Retraction: Development of retrotransposon insertion polymorphic markers and application in the genetic variation evaluation of Chinese Bama miniature pigs

Retrotransposons are genetic elements that can amplify themselves in a genome and are abundant in many eukaryotic organisms. In this study, we established some new short interspersed nuclear elements (SINE) and endogenous retroviruses (ERV) retrotransposons insertion polymorphism (RTIP) markers based on BLAT alignment tool strategy, and followed by PCR evaluation. We investigated the genetic variations among four subpopulations of Chinese Bama miniature pigs (BM), including BM in national conservation farm (BM-cov), BM inbreeding population (BM-inb) and BM closed Herd (BM-clo) in Guangxi University, and BM in the Experimental pig farm of Yangzhou University (BM-yzu). Genetic distance, polymorphism information content (PIC) and heterozygosity (He) of these markers in four of BM subpopulations were measured. Twelve SINE and twenty-eight ERV polymorphic molecular markers were identified in the four subpopulations. The BM-cov pigs represented the highest He and PIC, which indicated that BM-cov pigs maintain relatively highly genetic diversity. BM-inb pigs represented the lowest He and PIC indicating less variation and a high degree of inbreeding. Microsatellites polymorphism in four BM populations also well supported the results of these RTIP markers. In summary, retrotransposons insertion polymorphic markers could be a useful tool for population genetic variation analysis. Current SINE and ERV variation data may also provide a reference guide for the conservation and utilization of the BM miniature pig resource.

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Genetic Diversity of Two Evergreen Oaks [Quercus suber (L.) and Quercus ilex subsp. rotundifolia (Lam.)] in Portugal using AFLP Markers

Silvae Genetica ◽

10.1515/sg-2006-0016 ◽

2006 ◽

Vol 55 (1-6) ◽

pp. 105-118 ◽

Cited By ~ 17

Author(s):

A. C. Coelho ◽

M. B. Lima ◽

D. Neves ◽

A. Cravador

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Numerical Taxonomy ◽

Quercus Ilex ◽

Quercus Suber ◽

Cork Oak ◽

Holm Oak ◽

Genetic Profile ◽

Polymorphic Markers ◽

High Level

Abstract The genetic variability of cork oak (Quercus suber, L.) in Portugal was evaluated by AFLP using five primer combinations. Three hundred and thirteen trees from three geographically contrasting regions exhibited a high level of genetic variation. The genetic profile of each individual is composed of 291 loci, randomly positioned in the genome and consists of monomorphic and polymorphic fragments. Similarities and dissimilarities among the individuals were quantitatively evaluated by numerical taxonomy. The overall sample shows a proportion of AFLP polymorphic markers of 71%, denoting a high level of variability. Ninety percent of the polymorphic markers identified in cork oak genotypes are uniformly distributed throughout the cork oak populations of Algarve, Alentejo and Trás-os-Montes regions. The coefficients of genetic similarity vary from 0.61 to 0.88 implying that 60% of fragments found are common. A sample of 52 holm oak [Quercus ilex subsp. rotundifolia (Lam.)] trees from overlapping areas was also analysed by AFLP with the same five primer combinations. However the codification of markers together with those selected on cork oak profiles was feasible with only one primer combination due to an apparent much higher polymorphism. AFLP and numerical taxonomy analysis enabled to differentiate the taxa and showed that the level of similarity observed between the profiles of the individuals from holm oak species was lower than that observed in cork oak, implying that apparently the degree of polymorphism is higher in Q. ilex subsp. rotundifolia than that quantified in Q. suber. A Bayesian approach was used to assess Q. suber total genetic diversity (Ht = 0.2534, P < 0.001) of which 1.7% (Fst = 0.0172, P < 0.001) was assigned to differences among populations. Analysis of molecular variance (AMOVA) showed that most genetic variation is comprised within populations (96%) while 3.6% is among populations (Φst = 0.036, P < 0.001). Differences among populations within geographic regions account for 2.6% (Φsc = 0.026, P < 0.001) of the total variation and only 1.3% (Φct = 0.013, P = 0.007) is attributed to variation among regions denoting little differentiation of populations over a range of 700 km.

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Microsatellite Diversity of Androgenic Black Poplar (Populus nigra)

Acta Agraria Debreceniensis ◽

10.34101/actaagrar/27/3104 ◽

2007 ◽

pp. 60-67

Author(s):

András Bittsánszky ◽

Gábor Gyulai ◽

József Kiss ◽

Gábor Gullner ◽

László Heszky ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Resources ◽

Genetic Stability ◽

Genetic Similarity ◽

Populus Nigra ◽

Clonal Variation ◽

Polymorphic Markers ◽

Black Poplar ◽

Poplar Breeding ◽

Microsatellite Diversity

Genetic variation of somatic clones (1 to 35) of black poplar (Populus nigra) developed from two anther-donor trees N-SL and N-309 was determined by five SSR primer pairs. Twenty SSR alleles were detected, the number of alleles per marker ranged from 1 to 6, with an average of 3.3 including WPMS-2 (5 alleles), WPMS-4 (6 alleles), WPMS-6 (2 alleles), WPMS-20 (6 alleles) and PTR-4 (1 allele) detected by ALF (automatic laser fluorometer). Adendrogram produced by SPSS11 based on the presence versus absence of SSR alleles discriminated the groups of somatic clones of N-SL from somatic clones of N-309. The polymorphic markers of WPMS-2 (5 alleles), WPMS-4 (6 alleles) and WPMS-20 (6 alleles) revealed clonal variation in 1 clone (37) out of the 6 from the N-309 tree, and three subgroups out of the 29 somatic clones from the N-SL tree (17 and 24), (2 and 14) and (10 and 15). The remaining 23 of the 29 N-SL somatic clones with uniform genetic similarity suggests a good degree of genetic stability in black poplar. Nevertheless, the new SSR-clones may provide useful new genetic resources for poplar breeding.

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Genetic Diversity in Domestic and Introduced Wheats

Agriculture (Pol nohospodárstvo) ◽

10.2478/agri-2013-0009 ◽

2013 ◽

Vol 59 (3) ◽

pp. 101-110

Author(s):

Martina Hudcovicová ◽

Katarína Ondreičková ◽

Pavol Hauptvogel ◽

Ján Kraic

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Bread Wheat ◽

Ssr Markers ◽

Gene Diversity ◽

Polymorphic Markers ◽

Wheat Genotypes ◽

Average Gene Diversity ◽

Average Gene

Abstract A set of 33 wheat EST-SSR markers was designed and 18 from them were polymorphic and used for assessment of genetic diversity within 36 introduced genotypes of hexaploid bread wheat. Altogether 105 alleles were detected, in average 3.18 alleles per locus. Maximum number of alleles 14 was detected at the locus TDI389708. Five the most polymorphic markers were used for the evaluation and comparison of genetic variation within 46 domestic (Slovak) wheat genotypes and 36 introduced (foreign) wheat genotypes. The number of alleles per used primer pair within domestic genotypes varied from 7 to 19, with an average of 13.2 alleles, an average gene diversity 0.846 and PIC 0.980 per locus. The number of alleles per primer within introduced genotypes varied from 7 to 14, with an average of 10.8 alleles, an average gene diversity 0.780 and PIC 0.958 per locus. The level of polymorphism in EST- SSRs was sufficient for discrimination between genotypes and variation within domestic genotypes was slightly higher than in introduced genotypes. Variation revealed by 5 selected EST-SSR markers clustered genotypes according to origin. Domestic and introduced wheats were grouped distinctly into two separate groups.

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