Simple sequence repeat

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

F. P. Li, Lee, Y. S., Kwon, S. W., Li, G., and Park, Y. J., Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.), vol. 13, pp. 6316-6331, 2014.

This study analyzed 394 Korean rice landrace accessions, including 93 waxy varieties, for polymorphisms using 29 simple sequence repeat (SSR) markers. In total, 381 alleles served as raw data for estimating the genetic diversity (GD) and population structure. The number of alleles per locus ranged from 3 to 44 (average = 13.14). The expected heterozygosity and polymorphism information content (PIC) ranged from 0.0341 to 0.9358 (mean = 0.5623) and from 0.0783 to 0.9367 (mean = 0.5839), respectively.

Development and characterization of novel SSR markers in Siniperca kneri Garman

M. Yang, Zheng, H. Z., Liang, X. - F., Tian, C. X., Dou, Y. Q., Zhu, K. C., and Yuan, Y. C., Development and characterization of novel SSR markers in Siniperca kneri Garman, vol. 13, pp. 7593-7606, 2014.

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. The average allele number per locus was 5.1 (range: 2-8) for transcriptome-derived SSRs and 3.8 (range: 2-5) for genomic SSRs. The average observed and expected heterozygosities were 0.666 (range: 0.000-1.000) and 0.692 (range: 0.230-0.857) for transcriptome-derived SSRs, respectively. These values were 0.380 (range: 0.000-1.000) and 0.527 (range: 0.201-0.799) for genomic SSRs, respectively.

Identification of apple cultivars on the basis of simple sequence repeat markers

G. S. Liu, Zhang, Y. G., Tao, R., Fang, J. G., and Dai, H. Y., Identification of apple cultivars on the basis of simple sequence repeat markers, vol. 13, pp. 7377-7387, 2014.

DNA markers are useful tools that play an important role in plant cultivar identification. They are usually based on polymerase chain reaction (PCR) and include simple sequence repeats (SSRs), inter-simple sequence repeats, and random amplified polymorphic DNA. However, DNA markers were not used effectively in the complete identification of plant cultivars because of the lack of known DNA fingerprints. Recently, a novel approach called the cultivar identification diagram (CID) strategy was developed to facilitate the use of DNA markers for separate plant individuals.

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.

Screening of highly informative and representative microsatellite markers for genotyping of major cultivated cotton varieties

M. Kuang, Yang, W. H., Wang, F., Xu, H. X., Wang, Y. Q., Zhou, D. Y., Fang, D., Ma, L., and Feng, X. A., Screening of highly informative and representative microsatellite markers for genotyping of major cultivated cotton varieties, vol. 13, pp. 9777-9786, 2014.

We screened and assessed published cotton simple sequence repeat (SSR) primers to establish a set of core SSR markers suitable for cotton major cultivars in China and analyzed genetic diversity based on the core marker set. Using a stepwise screening strategy, 12 leading cultivars for preliminary screening and 96 cultivars for rescreening were evaluated. A total of 184 polymorphic SSR markers were initially screened from 3299 candidates, and a core set of 52 SSR markers with wide genome coverage (2 markers per chromosome) was obtained.

Isolation and characterization of polymorphic microsatellite loci from Zelkova schneideriana Hand.-Mazz.

H. L. Liu, Zhang, R. Q., Geng, M. L., Zhu, J. Y., and Ma, J. L., Isolation and characterization of polymorphic microsatellite loci from Zelkova schneideriana Hand.-Mazz., vol. 13, pp. 10062-10066, 2014.

Zelkova schneideriana is a highly valued hardwood species. An improved technique for isolating codominant compound microsatellite markers was used to develop simple sequence repeat markers for Z. schneideriana. A total of 12 microsatellite loci were identified. Overall, the number of alleles per locus ranged from 8-19, with an average of 11.75. Observed heterozygosity and expected heterozygosity values ranged from 0.109-0.709 and 0.832-0.929, respectively. Polymorphic information content is from 0.803-0.915, with an average of 0.854.

Development and characterization of novel microsatellite markers in Hyptis pectinata (Lamiaceae)

A. F. Blank, Jesus, A. S., Santos, C. P., Grando, C., Pinheiro, J. B., Zucchi, M. I., and Arrigoni-Blank, M. F., Development and characterization of novel microsatellite markers in Hyptis pectinata (Lamiaceae), vol. 13, pp. 10173-10176, 2014.

A microsatellite-enriched library was constructed and a set of 19 SSR markers were developed to characterize a germplasm collection of Hyptis pectinata (L.) Poit., maintained at the Universidade Federal de Sergipe (UFS). Fifteen markers of 19 ranged from moderately to highly polymorphic. A total of 113 alleles were identified, with a mean of 7.52 alleles per locus. The mean HO and HE were 0.582 and 0.657, respectively.

Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot

U. Hameed, Pan, Y. - B., Muhammad, K., Afghan, S., and Iqbal, J., Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot, vol. 11, pp. 1195-1204, 2012.

Red rod is an economically important disease of sugarcane caused by the fungus Colletotrichum falcatum. We used a simple sequence repeat (SSR)-based marker system to identify and analyze genetic relationships of red rot resistant and susceptible sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of 20 sugarcane cultivars. These SSR markers were found to be highly robust; we identified 144 alleles, with 3-11 alleles per marker and a mean of 6.8.

Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast

F. A. S. Aragão, J. Filho, T., Nunes, G. H. S., Queiróz, M. A., Bordallo, P. N., Buso, G. S. C., Ferreira, M. A., Costa, Z. P., and F. Neto, B., Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast, vol. 12, pp. 6356-6371, 2013.

The genetic divergence of 38 melon accessions from traditional agriculture of the Brazilian Northeast and three commercial hybrids were evaluated using fruit descriptors and microsatellite markers. The melon germplasm belongs to the botanic varieties cantalupensis (19), momordica (7), conomon (4), and inodorus (3), and to eight genotypes that were identified only at the species level.

Genetic characterization of pea (Pisum sativum) germplasm from Turkey using morphological and SSR markers

G. Sarıkamış, Yanmaz, R., Ermiş, S., Bakır, M., Bakır, M., and Yüksel, C., Genetic characterization of pea (Pisum sativum) germplasm from Turkey using morphological and SSR markers, vol. 9, pp. 591-600, 2010.

The need for the conservation of plant genetic resources has been widely accepted. Germplasm characterization and evaluation yield information for more efficient utilization of these valuable resources. The aim of the present study was to characterize the pea germplasm conserved at the Aegean Agricultural Research Institute of Turkey using morphological and simple sequence repeat (SSR)-based molecular approaches.

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