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

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.

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Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

10.21203/rs.3.rs-669769/v1 ◽

2021 ◽

Author(s):

Rafael Oliveira Moreira ◽

Eduardo de Andrade Bressan ◽

Horst Bremer Neto ◽

Angelo Pedro Jacomino ◽

Antonio Figueira ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Microsatellite Markers ◽

Native Species ◽

Genetic Parameters ◽

Genomic Library ◽

Conservation Strategies ◽

Paulo State ◽

Allele Number ◽

Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

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

World Rabbit Science ◽

10.4995/wrs.2018.7362 ◽

2018 ◽

Vol 26 (1) ◽

pp. 57 ◽

Cited By ~ 2

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 (HE), and Wright’s fixation index (FIS) 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 (FST=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 FIS (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.

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A study on genetic diversity of bagrid catfish (Hemibagrus guttatus Lacepede, 1803) using microsatellite markers

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/16/1/9203 ◽

2018 ◽

Vol 16 (1) ◽

pp. 59-65

Author(s):

Bùi Hà My ◽

Nguyễn Thị Hương ◽

Nguyễn Hữu Đức ◽

Trần Thị Thúy Hà

Keyword(s):

Microsatellite Markers ◽

Economic Value ◽

Low Frequency ◽

Wild Populations ◽

Genetic Characteristics ◽

Allele Number ◽

Expected Heterozygosity ◽

Artificial Breeding ◽

The Mean ◽

High Level

Bagrid catfish (Hemibagrus guttatus Lacepede, 1803) is a wild species of high economic value in Northern Vietnam. Artificial reproduction of bagrid catfish requires sources of quality fingerlings in terms of genetics. In fact, bagrid catfish is endangered due to overhunting. Until now, studying on bagrid catfish was mainly focused on biology characterictics and artificial breeding. In this study, three microsatellite markers were used to assess the genetic characteristics of four bagrid catfish populations (three wild populations collected in Tuyên Quang, Phu Tho, Ha Giang and a cultured population in Hai Duong). These markers were registed Genbwith the code of KJ873116, KJ873117 and NC 023976 for HM7, HM8 and SS1, respectively. All of the loci showed high level of polymorphism with 16 alleles in total which were 5 at locus HM7, 5 at locus HM8, and 6 at locus SS1. Total allele number in population collected in Ha Giang was higher than that of Tuyen Quang, Phu Tho and Hai Duong populations. The mean of number of observed alleles (Na = 3,83 ± 0,24) was higher than the mean number of effective alleles (Ne = 2,14 ± 0,13) and low frequency alleles (< 0,1) were observed in all loci. The value of the expected heterozygosity (He = 0,38- 0,63) was lower than that of the observed heterozygosity (Ho = 0,51-0,71). FIS value was low and the genetic differences between four populations was insignificant as FST < 0,05. The results provide useful information for breeding program and conservation of the bagrid catfish in the future.

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Molecular characterization of Iranian dromedaries using microsatellite markers

Acta Agronómica ◽

10.15446/acag.v69n4.64487 ◽

2021 ◽

Vol 69 (4) ◽

pp. 321-330

Author(s):

Mohammadreza Mohammadabadi ◽

Mehrdad Ghasemi Meymandi ◽

Mahdieh Montazeri ◽

Volodymyr Afanasenko ◽

Oleksandr Kalashnyk

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Camelus Dromedarius ◽

Conservation Strategies ◽

The North ◽

Allele Number ◽

Total Genetic Diversity ◽

Hardy Weinberg Equilibrium ◽

Different Populations ◽

Future Direction

Considering the importance of maintaining the genetic diversity in native animals, this study conducted to analyse genetic diversity in dromedary populations in the north of Kerman province, Iran, using eight autosomal microsatellite markers. Eighty-one blood samples were collected from five different populations and DNA was extracted. The highest and the lowest allele number and effective alleles were shown in YWLL08 (21 and 4) and VOLP32 (14.97 and 3.11), respectively. The expected heterozygosity varied from 0.778 in Sahra-e Jahad population to 0.847 in Nogh population. The test for Hardy-Weinberg equilibrium showed significant deviations in most loci. The mean multilocus FST value (0.057) suggested that differentiation is moderate between populations. From total genetic diversity, only 6% were due to differentiation among populations, while the remaining 94% corresponded to differences among individuals within each population. The results of the current study indicated that the Camelus dromedarius populations in the north of Kerman province have a relativity high genetic variation and the data could be useful for designing the breeding strategies and conservation. The degree of variability demonstrated implies that studied populations are rich reservoirs of genetic diversity that must be preserved. A future direction to our study can be studying all of the Iranian Camelus dromedarius populations to better evaluate the level of inbreeding and establish the appropriate conservation strategies aimed to avoid losses of genetic diversity.

