Microsatellites

Polymorphic microsatellite loci for the razor clam, Sinonovacula constricta

H. - T. Ma, Jiang, H. - B., Liu, X. - Q., Wu, X. - P., and Wei, X. - M., “Polymorphic microsatellite loci for the razor clam, Sinonovacula constricta”, vol. 14, pp. 145-148, 2015.

The razor clam, Sinonovacula constricta, is an important commercial bivalve and a popular mollusca food in China. Twelve polymorphic microsatellite markers were isolated from the razor clam using a partial genomic library enriched for tandem repeat sequences of (CA)16, (GA)16. Polymorphisms of these loci were evaluated in a wild population of 30 individuals. The allele number of these polymorphic markers ranged from 5-15 per locus with an average of 9.333. Observed and expected heterozygosity values ranged from 0.192-1.000 and 0.219-0.906.

Comparison of DNA extraction methods for polymerase chain reaction amplification of guanaco (Lama guanicoe) fecal DNA samples

M. I. Espinosa, Bertin, A., Squeo, F. A., Cortés, A., and Gouin, N., “Comparison of DNA extraction methods for polymerase chain reaction amplification of guanaco (Lama guanicoe) fecal DNA samples”, vol. 14, pp. 400-406, 2015.

Feces-based population genetic studies have become increasingly popular. However, polymerase chain reaction (PCR) amplification rates from fecal material vary depending on the species, populations, loci, and extraction protocols. Here, we assessed the PCR amplification success of three microsatellite markers and a segment of the mitochondrial control region of DNA extracted from field-collected feces of guanaco (Lama guanicoe) using two protocols - Qiagen DNA Stool Kit and 2 cetyltrimethylammonium bromide/phenol:chloroform:isoamyl alcohol (2CTAB/PCI) method.

Isolation and characterization of microsatellite loci for Cunninghamia lanceolata (Lamb.) Hook

Y. X. Li, Wang, Z. S., Sui, J. K., Zeng, Y. F., Duan, A. G., and Zhang, J. G., “Isolation and characterization of microsatellite loci for Cunninghamia lanceolata (Lamb.) Hook”, vol. 14, pp. 453-456, 2015.

As a result of human activities, wild populations of Cunninghamia lanceolata (Cupressaceae) have sharply declined in recent years. The development and implementation of a valid conservation strategy require a clear understanding of the genetic makeup of this species. Eleven polymorphic microsatellite loci were isolated and characterized from samples of 52 individuals from the Provenance Test Plantation in Fenyi, Jiangxi Province, China. Among the loci, 10 were polymorphic and 1-34 (average 18.182) alleles per locus were identified.

Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

G. C. Yu, Tang, Q. Z., Long, K. R., Che, T. D., Li, M. Z., and Shuai, S. R., “Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs”, vol. 14, pp. 1362-1370, 2015.

Parentage analysis and individual identification are recent, promising methods that have been applied to evolutionary and ecological studies, as well as conservation management. Parental exclusion relying on polymorphic microsatellites has been used worldwide in parentage determination, while the low mutation rate and genotyping error rate of single nucleotide polymorphisms (SNPs) make them another important marker for pedigree tracing. Here, we compared the effectiveness of microsatellites and SNP markers in European pigs.

Development of novel microsatellite markers for conservation genetic studies of Vulpes vulpes (Canidae) by using next-generation sequencing method

J. - N. Yu, Chung, C. - U., Oh, K. H., Lee, B. - K., and Lim, C. E., “Development of novel microsatellite markers for conservation genetic studies of Vulpes vulpes (Canidae) by using next-generation sequencing method”, vol. 14. pp. 3980-3983, 2015.

The red fox, Vulpes vulpes (Canidae), is the most widely distributed terrestrial carnivore worldwide, but this species is classified as endangered in Korea. In this study, we developed 25 polymorphic microsatellite markers that included 3-13 (mean = 6.32) alleles per locus using 22 red fox individuals. The most polymorphic locus was FR(59)TG (13 alleles) and the least polymorphic loci were FR(70)TG and FR(182)AG (3 alleles each).

