Assessment of the Genetic Potential of the Peregrine Falcon (Falco peregrinus peregrinus) Population Used in the Reintroduction Program in Poland

Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1–15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population.

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Genetic analysis of a heritage variety collection

Plant Genetic Resources ◽

10.1017/s1479262118000448 ◽

2018 ◽

Vol 17 (03) ◽

pp. 232-244 ◽

Cited By ~ 2

Author(s):

J. M. Preston ◽

B. V. Ford-Lloyd ◽

L. M. J. Smith ◽

R. Sherman ◽

N. Munro ◽

...

Keyword(s):

Genetic Analysis ◽

Group Method ◽

Niche Markets ◽

Principal Coordinates Analysis ◽

Pair Group ◽

Landrace Diversity ◽

Principal Coordinates ◽

Length Polymorphisms ◽

Seed Saving ◽

History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

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Genetic diversity among Mycobacterium tuberculosis isolates from Mexican patients

Canadian Journal of Microbiology ◽

10.1139/w08-051 ◽

2008 ◽

Vol 54 (8) ◽

pp. 610-618

Author(s):

G. Vázquez-Marrufo ◽

D. Marín-Hernández ◽

M. G. Zavala-Páramo ◽

G. Vázquez-Narvaez ◽

C. Álvarez-Aguilar ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Gene Diversity ◽

Group Method ◽

Tuberculosis Complex ◽

Principal Coordinates Analysis ◽

Strain Distribution Pattern ◽

Pair Group ◽

Principal Coordinates ◽

Unweighted Pair Group Method

Forty-six isolates of the Mycobacterium tuberculosis complex were typified by PCR of the IS6110 region and by Mycobacterium bovis specific primers JB21/JB22. Isolate MVG01 was typified as M. bovis, being the first record of a case of human tuberculosis caused by this species in Mexico. RAPD–PCR was used to describe the genetic diversity of the remaining 45 M. tuberculosis complex isolates. The corrected genotypic diversity value calculated for the analyzed population was 0.96, the estimated mean gene diversity was 0.235, and the corrected Shannon–Weiner index was 2.15. All allele–loci combinations generated showed significant linkage disequilibria. The distribution of genetic variation was analyzed both by the unweighted pair group method with arithmetic averages clustering and by principal coordinates analysis. Unweighted pair group method with arithmetic averages clustering resulted in a tree with four main clusters and one unclustered strain (MVG20), the principal coordinates analysis strain distribution pattern being consistent with this grouping. The obtained results suggest that the studied isolates belong to a clonal population having significant genetic diversity. Our genetic diversity results are comparable with those reported for other populations of M. tuberculosis, although only three RAPD primers were used.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.3.309 ◽

2001 ◽

Vol 126 (3) ◽

pp. 309-317 ◽

Cited By ~ 59

Author(s):

O. Gulsen ◽

M.L. Roose

Keyword(s):

Simple Sequence Repeats ◽

Phylogenetic Trees ◽

Nuclear Genome ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Inter Simple Sequence Repeats ◽

Ssr Loci ◽

High Level ◽

Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

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Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

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Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽

10.3390/ani11092633 ◽

2021 ◽

Vol 11 (9) ◽

pp. 2633

Author(s):

Poh Chiang Chew ◽

Annie Christianus ◽

Jaapar M. Zudaidy ◽

Md Yasin Ina-Salwany ◽

Chou Min Chong ◽

...

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Differentiation ◽

Genetic Relatedness ◽

Genetic Distances ◽

Group Method ◽

Genetic Management ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

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Identification and structure analysis of three tilapia species using microsatellite markers

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236209990258 ◽

2009 ◽

Vol 6 (2) ◽

pp. 119-125

Author(s):

Song Hong-Mei ◽

Bai Jun-Jie ◽

Quan Ying-Chun ◽

Li Sheng-Jie

Keyword(s):

Microsatellite Markers ◽

Clustering Analysis ◽

Phylogenetic Trees ◽

Mean Value ◽

Group Method ◽

Oreochromis Aureus ◽

Arithmetic Average ◽

Pair Group ◽

Expected Heterozygosity ◽

The Mean

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

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Application of RAPD and ISSR markers to analyse molecular relationships in Grevillea (Proteaceae)

Australian Systematic Botany ◽

10.1071/sb03016 ◽

2004 ◽

Vol 17 (1) ◽

pp. 49 ◽

Cited By ~ 22

Author(s):

M. Pharmawati ◽

G. Yan ◽

I. J. McFarlane

Keyword(s):