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THE ROLE OF PHAGE THERAPY IN THE FORMATION OF THE INTESTINAL MICROECOSYSTEM

"Medical & pharmaceutical journal "Pulse" ◽

10.26787/nydha-2686-6838-2020-22-12-183-191 ◽

2020 ◽

pp. 183-191

Author(s):

Gladkov S.F. ◽

Perevoshchikova N.K. ◽

Chernykh N.S. ◽

Pichugina Yu.S. ◽

Surkova M.A.

Keyword(s):

Intestinal Microbiota ◽

Allergic Diseases ◽

Evidence Base ◽

Immunological Tolerance ◽

Convincing Evidence ◽

Selective Decontamination ◽

Genetic Characteristics ◽

Treatment And Prevention ◽

Intestinal Infections ◽

The Individual

The current adverse situation associated with the presence of a pandemic of allergic diseases is due to the lack of a scientifically based concept of treatment and prevention. The increased interest of researchers from different countries in the formation of immunological tolerance by modeling the intestinal microbiota is of high importance. Methods of influence on the microbial communities of the child's intestine should be as delicate as possible, taking into account the individual genetic characteristics of the microecosystem and the possibility of anaphylaxis. Until now, probiotic drugs have been widely used to correct dysbiosis, but data is gradually accumulating that there is no convincing evidence base for their use for the treatment and prevention of atopy. The use of bacteriophages is very relevant and one of the promising, actively studied areas of correction of intestinal biocenosis today, which are an alternative to antibiotic and probiotic medications. Selective decontamination of representatives of opportunistic flora, as the main factor in the implementation of the atopic phenotype, makes it possible to preserve and accelerate the formation of a unique and individual composition of the intestinal microbiota of the child, which can form an immunoregulatory balance. More than a century of experience in the use of bacteriophages indicates the safety of their use. Today, bacteriophages are actively used in various fields of practical medicine − obstetrics-gynecology, perinatology, urology, pediatric otorhinolaryngology, in the treatment of purulent-septic and intestinal infections. In some cases, bacteriophages are very effective against antibiotic-resistant pathogens. The active personalized use of bacteriophages in real clinical practice will make it possible to solve a number of serious, long-standing health problems in the Russian Federation and to win a world priority in this direction.

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Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽

10.3390/agriculture11070680 ◽

2021 ◽

Vol 11 (7) ◽

pp. 680

Author(s):

Thuy T. P. Mai ◽

Craig M. Hardner ◽

Mobashwer M. Alam ◽

Robert J. Henry ◽

Bruce L. Topp

Keyword(s):

Genetic Diversity ◽

Growth Traits ◽

Principal Component ◽

Conservation Strategies ◽

Wild Germplasm ◽

Phenotypic Characterisation ◽

Wide Range ◽

Genetic And Environmental Factors ◽

Positive Correlations ◽

Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Biochemical Genetics ◽

10.1007/s10528-021-10090-7 ◽

2021 ◽

Author(s):

Júlia Halász ◽

Noémi Makovics-Zsohár ◽

Ferenc Szőke ◽

Sezai Ercisli ◽

Attila Hegedűs

Keyword(s):

Simple Sequence Repeat ◽

Principal Component ◽

Sequence Repeat ◽

Breeding Programs ◽

Allele Number ◽

Genetic Potential ◽

Ssr Loci ◽

High Level ◽

Diversity Studies ◽

Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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Phylogeographic Investigation of an Endangered Longhorn Beetle, Callipogon relictus (Coleoptera: Cerambycidae), in Northeast Asia: Implications for Future Restoration in Korea

Insects ◽

10.3390/insects12060555 ◽

2021 ◽

Vol 12 (6) ◽

pp. 555

Author(s):

