Microsatellites

Isolation and characterization of polymorphic microsatellite loci in the ridgetail white prawn Exopalaemon carinicauda

S. W. Jia, Liu, P., Li, J., Li, J. T., and Pan, L. Q., “Isolation and characterization of polymorphic microsatellite loci in the ridgetail white prawn Exopalaemon carinicauda”, vol. 12, pp. 2816-2820, 2013.

The ridgetail white prawn Exopalaemon carinicauda is one of the major economic shrimp species cultured in China. In this study, 30 microsatellite loci were isolated and characterized for the ridgetail white prawn E. carinicauda using a microsatellite-enriched library. Polymorphisms were tested in 30 individuals from a single wild population. The number of alleles at each locus ranged from 2 to 14. The observed and expected heterozygosities varied from 0.1000 to 0.8000 and from 0.2299 to 0.9228, respectively. The PIC value ranged from 0.2002 to 0.8939.

Segregation and genetic linkage analyses of river catfish, Mystus nemurus, based on microsatellite markers

B. P. Hoh, Siraj, S. S., Tan, S. G., and Yusoff, K., “Segregation and genetic linkage analyses of river catfish, Mystus nemurus, based on microsatellite markers”, vol. 12, pp. 2578-2593, 2013.

The river catfish Mystus nemurus is an important fresh water species for aquaculture in Malaysia. We report the first genetic linkage map of M. nemurus based on segregation analysis and a linkage map using newly developed microsatellite markers of M. nemurus. A total of 70 of the newly developed polymorphic DNA microsatellite markers were analyzed on pedigrees generated using a pseudo-testcross strategy from 2 mapping families.

Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines

A. A. Leal, Mangolin, C. A., Júnior, A. Tdo Amaral, Gonçalves, L. S. A., Scapim, C. A., Mott, A. S., Eloi, I. B. O., Cordovés, V., and da Silva, M. F. P., “Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines”, vol. 9, pp. 9-18, 2010.

Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S7 inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes.

Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

I. A. Arif, Khan, H. A., Shobrak, M., Homaidan, A. A. Al, M. Sadoon, A., Farhan, A. H. Al, and Bahkali, A. H., “Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx”, vol. 9, pp. 259-265, 2010.

Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx.

Worldwide diversity of the Y-chromosome tetra-local microsatellite DYS464

F. S. G. Kehdy and Pena, S. D. J., “Worldwide diversity of the Y-chromosome tetra-local microsatellite DYS464”, vol. 9, pp. 1525-1534, 2010.

Of all DNA markers on the human Y-chromosome, the tetra-local Y-linked microsatellite DYS464 is the most polymorphic. We genotyped DYS464 in 677 male samples collected worldwide, maintained in the HGDP-CEPH Human Genome Diversity Cell Line Panel. Fourteen different alleles were found, with allele lengths varying from 9 to 23 repeats. One hundred and seventy-five different genotypes were detected, of which 90 appeared to be continent-specific. The region with the highest percentage of unique genotypes was Africa.

Isolation and characterization of 21 novel polymorphic microsatellite loci in the Chinese soft-shelled turtle Pelodiscus sinensis

X. J. Bu, Liu, L., Wang, L., and Nie, L. W., “Isolation and characterization of 21 novel polymorphic microsatellite loci in the Chinese soft-shelled turtle Pelodiscus sinensis”, vol. 10. pp. 1006-1010, 2011.

Twenty-one novel polymorphic microsatellite loci were isolated from the Chinese soft-shelled turtle, Pelodiscus sinensis (Trionychidae). This is a commonly consumed Asian species, especially in China, where it is reared in large numbers on farms. We screened 34 unrelated individuals from Wuhu of Anhui province in China and detected high levels of polymorphism for all 21 loci, with the number of alleles/locus ranging from 5 to 23 (mean 15.67). The expected and observed heterozygosities ranged from 0.421 to 0.946 and from 0.324 to 0.941, respectively.

Polymorphisms of the cocaine-amphetamine-regulated transcript (CART) gene and their association with reproductive traits in Chinese goats

P. Q. Wang, Deng, L. M., Zhang, B. Y., Chu, M. X., and Hou, J. Z., “Polymorphisms of the cocaine-amphetamine-regulated transcript (CART) gene and their association with reproductive traits in Chinese goats”, vol. 10, pp. 731-738, 2011.

Polymorphisms of the CART gene were investigated by PCR-single-strand conformation polymorphism analysis in 540 samples from 10 goat breeds. Ten novel single-nucleotide polymorphisms as well as three microsatellites were detected; a mutation, 77T→C, led to an amino acid change (Leu→Ser). Associations between polymorphic loci and reproductive traits were analyzed in Chuandong White, Guizhou White and Gulin Ma breeds. Mutation at position 524 had no significant effect on litter size in these three goat breeds.

Isolation and characterization of novel microsatellite markers in commercial selected golden Malaysian arowana fish, Scleropages formosus (Osteoglossidae)

B. Manoharan, Sulaimen, Z., Omar, F., Othman, R. Y., Mohamed, S. Z., and Bhassu, S., “Isolation and characterization of novel microsatellite markers in commercial selected golden Malaysian arowana fish, Scleropages formosus (Osteoglossidae)”, vol. 10. pp. 712-716, 2011.

Malaysian arowana (dragonfish; Scleropages formosus) is an ancient osteoglossid fish from southeast Asia. Due to the high demand of the ornamental fish trade and because of habitat loss, the species is close to extinction. We isolated and characterized 10 polymorphic microsatellites of this species, using 5'-anchored PCR. The number of alleles at the 10 microsatellite loci ranged from 2 to 28, with a mean of 7.8/locus. The observed heterozygosity ranged from 0.03 to 0.93 (mean: 0.39), whereas the expected heterozygosity ranged from 0.03 to 0.94 (mean: 0.46).

Genetic diversity in wild sweet cherries (Prunus avium) in Turkey revealed by SSR markers

S. Ercisli, Agar, G., Yildirim, N., Karlidag, H., Duralija, B., and Vokurka, A., “Genetic diversity in wild sweet cherries (Prunus avium) in Turkey revealed by SSR markers”, vol. 10, pp. 1211-1219, 2011.

Wild sweet cherry (Prunus avium) trees are abundant in the northern part of Turkey, including the Coruh Valley. We analyzed 18 wild sweet cherry genotypes collected from diverse environments in the upper Coruh Valley in Turkey to determine genetic variation, using 10 SSR primers. These SSR primers generated 46 alleles; the number of alleles per primer ranged from 3 to 7, with a mean of 4.6. The primer PS12A02 gave the highest number of polymorphic bands (N = 7), while CPSCT010, UDAp-401 and UDAp-404 gave the lowest number (N = 3).

Study of closely related species within the Physalaemus cuvieri group (Anura): contribution of microsatellite markers

M. Conte, Zucchi, M. I., Andrade, G. V., Souza, A. P., and Recco-Pimentel, S. M., “Study of closely related species within the Physalaemus cuvieri group (Anura): contribution of microsatellite markers”, vol. 10, pp. 1434-1444, 2011.

Various species of the Physalaemus cuvieri group of frogs are difficult to distinguish morphologically, making molecular analysis an attractive alternative for indentifying members of this group, which is considered to be at risk because of loss of habitat. The genetic structure of natural populations of P. ephippifer and P. albonotatus species was investigated and analyzed, together with that of five previously studied populations of P. cuvieri. Nine microsatellite loci were used in the analyses.

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