Phylogenetic Trees ◽

Genetic Relationships ◽

Initial Point ◽

Morphological Characteristics ◽

Issr Markers ◽

Group Method ◽

Pair Group ◽

Molecular Relationships ◽

Group B ◽

Rapd And Issr

The potential of RAPD and ISSR markers to construct molecular relationships of Grevillea was evaluated with 23 RAPD and 12 ISSR primers. The 16 genotypes representing 12 species and 3 subspecies of Grevillea were sampled from the collection of the Mt Anann Botanic Garden, NSW. RAPD and ISSR assays generated a total of 401 RAPD and 280 ISSR fragments. High frequencies of polymorphisms, 99.39% for RAPD and 99.51% for ISSR, were detected by both markers. Three statistical approaches were employed to construct phylogenetic relationships from combined RAPD and ISSR data. Cluster analysis by the unweighted pair group method (UPGMA) of Jaccard's similarity and Neighbour-Joining analysis of total character difference generated dendograms with similar topology. Parsimony analysis also generated a tree that was in broad agreement with the two dendograms. The phylogenetic trees divided the Grevillea species studied into three groups. Group A consisted of G. buxifolia subsp. buxifolia, G. phylicoides and G. sphacelata. In group B, G. mucronulata was grouped together with G. montana, while G. diffusa, G. humilis, G. linearifolia, G. molyneuxii, G. oldei, G. sericea and G. speciosa formed group C. This molecular result was comparable to groupings suggested by a previous author (Makinson 2000) based on morphological characteristics. However, in contrast to the morphological taxonomy, molecular phylogeny suggests that G. oldei and G. speciosa belong to the same subgroup sensu Makinson (2000), whereas G. linearifolia and G. molyneuxii should not be placed in their originally suggested subgroups sensu Makinson (2000). The present study is the first published report on molecular relationships of Grevillea and can be considered as an initial point for further research on the genetic relationships and evolution of Grevillea.

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A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare)

Canadian Journal of Plant Science ◽

10.4141/cjps10203 ◽

2011 ◽

Vol 91 (4) ◽

pp. 717-723 ◽

Cited By ~ 1

Author(s):

Benjamin Clasen ◽

Nicole Moss ◽

Monika Chandler ◽

Alan Smith

Keyword(s):

Genetic Structure ◽

North America ◽

Small Variation ◽

Structure Study ◽

Inter Simple Sequence Repeat ◽

Principal Coordinates Analysis ◽

Tanacetum Vulgare ◽

Pair Group ◽

Principal Coordinates ◽

Disturbed Areas

Clasen, B. M., Moss, N. G., Chandler, M. A. and Smith, A. G. 2011. A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare). Can. J. Plant Sci. 91: 717–723. Common tansy is an herbaceous perennial member of the Asteraceae and is considered a weed in North America. Common tansy was introduced deliberately for use as a funerary herb, medicine, preservative, and animal and insect repellent. It is known to escape cultivation and invade disturbed areas, spreading both sexually and asexually. This paper reports a preliminary analysis of the genetic structure of 10 invasive common tansy populations in Minnesota and Montana, USA, and Alberta, Canada. Ninety polymorphic loci were found using six inter simple sequence repeat (ISSR) primers used to amplify DNA from 40 individuals from 10 discrete populations. The diversity within and among populations was assessed using the Dice coefficient of similarity and AMOVA. The AMOVA showed that diversity within populations was generally high and that there was relatively small variation among populations. An unweighted pair-group with arithmetic mean (UPGMA) dendrogram was constructed based on the distance between populations, and demonstrated substantial and distinct clustering of a population from Ramsey County, Minnesota. A principal coordinates analysis clustered all individuals from Ramsey County distinctly from other individuals, indicating a possible limited gene flow among this population and the other populations sampled in this study. Understanding genetic diversity and the distribution of diversity within and among populations may help predict the potential for successful management of common tansy populations in North America.

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Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection

Plants ◽

10.3390/plants9080989 ◽

2020 ◽

Vol 9 (8) ◽

pp. 989

Author(s):

Maria Carola Fiore ◽

Francesco Maria Raimondo ◽

Francesco Mercati ◽

Ignazio Digangi ◽

Francesco Sunseri ◽

...

Keyword(s):

Common Bean ◽

Rural Areas ◽

Germplasm Collection ◽

Genetic Distances ◽

Ex Situ ◽

Group Method ◽

Gene Pools ◽

Mountain Areas ◽

Pair Group ◽

Principal Coordinates

The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the “Living Plants Germplasm Bank” at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the “Sicilian Plant Germplasm Repository” of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.

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