Microsatellite

Development and cross-species amplification of microsatellite loci for Puccinellia maritima, an important engineer saltmarsh species

R. Rouger, Vallejo-Marin, M., and Jump, A. S., “Development and cross-species amplification of microsatellite loci for Puccinellia maritima, an important engineer saltmarsh species”, vol. 13, pp. 3426-3431, 2014.

The grass Puccinellia maritima is an important saltmarsh ecosystem engineer exhibiting wide morphological variation, which is partially genetically determined. Nevertheless, nothing is known about its population genetics or how neutral genetic variation is distributed throughout its geographical range. Here, we describe 12 polymorphic microsatellites pooled into two multiplexes for this octoploid species. Assessment of 24 samples from three populations revealed 4 to 29 alleles per locus, with variation in allele presence and abundance between populations.

Geographical genetics of Pseudoplatystoma punctifer (Castelnau, 1855) (Siluriformes, Pimelodidae) in the Amazon Basin

M. P. C. Telles, Collevatti, R. G., Braga, R. S., Guedes, L. B. S., Castro, T. G., Costa, M. C., Silva-Júnior, N. J., Barthem, R. B., and Diniz-Filho, J. A. F., “Geographical genetics of Pseudoplatystoma punctifer (Castelnau, 1855) (Siluriformes, Pimelodidae) in the Amazon Basin”, vol. 13, pp. 3656-3666, 2014.

Geographical genetics allows the evaluation of evolutionary processes underlying genetic variation within and among local populations and forms the basis for establishing more effective strategies for biodiversity conservation at the population level. In this study, we used explicit spatial analyses to investigate molecular genetic variation (estimated using 7 microsatellite markers) of Pseudoplatystoma punctifer, by using samples obtained from 15 localities along the Madeira River and Solimões, Amazon Basin.

Polymorphic microsatellite loci isolated from Cervus unicolor (Cervidae) show inbreeding in a domesticated population of Taiwan Sambar deer

D. Y. Lin, Chiang, T. Y., Huang, C. C., Lin, H. D., Tzeng, S. J., Kang, S. R., Sung, H. M., and Wu, M. C., “Polymorphic microsatellite loci isolated from Cervus unicolor (Cervidae) show inbreeding in a domesticated population of Taiwan Sambar deer”, vol. 13, pp. 3967-3971, 2014.

Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesticated Formosan Sambar deer (Cervus unicolor swinhoei). All loci were polymorphic, with 10-19 alleles per locus. The average observed heterozygosity across loci and samples was 0.310, ranging from 0 to 0.750 at each locus. All loci but one, CU18, deviated from Hardy-Weinberg equilibrium due to excessive homozygosity in these domesticated broodstocks, reflecting inbreeding.

Development of eight novel microsatellite markers for Huoyan geese

Z. Z. Cao, Su, D., Zhao, Y. Y., Liu, M., Gao, M., and Luan, X. H., “Development of eight novel microsatellite markers for Huoyan geese”, vol. 13, pp. 5562-5565, 2014.

In this study, we isolated microsatellite DNA from the Huoyan goose genome with magnetic beads. As a result, 150 positive clones were identified, and 148 microsatellites were found. Among the 148 microsatellites, 69.6% were perfect, 17.6% were imperfect, and the rest were compound type (12.8%). Twenty microsatellite primers were used to screen 90 individuals from 3 Huoyan goose populations. Eight loci were polymorphic with a low number of alleles (2 to 4). The observed and expected heterozygosities ranged from 0.3556 to 1 and from 0.2923 to 0.6868, respectively.

Isolation and characterization of 32 microsatellite loci for topmouth culter (Culter alburnus Basilewsky)

S. - L. Liu, Gu, Z. - M., Jia, Y. - Y., Zhao, J. - L., Jiang, W. - P., Li, Q., and Li, F., “Isolation and characterization of 32 microsatellite loci for topmouth culter (Culter alburnus Basilewsky)”, vol. 13, pp. 7480-7483, 2014.

The topmouth culter (Culter alburnus) is an economically important freshwater fish, which is widely distributed throughout large rivers, reservoirs, and lake areas of China. We report here the isolation and characterization of 32 new polymorphic microsatellite loci isolated from genomic DNA in this species enriched by (CA)12 and (GA)12 probes. The variability of these microsatellites was tested on 30 individuals cultured. The average allele number was 6.6 per locus, ranging from 3 to 12.

Isolation and characterization of novel microsatellite markers from Siamese fighting fish (Betta splendens, Osphronemidae, Anabantoidei) and their transferability to related species, B. smaragdina and B. imbellis

V. Chailertrit, Swatdipong, A., Peyachoknagul, S., Salaenoi, J., and Srikulnath, K., “Isolation and characterization of novel microsatellite markers from Siamese fighting fish (Betta splendens, Osphronemidae, Anabantoidei) and their transferability to related species, B. smaragdina and B. imbellis”, vol. 13, pp. 7157-7162, 2014.

Ten novel microsatellite markers were developed and characterized from Siamese fighting fish (Betta splendens). Nine of ten markers were polymorphic, exhibiting an allelic number (NA) from 2 to 6 alleles per locus. The effective number of alleles (NE) ranged from 1.60 to 3.08 (average of 2.30). The observed (HO) and expected (HE) heterozygosities ranged from 0.13 to 0.67 (average of 0.39) and 0.29 to 0.63 (average of 0.50), respectively.

Inverted migration of rare whisker sheatfish in Nong-Han Lake, northeastern Thailand: Implications for conservation

P. Phongkaew, Arunyawat, U., Swatdipong, A., and Hongtrakul, V., “Inverted migration of rare whisker sheatfish in Nong-Han Lake, northeastern Thailand: Implications for conservation”, vol. 13, pp. 7492-7502, 2014.

Nong-Han Lake, Thailand, sustains the whisker sheatfish (Micronema bleekeri Günther, 1864), which is a rare species of freshwater catfish. Wild-caught whisker sheatfish has been intensively harvested to meet market demand; yet, genetic information about this species remains unknown. To assist with the in situ conservation of whisker sheatfish populations in Nong-Han Lake, 35 and 34 individuals from the middle (MN) and lower (LN) areas of the lake, respectively, were studied using 7 microsatellite loci.

Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China

S. - R. Zhu, Li, J. - L., Xie, N., Zhu, L. - M., Wang, Q., and Yue, G. - H., “Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China”, vol. 13, pp. 8046-8054, 2014.

The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci.

Genetic diversity among Puccinia melanocephala isolates from Brazil assessed using simple sequence repeat markers

R. F. Peixoto-Junior, Creste, S., Landell, M. G. A., Nunes, D. S., Sanguino, A., Campos, M. F., Vencovsky, R., Tambarussi, E. V., and Figueira, A., “Genetic diversity among Puccinia melanocephala isolates from Brazil assessed using simple sequence repeat markers”, vol. 13, pp. 7852-7863, 2014.

Brown rust (causal agent Puccinia melanocephala) is an important sugarcane disease that is responsible for large losses in yield worldwide. Despite its importance, little is known regarding the genetic diversity of this pathogen in the main Brazilian sugarcane cultivation areas. In this study, we characterized the genetic diversity of 34 P. melanocephala isolates from 4 Brazilian states using loci identified from an enriched simple sequence repeat (SSR) library.

Unraveling the variability and genetic structure of barker frog Physalaemus cuvieri (Leiuperinae) populations from different regions of Brazil

M. Conte, Targueta, C. P., Zucchi, M. I., Souza, A. P., and Recco-Pimentel, S. M., “Unraveling the variability and genetic structure of barker frog Physalaemus cuvieri (Leiuperinae) populations from different regions of Brazil”, vol. 13, pp. 8055-8065, 2014.

The barker frog Physalaemus cuvieri is widely distributed in South America and is found in all regions of Brazil. Significant intraspecific morphological variation in this species has been reported. To determine the genetic structure of the natural Brazilian populations of P. cuvieri, 10 different populations geographically separated by 99.41 to 2936.75 km were evaluated using 10 polymorphic microsatellite loci. In addition, mitochondrial DNA data were analyzed to determine genetic distance between the populations.

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