Ji-Hyoun Kang ◽

Dae-Am Yi ◽

Alexander V. Kuprin ◽

Chang-Do Han ◽

Yeon-Jae Bae

Keyword(s):

South Korea ◽

Mitochondrial Gene ◽

Northeast Asia ◽

Haplotype Network ◽

Conservation Strategies ◽

Genetic Characteristics ◽

Linear Pattern ◽

Wide Range ◽

Longhorn Beetle ◽

High Level

The longhorn beetle, Callipogon (Eoxenus) relictus Semenov, is the only remnant species found in the Palearctic region, while all other Callipogon species are distributed mainly in Central America and partly in South America. This species has been placed in the first category (as ‘critically endangered’) of the Red Data Book in Russia and designated as one of the top-priority target species among all endangered invertebrate species for restoration in South Korea since 2006. Although its restricted distribution in Northeast Asia with a high conservational value has been highlighted, genetic features of C. relictus from different geographic regions remain unexplored. We first investigated the level of genetic diversity and phylogeographic patterns of C. relictus to evaluate the current conservational status and the feasibility of the implementation of a restoration program. The average genetic divergence of mitochondrial gene COI based on Kimura-2-parameter distance among the four regions in Russia, China, North Korea, and South Korea was 2.2%, which lies within the range of intraspecific levels. However, two separate clades with 3.8% divergence were identified, despite no geographical clustering of haplotypes. The linear pattern of the haplotype network with a high level of haplotype and nucleotide diversities suggests that the wide range of currently fragmented populations might be the remnant of genetically diverse populations in the past. This study will provide crucial information on the genetic characteristics and phylogeographic history of C. relictus, which will help to establish conservation strategies for this cherished insect species in Northeast Asia.

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Bioactive Phenolic Metabolites from Adriatic Brown Algae Dictyota dichotoma and Padina pavonica (Dictyotaceae)

Foods ◽

10.3390/foods10061187 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1187

Author(s):

Ivana Generalić Mekinić ◽

Vida Šimat ◽

Viktorija Botić ◽

Anita Crnjac ◽

Marina Smoljo ◽

...

Keyword(s):

Total Phenolics ◽

Antioxidant Activities ◽

Principal Component ◽

Ultrasound Assisted Extraction ◽

Antioxidant Power ◽

Dictyota Dichotoma ◽

Assisted Extraction ◽

Sample Data ◽

Ferric Reducing Antioxidant Power ◽

The Individual

In this study, the influences of temperature (20, 40 and 60 °C) and extraction solvents (water, ethanol) on the ultrasound-assisted extraction of phenolics from the Adriatic macroalgae Dictyota dichotoma and Padina pavonica were studied. The extracts were analysed for major phenolic sub-groups (total phenolics, flavonoids and tannins) using spectrometric methods, while the individual phenolics were detected by HPLC. The antioxidant activities were evaluated using three methods: Ferric Reducing/Antioxidant Power (FRAP), scavenging of the stabile 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and Oxygen Radical Antioxidant Capacity (ORAC). The aim of the study was also to find the connection between the chemical composition of the extracts and their biological activity. Therefore, principal component analysis (PCA), which permits simple representation of different sample data and better visualisation of their correlations, was used. Higher extraction yields of the total phenolics, flavonoids and tannins were obtained using an alcoholic solvent, while a general conclusion about the applied temperature was not established. These extracts also showed good antioxidant activity, especially D. dichotoma extracts, with high reducing capacity (690–792 mM TE) and ORAC values (38.7–40.8 mM TE in 400-fold diluted extracts). The PCA pointed out the significant influence of flavonoids and tannins on the investigated properties. The results of this investigation could be interesting for future studies dealing with the application of these two algae in foods, cosmetics and pharmaceuticals.

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Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

Plant Genetic Resources ◽

10.1017/s1479262114000525 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S125-S129

Author(s):

Gi-An Lee ◽

Sok-Young Lee ◽

Ho-Sun Lee ◽

Kyung-Ho Ma ◽

Jae-Gyun Gwag ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Management ◽

Underutilized Crops ◽

Crop Species ◽

Closely Related Species ◽

Polymorphic Loci ◽

Allele Number ◽

The Mean ◽

Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

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