SSR

Population structure of the blood clam (Tegillarca granosa) in China based on microsatellite markers

Y. J. Wang, Zeng, Q. G., and Xu, L. N., “Population structure of the blood clam (Tegillarca granosa) in China based on microsatellite markers”, vol. 12, pp. 892-900, 2013.

The blood clam, Tegillarca granosa, is widely cultivated in China. We isolated 6 microsatellite loci from T. granosa and used them to investigate genetic diversity and population structure of 5 widely distributed populations of blood clam collected from eastern and southeastern China. The allele number per locus varied from 4 to 9, and the polymorphism information content value was 0.301 to 0.830.

Analysis of genetic diversity among Chinese wild Vitis species revealed with SSR and SRAP markers

Z. B. Jing, Wang, X. P., and Cheng, J. M., “Analysis of genetic diversity among Chinese wild Vitis species revealed with SSR and SRAP markers”, vol. 12, pp. 1962-1973, 2013.

The genetic diversity among 80 Vitis materials including 62 indigenous accessions of 17 wild Vitis species in China and 7 interspecific hybrids, 10 V. vinifera L. cultivars, and 1 V. riparia Michaux were evaluated by simple sequence repeat and sequence-related amplified polymorphism markers. A total of 10 simple sequence repeat primers and 11 sequence-related amplified polymorphism primer combinations were amplified, and 260 bands were generated, of which 252 were polymorphic with an average polymorphism rate of 97.02%.

Development and characterization of microsatellite primers in Pogostemon cablin (Lamiaceae)

S. S. Sandes, Pinheiro, J. B., Zucchi, M. I., Monteiro, M., Arrigoni-Blank, M. F., and Blank, A. F., “Development and characterization of microsatellite primers in Pogostemon cablin (Lamiaceae)”, vol. 12. pp. 2837-2840, 2013.

Microsatellite primers were developed and optimized for patchouli (Pogostemon cablin) to characterize the patchouli Active Germplasm Bank of Universidade Federal de Sergipe. Creation of a genomic library for patchouli enabled the design of 12 microsatellite primers. Six of these microsatellites were polymorphic, revealing two well-defined groups of individuals that possess exclusive alleles. The data allowed us to characterize the patchouli active Germplasm Bank, identify its genetic diversity, and provide new information for researching this species.

Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs

X. Q. Wang, Yu, Y., Li, W., Guo, H. L., Lin, Z. X., and Zhang, X. L., “Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs”, vol. 12, pp. 3353-3362, 2013.

Cotton is an important cash crop. Mining for quantitative trait loci related to yield and fiber quality traits using association analysis has many advantages for cotton research. In this study, 170 simple sequence repeats (SSRs) and 258 sequence-related amplified polymorphisms (SRAPs) were used to analyze the association of 3 yield component traits and 5 fiber quality traits of 55 Gossypium barbadense accessions in 2009 and 2010. Principal component analysis of SSRs and SRAPs showed 3 and 2 subgroups, respectively.

Genomic DNA isolation of Acrocomia aculeata (Arecaceae) from leaf and stipe tissue samples for PCR analysis

E. C. M. Lanes, Nick, C., Kuki, K. N., Freitas, R. D., and Motoike, S. Y., “Genomic DNA isolation of Acrocomia aculeata (Arecaceae) from leaf and stipe tissue samples for PCR analysis”, vol. 12, pp. 3905-3911, 2013.

Macaw palm, Acrocomia aculeata is an oleaginous species of the Arecaceae family; it has been identified as one of the most promising plants for sustainable production of renewable energy, especially biodiesel. We developed an efficient protocol of genomic DNA extraction for A. aculeata using leaf and stipe tissues, based on the cationic hexadecyltrimethylammonium bromide method, and we evaluated the quantity, purity, and integrity of the resultant DNA. We also determined whether these procedures interfere with PCR amplification using SSR molecular markers.

Production and identification of doubled haploids in tropical maize

G. M. Battistelli, Von Pinho, R. G., Justus, A., Couto, E. G. O., and Balestre, M., “Production and identification of doubled haploids in tropical maize”, vol. 12, pp. 4230-4242, 2013.

The production of maize doubled haploid (DH) lines is a technique commonly used by private companies, but not by Brazilian public institutions. Research on this technique is essential to develop and improve the production of DH lines grown under tropical conditions.

Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers

M. H. Öz, Vurgun, H., Bakir, M., Büyük, İ., Yüksel, C., Ünlü, H. M., Çukadar, K., Karadoğan, B., Köse, Ö., and Ergül, A., “Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers”, vol. 12, pp. 5310-5320, 2013.

We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships.

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers

A. A. Khaing, Moe, K. T., Hong, W. J., Park, C. S., Yeon, K. H., Park, H. S., Kim, D. C., Choi, B. J., Jung, J. Y., Chae, S. C., Lee, K. M., and Park, Y. J., “Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers”, vol. 12, pp. 5335-5347, 2013.

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus.

Characterization of Anatolian traditional quince cultivars, based on microsatellite markers

C. Yüksel, Mutaf, F., Demirtaş, İ., Öztürk, G., Pektaş, M., and Ergül, A., “Characterization of Anatolian traditional quince cultivars, based on microsatellite markers”, vol. 12, pp. 5880-5888, 2013.

We conducted simple sequence repeat (SSR) analyses of 15 traditional quince (Cydonia oblonga) cultivars from Anatolian gene sources for molecular characterization and investigation of genetic relationships. Three pear and two apple cultivars were used as references for SSR locus data analysis and to determine allele profiles between species. Eight SSR loci that were developed from apple and pear were used, and a total of 44 alleles were found among quince cultivars.

Genetic diversity of Saccharum spontaneum from geographical regions of China assessed by simple sequence repeats

L. N. Fan, Deng, H. H., Luo, Q. W., He, H. Y., Li, Y., Wang, Q. N., Huang, Z. X., Wu, J. T., Li, Q. W., Liu, S. M., and Qi, Y. W., “Genetic diversity of Saccharum spontaneum from geographical regions of China assessed by simple sequence repeats”, vol. 12, pp. 5916-5925, 2013.

Saccharum spontaneum is the most variable wild relative of sugarcane with potential for use in sugarcane improvement programs. In order to help preserve and exploit this species, 152 accessions from eight major geographical regions in China, including Hainan, Guangdong, Guangxi, Yunnan, Sichuan, Guizhou, Fujian, and Jiangxi provinces, were investigated by analyzing 20 simple sequence repeats (SSRs), including 11 genomic SSRs (gSSRs) and nine SSRs developed from expressed sequence tags (EST-SSRs).