SSR

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

M. R. Bakhtiarizadeh, Arefnejad, B., Ebrahimie, E., and Ebrahimi, M., “Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)”, vol. 11, pp. 1558-1574, 2012.

Many years of domestication and breeding have given rise to the wide range of chicken breeds that exist today; however, an increasing number of local chicken breeds are under threat of extinction. A comprehensive characterization of chicken markers (especially type I markers) is needed to monitor and conserve genetic diversity in this species. The explosion of genomics and functional genomics information in recent years has opened new possibilities for the generation of molecular markers.

Mapping of HtNB, a gene conferring non-lesion resistance before heading to Exserohilum turcicum (Pass.), in a maize inbred line derived from the Indonesian variety Bramadi

H. Wang, Xiao, Z. X., Wang, F. G., Xiao, Y. N., Zhao, J. R., Zheng, Y. L., and Qiu, F. Z., “Mapping of HtNB, a gene conferring non-lesion resistance before heading to Exserohilum turcicum (Pass.), in a maize inbred line derived from the Indonesian variety Bramadi”, vol. 11, pp. 2523-2533, 2012.

The gene HtNB confers non-lesion resistance to the fungal pathogen Exserohilum turcicum in maize. To map this gene, we developed two F₂ populations, P111 (resistant line) x HuangZao 4 (susceptible line) and P111 x B73 (susceptible). HtNB was located on chromosome 8.07 bin, flanked by MAC216826-4 and umc2218 at distances of 3.3 and 3.4 cM, respectively. HtNB appears to be a new gene responsible for resistance to northern corn leaf blight. Functions of the genes in the region between umc1384 and umc2218 were predicted.

Characterization of nine microsatellite loci for the tree species Parapiptadenia rigida

B. F. Costa, Rodrigues, L. A., Ruas, E. A., Souza, L. B., Ruas, C. F., Vieira, B. G., Conson, A. R. O., and Ruas, P. M., “Characterization of nine microsatellite loci for the tree species Parapiptadenia rigida”, vol. 11. pp. 2338-2342, 2012.

Parapiptadenia rigida, locally known as angico, is a tropical tree common in the semideciduous Brazilian forest. Its wood is naturally resistant to insect attack and is useful for construction. Extracts from the tree have medicinal properties. We characterized nine microsatellite loci for P. rigida. Thirty-five alleles were detected in a sample of 45 individuals from 3 different populations, with an average of 3.9 alleles per locus. The average polymorphic information content ranged from 0.099 to 0.640.

Genetic diversity of Lagerstroemia (Lythraceae) species assessed by simple sequence repeat markers

D. He, Liu, Y., Cai, M., Pan, H. T., Zhang, Q. X., Wang, X. Y., and Wang, X. J., “Genetic diversity of Lagerstroemia (Lythraceae) species assessed by simple sequence repeat markers”, vol. 11, pp. 3522-3533, 2012.

Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration, and diverse colors. However, little is known about the genetic structure and diversity of germplasm in Lagerstroemia. We genotyped 81 L. indica cultivars, five other species of Lagerstroemia, and 10 interspecific hybrids using 30 simple sequence repeat markers; 275 alleles were generated with a mean of nine alleles per locus.

Isolation and characterization of 25 microsatellite DNA loci for Anopheles albitarsis sensu lato and inter-specific amplification in 5 congeneric species

G. M. Guimarães-Marques, Batista, J. S., Guimarães, H. M., Naice-Daou, M. V., Lima, M. P., Formiga, K. M., Santos, J. M. M., Lima, C. A. P., and Rafael, M. S., “Isolation and characterization of 25 microsatellite DNA loci for Anopheles albitarsis sensu lato and inter-specific amplification in 5 congeneric species”, vol. 11, pp. 4198-4203, 2012.

The Anopheles albitasis complex includes 6 species, and 3 are considered as malaria vectors in Brazil. Twenty-five polymorphic microsatellite DNA loci were isolated and characterized in 24-36 individuals from the neighborhood of Puraquequara, Manaus, Amazonas State, Brazil. The number of estimated alleles ranged from 2 to 10, the observed heterozygosity ranged from 0.182 to 0.897, and the expected heterozygosity ranged from 0.260 to 0.854. Eleven loci showed significant deviation from Hardy-Weinberg equilibrium.

Analysis of genetic diversity among wild bermudagrass germplasm from southwest China using SSR markers

Y. Ling, Zhang, X. - Q., Ma, X., Chen, S. - Y., Chen, T. - T., and Liu, W., “Analysis of genetic diversity among wild bermudagrass germplasm from southwest China using SSR markers”, vol. 11, pp. 4598-4608, 2012.

Fifty-five wild accessions of bermudagrass (Cynodon dactylon) were collected from southwest China (Sichuan, Chongqing, Yunnan, Guizhou, and Tibet), and their genetic diversity was analyzed using simple sequence repeat markers. A total of 267 polymorphic bands were detected with 18 primer combinations. The genetic similarity among the accessions ranged from 0.688 to 0.894 with an average of 0.797. All 55 wild accessions were clustered into 7 eco-geographic groups.

Identification of earl millet cultivars using both microsatellites and enzymatic markers

R. P. Mendonça Neto, Von Pinho, E. V. R., Carvalho, B. L., and Pereira, G. S., “Identification of earl millet cultivars using both microsatellites and enzymatic markers”, vol. 12, pp. 1-14, 2013.

The increasing number of protected and registered cultivars and problems involving seed commercialization make distinction and identification of cultivars imperative. Millet (Pennisetum glaucum), a crop species with protected cultivars in Brazil, has been the target of seed piracy.

A protocol for high-quality genomic DNA extraction from legumes

I. O. Agbagwa, Datta, S., Patil, P. G., Singh, P., and Nadarajan, N., “A protocol for high-quality genomic DNA extraction from legumes”, vol. 11, pp. 4632-4639, 2012.

Current DNA extraction protocols, which require liquid nitrogen, lyophilization and considerable infrastructure in terms of instrumentation, often impede the application of biotechnological tools in less researched crops in laboratories in developing countries. We modified and optimized the existing CTAB method for plant genomic DNA extraction by avoiding liquid nitrogen usage and lyophilization. DNA was extracted directly from freshly harvested leaves ground in pre-heated CTAB buffer.

Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers

Z. Noormohammadi, Y. Farahani, H. - A., Sheidai, M., Ghasemzadeh-Baraki, S., and Alishah, O., “Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers”, vol. 12. pp. 256-269, 2013.

Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F₂ progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism.

Genetic variability of watermelon accessions based on microsatellite markers

R. N. Cde S. Gama, Santos, C. A. F., and R. Dias, deC. S., “Genetic variability of watermelon accessions based on microsatellite markers”, vol. 12, pp. 747-754, 2013.

We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci.