Genetic diversity and population structure of Zackel sheep and other Hungarian sheep breeds

Abstract. More than 6000 samples of 18 different Hungarian sheep breeds were genotyped for 10 unlinked microsatellite loci. After data cleaning, 5434 sheep remained in the analysis. Some locus–breed combinations show deviation from Hardy–Weinberg equilibrium, possibly due to null alleles or the Wahlund effect. All breeds show high genetic variability; the lowest expected heterozygosity is that of the British Milksheep (He = 0.588). The Transylvanian Zackel has the highest expected heterozygosity (He = 0.790). It is also the least differentiated breed (Fst = 0.020). Pairwise genetic distances among breeds range from 0.021 between Hungarian Merino and both Mutton Merino and Transylvanian Zackel to greater than 0.105 between British Milksheep and all other breeds. The three Zackel populations – white, black, and Transylvanian Zackel – show small genetic distances among each other, with pairwise Fst values from 0.030 to 0.058. The Transylvanian Zackel tended to have close relationships to some other breeds too, probably due to its low differentiation. Given the individual genotypic information, a Bayesian analysis assigned individuals to breeds generally correctly.

Download Full-text

New Microsatellite Markers for Two Sympatric Tinamou Species, the Ornate Tinamou (Nothoprocta ornata) and Darwin's Nothura (Nothura darwinii)

Avian Biology Research ◽

10.3184/175815515x14503747783157 ◽

2016 ◽

Vol 9 (3) ◽

pp. 139-146 ◽

Cited By ~ 2

Author(s):

Lina Maria Giraldo Deck ◽

Jan Christian Habel ◽

Manuel Curto ◽

Martin Husemann ◽

Sarah Sturm ◽

...

Keyword(s):

Microsatellite Loci ◽

Life History Traits ◽

Null Alleles ◽

Genetic Population ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite ◽

Successful Amplification ◽

Low Coverage ◽

Candidate Loci

Tinamous (Tinamidae) represent one of the most ancient living avian lineages but their life history traits are relatively unstudied. Here we identified microsatellite loci for two sympatric tinamou species, the Ornate Tinamou ( Nothoprocta ornata) and the Darwin's Nothura ( Nothura darwinii) from low coverage Illumina sequencing of genomic DNA. The experiment yielded a large number of candidate loci. We designed primers and tested them for successful amplification in 1 to 2 populations of the target species, tested for deviation from the Hardy–Weinberg equilibrium and the presence of null alleles, the levels of polymorphism and potential cross-amplification. All 30 and 24 loci amplified consistently, in the Ornate Tinamou and in Darwin's Nothura, respectively. In the Ornate Tinamou, 25 loci were polymorphic and in the Darwin's Nothura 12, with 2 to 14 alleles per locus in both species. The expected heterozygosity ranged from 0.054 to 0.917 in the Ornate Tinamou and from 0.044 to 0.908 in the Darwin's Nothura. 23 (40%) of 54 loci were successfully cross-amplified. These newly discovered, polymorphic microsatellite loci represent a valuable tool for future studies on social behaviour, parentage and genetic population structure in tinamous.

Download Full-text

Personal Goals of Older Female Twins

European Psychologist ◽

10.1027/1016-9040.14.2.160 ◽

2009 ◽

Vol 14 (2) ◽

pp. 160-167 ◽

Cited By ~ 14

Author(s):

Katariina Salmela-Aro ◽

Sanna Read ◽

Jari-Erik Nurmi ◽

Markku Koskenvuo ◽

Jaakko Kaprio ◽

...

Keyword(s):

Physical Exercise ◽

Independent Living ◽

Environmental Effect ◽

Close Relationships ◽

Environmental Influence ◽

Genetic Effect ◽

Additive Genetic Effect ◽

Personal Goals ◽

Cultural Activities ◽

The Individual

This study examined genetic and environmental influences on older women’s personal goals by using data from the Finnish Twin Study on Aging. The interview for the personal goals was completed by 67 monozygotic (MZ) pairs and 75 dizygotic (DZ) pairs. The tetrachoric correlations for personal goals related to health and functioning, close relationships, and independent living were higher in MZ than DZ twins, indicating possible genetic influence. The pattern of tetrachoric correlations for personal goals related to cultural activities, care of others, and physical exercise indicated environmental influence. For goals concerning health and functioning, independent living, and close relationships, additive genetic effect accounted for about half of the individual variation. The rest was the result of a unique environmental effect. Goals concerning physical exercise and care of others showed moderate common environmental effect, while the rest of the variance was the result of a unique environmental effect. Personal goals concerning cultural activities showed unique environmental effects only.

Download Full-text

Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences

Genome ◽

10.1139/g01-106 ◽

2001 ◽

Vol 44 (6) ◽

pp. 1041-1045 ◽

Cited By ~ 25

Author(s):

J C Glaubitz ◽

L C Emebiri ◽

G F Moran

Keyword(s):

Base Pair ◽

Mendelian Inheritance ◽

Null Alleles ◽

Fixation Index ◽

Eucalyptus Nitens ◽

Internal Reference ◽

Single Base ◽

Hardy Weinberg Equilibrium ◽

Single Base Pair ◽

Flanking Regions

Eight dinucleotide microsatellites were developed in Eucalyptus sieberi L. Johnson (silvertop ash), a member of the subgenus Eucalyptus. Transfer of six of these to the subgenus Symphyomyrtus and their Mendelian inheritance are demonstrated using a full-sib cross in Eucalyptus nitens. Genetic diversity parameters are presented for the eight loci based on a sample of 100 old-growth E. sieberi trees from a single natural stand. One locus, Es266, had an atypically high fixation index, and significantly deviated from Hardy-Weinberg equilibrium genotypic proportions, indicating the likely presence of null alleles. Two of the loci, Es076 and Es140, had many alleles that differed in size by only a single base pair, possibly because of short poly(A) or poly(T) stretches in their flanking regions. These two loci were by far the most polymorphic, but were difficult to score reliably on a capillary DNA sequencer. Reliability of scoring of these two one-base microsatellite loci was markedly improved by the incorporation of internal reference alleles into each sample analysed.Key words: SSRs, single base pair alleles, null alleles, internal reference alleles.

Download Full-text

Genetic polymorphism of milk protein loci in Argentinian Holstein cattle

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400019 ◽

2000 ◽

Vol 23 (4) ◽

pp. 819-823 ◽

Cited By ~ 5

Author(s):

Adriana Gloria Bonvillani ◽

Miguel Angel Di Renzo ◽

Iván Nicolás Tiranti

Keyword(s):

Genetic Polymorphism ◽

Milk Protein ◽

Genotypic Diversity ◽

Genetic Distances ◽

Holstein Cattle ◽

Starch Gel Electrophoresis ◽

Beta Casein ◽

Hardy Weinberg Equilibrium ◽

Quality Of Milk ◽

Beta Lactoglobulin

Some alleles of milk protein loci are associated with superior cheese production characteristics. The genetic polymorphism of the milk protein loci alphas1-casein, beta-casein, k-casein and beta-lactoglobulin was examined in Argentinian Holstein cattle. Samples from 12 herds of four regions of Córdoba were analyzed by starch gel electrophoresis. The chi² test was used to assess whether the populations were in Hardy-Weinberg equilibrium. Genotypic diversity was analyzed by the Shannon-Weaver index. The observed genotypic frequencies were analyzed by Hedrick's genetic identity and the genetic distance of Balakrishnan and Sanghvi. The allelic and genotypic frequencies were similar to those of other Holstein populations. The genotypic frequencies of the alphas1-casein and beta-casein loci were in equilibrium, whereas in some populations the k-casein and beta-lactoglobulin loci were not. According to the Shannon-Weaver index the total genetic diversity within each herd was greater than 96%. The high values of identity agreed with the low genetic distances among populations. We conclude that there is extensive genetic homogeneity in Holstein cattle in Córdoba Province and that it would be feasible to select for B alleles at the k-casein and b-lactoglobulin loci in order to improve the quality of milk available for cheese manufacturing.

Download Full-text

ISOLATION AND CHARACTERIZATION OF NEW MICROSATELLITE MARKERS FOR THE CORTÉS GEODUCK (Panopea globosa)

CICIMAR Oceánides ◽

10.37543/oceanides.v31i1.162 ◽

2016 ◽

Vol 31 (1) ◽

pp. 17

Author(s):

Celia Isabel Bisbal -Pardo ◽

Miguel Ángel Del Río -Portilla ◽

Ana Yonori Castillo -Paéz ◽

Axayácatl Rocha-Olivares

Keyword(s):

