 888-901
Author(s):  
Fang-Yu Lai ◽  
Yi-Ying Chang ◽  
Yi-Chen Chen ◽  
En-Chung Lin ◽  
Hsiu-Chou Liu ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
High Capacity ◽  
Principal Component ◽  
Conservation Strategies ◽  
Genetic Characteristics ◽  
Pekin Ducks ◽  
Allele Number ◽  
Limited Degree ◽  
The Individual ◽  
Genetic Structures

Objective: A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan.Methods: The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations.Results: In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population.Conclusion: According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Genetic Differentiation of Archachatina marginata Populations from Three Vegetation Zones Using Radom Amplified Polymorphic DNA Polymerase Chain Reaction

2015 ◽  
Vol 7 (3) ◽  
pp. 372-381
Author(s):  
Comfort O. AFOLAYAN ◽  
Michael Olugemi AWODIRAN
Keyword(s):  
Genetic Differentiation ◽  
Principal Component ◽  
Ammonium Bromide ◽  
Vegetation Zones ◽  
Suitable Parameter ◽  
Variable Feature ◽  
Canonical Variates ◽  
Cetyl Trimethyl Ammonium ◽  
High Level ◽  
Dna Profiles

The genetic differentiation of Archachatina marginata populations from three different zones of Nigeria was studied with a view to delimiting them into sub-species. One hundred and nineteen (119) snail specimens were collected, comprising of forty (40) specimens from Yenagoa (Mangrove forest) and from Kabba (Guinea Savanna) and thirty nine (39) specimens were from Ile-Ife (Rainforest). Eight parameters of the shell specimens of A. marginata which included height of shell, width of shell, aperture height, aperture width, spire length, spire width, penultimate whorl length and first whorl length were subjected to Principal Component Analysis (PCA) and Canonical Variates Analysis (CVA) to delimit the populations into sub-species. DNA of the various populations was extracted from the foot muscle using CTAB (Cetyl Trimethyl Ammonium Bromide) method, which was subjected to RAPD analysis. The RAPD studies employed five (5) oligonucleotide primers (OPB – 17, OPH – 12, OPH – 17, OPI – 06 and OPU – 14) to amplify DNA from 27 samples of A. marginata selected. All five primers produced different band patterns, and the number of fragments amplified per primer varied. Among them, OPB- 17 gave DNA profiles with more numerous bands than the others primers. Both PCA and CVA produced overlapped clusters of A. marginata specimens from the three vegetation zones. The height of shell was observed to be the most variable feature and preferably the most suitable parameter for population grouping. Analysis of the proportions of polymorphic loci and band sharing based on similarity indices for A. marginata samples indicated a relatively high level of genetic variation in the populations from the three areas.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Development of microsatellite markers for a giant water bug, Appasus japonicus, distributed in East Asia

2020 ◽  
Author(s):  
Tomoya Suzuki ◽  
Akira S. Hirao ◽  
Masaki Takenaka ◽  
Koki Yano ◽  
Koji Tojo
Keyword(s):  
Microsatellite Markers ◽  
East Asia ◽  
Local Level ◽  
Mainland China ◽  
Fixation Index ◽  
Japanese Archipelago ◽  
Red Data Book ◽  
Expected Heterozygosity ◽  
Data Book ◽  
Polymorphic Microsatellite

AbstractWe developed microsatellite markers for Appasus japonicus (Hemiptera: Belostomatidae). This belostomatid bug is distributed in East Asia (Japanese Archipelago, Korean Peninsula, and Mainland China), and often listed as endangered species in the ‘Red List’ or the ‘Red Data Book’ at the national and local level in Japan. Here we describe twenty novel polymorphic microsatellite loci developed for A. japonicus, and marker suitability was evaluated on 56 individuals from four A. japonicus populations (Nagano, Hiroshima, and Yamaguchi prefecture, Japan, and Chungcheongnam-do, Korea). The number of alleles per locus ranged 1–12 (mean = 2.5), and average observed and expected heterozygosity, and fixation index per locus were 0.270, 0.323, and 0.153, respectively. The 20 markers described here will be useful for investigating the genetic structure of A. japonicus populations, which can contribute in population genetics studies of this species.

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

Limited genetic differentiation in Labeo rohita (Hamilton 1822) populations as revealed by microsatellite markers

2014 ◽  
Vol 57 ◽  
pp. 427-431 ◽  
Author(s):  
L. Sahoo ◽  
B.P. Sahu ◽  
Sofia P. Das ◽  
Subrat K. Swain ◽  
D. Bej ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Labeo Rohita

scholarly journals Genetic characteristics of Giardia duodenalis from sheep in Inner Mongolia, China

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 60
Author(s):  
Letian Cao ◽  
Kelei Han ◽  
Luyang Wang ◽  
Surong Hasi ◽  
Fuchang Yu ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Inner Mongolia ◽  
Animal Health ◽  
Giardia Duodenalis ◽  
Small Subunit ◽  
Genetic Characteristics ◽  
Zoonotic Pathogen ◽  
Multilocus Genotyping ◽  
Sequences Analysis ◽  
World Information

Giardia duodenalis is an important zoonotic pathogen for both human and animal health. Although there have been reports on G. duodenalis infections in animals all over the world, information regarding the prevalence and genetic characteristics of G. duodenalis in sheep in Inner Mongolia, China, is limited. In this study, 209 sheep fecal specimens were collected in this autonomous region. We established that the prevalence of G. duodenalis was 64.11% (134/209), as determined using nested PCR detection and sequences analysis of the small subunit ribosomal RNA (SSU rRNA) gene. Based on the beta-giardin (bg) locus, the glutamate dehydrogenase (gdh) locus, and the triose phosphate isomerase (tpi) locus to study genetic characteristics, both assemblages A (2.99%, 4/134) and E (97.01%, 130/134) were found. Five novel nucleotide sequence of assemblage E were detected, two at the bg locus, two at the gdh locus, and one at the tpi locus. Multilocus genotyping yielded four assemblage E and two assemblage A multilocus genotypes (MLGs), including four novel assemblage E MLGs and one novel assemblage A MLG. Results of this study indicated that G. duodenalis was highly prevalent in sheep in Inner Mongolia. This study is the first to use the multilocus genotyping approach to identify G. duodenalis in sheep from this region.

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