Molecular phylogenetics of the white-lipped peccary (Tayassu pecari) did not confirm morphological subspecies in northwestern South America

M. Ruiz-García, Pinedo-Castro, M., Luengas-Villamil, K., Vergara, C., Rodriguez, J. A., and Shostell, J. M., “Molecular phylogenetics of the white-lipped peccary (Tayassu pecari) did not confirm morphological subspecies in northwestern South America”, vol. 14, pp. 5355-5378, 2015.

We sequenced the mitochondrial DNA (mtDNA) control region of 59 peccaries (44 white-lipped peccaries, Tayassu pecari, and 15 collared peccaries, Pecari tajacu). We also genotyped 3 DNA microsatellites from 78 white-lipped peccaries representing the 4 putative morphological subspecies (i.e., spiradens, aequatoris, pecari, and albirostris) present in northwestern South America (i.e., Colombia, Ecuador, Peru, and Bolivia). Our results showed: 1) the estimated diversity of the mtDNA control region in the T.

Development of novel microsatellite markers in the Korean rockfish Sebastes schlegeli

H. - T. Ma, Jia, C. - F., Yang, J. - M., Wang, F., Xue, R., Han, C. - H., and Jiang, H. - B., “Development of novel microsatellite markers in the Korean rockfish Sebastes schlegeli”, vol. 14, pp. 5099-5102, 2015.

The Korean rockfish Sebastes schlegeli is a valuable recreational and commercial fish in China, and is cultured in land-based tanks and net cages. Fifteen microsatellite markers were developed for this species, and their polymorphisms were examined in a population. The allele number of the 15 markers ranged from 2 to 13, with an average of 5.933 per locus. The observed and expected heterozygosity values ranged from 0.063 to 0.938 (averaging 0.585), and 0.062 to 0.908 (averaging 0.642), respectively.

Effect of selective logging on genetic diversity and gene flow in Cariniana legalis sampled from a cacao agroforestry system

J. B. Leal, Santos, R. P., and Gaiotto, F. A., “Effect of selective logging on genetic diversity and gene flow in Cariniana legalis sampled from a cacao agroforestry system”, vol. 13, pp. 626-635, 2014.

The fragments of the Atlantic Forest of southern Bahia have a long history of intense logging and selective cutting. Some tree species, such as jequitibá rosa (Cariniana legalis), have experienced a reduction in their populations with respect to both area and density. To evaluate the possible effects of selective logging on genetic diversity, gene flow, and spatial genetic structure, 51 C. legalis individuals were sampled, representing the total remaining population from the cacao agroforestry system.

Genetic diversity and population structure of different varieties of Morada Nova hair sheep from Brazil

J. S. B. Ferreira, Paiva, S. R., Silva, E. C., McManus, C. M., Caetano, A. R., Façanha, D. A. E., and de Sousa, M. A. N., “Genetic diversity and population structure of different varieties of Morada Nova hair sheep from Brazil”, vol. 13, pp. 2480-2490, 2014.

The aim of this study was to analyze genetic diversity and population structure among varieties of White (N = 40), Red (N = 32), and Black (N = 31) Morada Nova hair sheep from flocks in the northeastern Brazilian semiarid region. Fifteen nuclear microsatellite markers and two regions of mitochondrial DNA were used. The intra-population analysis demonstrated that the White variety had higher diversity, while the Red variety had the lowest values.

Assessment of microsatellites in estimating inter- and intraspecific variation among Neotropical Crocodylus species

A. Bashyal, Gross, B. A., Venegas-Anaya, M., Lowrance, F., and Densmore, III, L. D., “Assessment of microsatellites in estimating inter- and intraspecific variation among Neotropical Crocodylus species”, vol. 13, pp. 5492-5502, 2014.

We tested microsatellites that were developed for the saltwater crocodile (Crocodylus porosus) for cross-species amplification and to provide an estimate of inter- and intraspecific variation among four species of Neotropical crocodiles (C. rhombifer, C. intermedius, C. acutus, and C. moreletii). Our results indicated that with the exception of 2 loci in C.

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