Fishery Management ◽

Genetic Research ◽

Isolation And Characterization ◽

Expected Heterozygosity ◽

Tetranucleotide Repeats ◽

Hardy Weinberg Equilibrium ◽

Increasing Demand ◽

Sustainable Fishery ◽

Generation Technology

The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of México that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management. Aislamiento y caracterización de nuevos marcadores microsatelitales en la almeja generosa (Panopea globosa) La almeja generosa Panopea globosa es una especie infáunica longeva y de gran tamaño que mantiene una pesquería creciente en la costa del Noroeste de México. A pesar de su demanda creciente en los mercados asiáticos, se conoce muy poco acerca de su biología. Con la finalidad de proveer nuevos marcadores genéticos para la caracterización de poblaciones silvestres, se desarrollaron nueve marcadores microsatelitales nuevos (con patrones repetidos de di-, tri-, y tetranucleotídicos) utilizando secuenciación genómica aleatoria con tecnología de secuenciación de siguiente generación (Illumina). El número de alelos por locus varió de 3 a 16 y los valores de heterocigosidad observada y esperada variaron de 0.286 a 0.650 y 0.504 a 0.906, respectivamente. Cinco microsatelites se desvían del equilibrio de Hardy-Weinberg y tres pares de microsatélites mostraron evidencia de desequilibrio de ligamiento. La mayoría de los loci son altamente informativos para estudios poblacionales y análisis de ligamiento de acuerdo con su contenido de información de polimorfismos (> 0.5) y serán útiles para incrementar el conocimiento de la estructura genética de las poblaciones silvestres de esta almeja y para coadyuvar en su pesquería sustentable.

Download Full-text

Genetic analysis of silver-fir populations in the Beskids

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2003.015 ◽

2011 ◽

Vol 72 (2) ◽

pp. 115-119 ◽

Cited By ~ 3

Author(s):

Leon Mejnartowicz

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Analysis ◽

Abies Alba ◽

Genetic Distances ◽

Silver Fir ◽

Geographical Distance ◽

Polymorphic Loci ◽

Expected Heterozygosity ◽

Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (Abies alba): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (I = 0.42), percentage of polymorphic loci (%PoL = 64.29) and number of rare alleles (NoRa = 5). Besides, the BM population has the highest observed heterozygosity (Ho = 0.291), which exceeds the expected heterozygosity (He = 0.254), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of He = 0.262 and Ho = 0.264.

Download Full-text

Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster,Panulirus guttatus

PeerJ ◽

10.7717/peerj.1467 ◽

2016 ◽

Vol 4 ◽

pp. e1467 ◽

Cited By ~ 3

Author(s):

Nathan Truelove ◽

Donald C. Behringer ◽

Mark J. Butler IV ◽

Richard F. Preziosi

Keyword(s):

Spiny Lobster ◽

Florida Keys ◽

Null Alleles ◽

Polymerase Chain Reaction Primer ◽

Genomic Libraries ◽

Genetics Research ◽

Isolation And Characterization ◽

Quality Control Testing ◽

Panulirus Guttatus ◽

Hardy Weinberg Equilibrium

Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster,Panulirus guttatususing 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs ofPanulirus argusmicrosatellite loci were also tested for cross-species amplification inPanulirus guttatus.In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research ofP. guttatus.

Download Full-text

Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽

10.7717/peerj.2936 ◽

2017 ◽

Vol 5 ◽

pp. e2936 ◽

Cited By ~ 13

Author(s):

Caroline E. Dubé ◽

Serge Planes ◽

Yuxiang Zhou ◽

Véronique Berteaux-Lecellier ◽

Emilie Boissin

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Natural Populations ◽

454 Sequencing ◽

Genetic Distances ◽

Null Alleles ◽

Future Research ◽

Significant Linkage ◽

Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Download Full-text

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Genes ◽

10.3390/genes11070743 ◽

2020 ◽

Vol 11 (7) ◽

pp. 743

Author(s):

Caiyong Yin ◽

Kaiyuan Su ◽

Ziwei He ◽

Dian Zhai ◽

Kejian Guo ◽

...

Keyword(s):

Tandem Repeats ◽

Forensic Analysis ◽

Copy Number Variations ◽

Null Alleles ◽

Nucleotide Polymorphisms ◽

Evolutionary Pathway ◽

Individual Level ◽

Population Comparisons ◽

Heated Debate ◽

The Individual

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

Download Full-text

A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

Plant Genetic Resources ◽

10.1017/s1479262117000193 ◽

2017 ◽

Vol 16 (3) ◽

pp. 284-287

Author(s):

Bruno C. Rossini ◽

Mariá B. Kampa ◽

Celso L. Marino ◽

Fernanda Bortolanza Pereira ◽

Fábio M. Alves ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Null Alleles ◽

Germplasm Resources ◽

Significant Linkage Disequilibrium ◽

Orchid Species ◽

Expected Heterozygosity ◽

Tropical Orchid ◽

Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

Download Full-text