Molecular markers

Molecular characterization of endophytes isolated from Saccharum spp based on esterase and ribosomal DNA (ITS1-5.8S-ITS2) analyses

A. C. Leme, Bevilaqua, M. R. R., Rhoden, S. A., Mangolin, C. A., Machado, M. F. P. S., and Pamphile, J. A., Molecular characterization of endophytes isolated from Saccharum spp based on esterase and ribosomal DNA (ITS1-5.8S-ITS2) analyses, vol. 12, pp. 4095-4105, 2013.

This study used esterases and ribosomal DNA (rDNA) markers to determine endophytic variability in order to better understand endophyte-host interactions. Polyacrylamide gel electrophoresis and esterase isoenzymes (EST; EC 3.1.1.3), with α-naphthyl acetate and β-naphthyl acetate as substrates, were used to assess relationships among endophytes. ITS1-5.8S-ITS2 sequencing data were used as rDNA markers. Thirty-two esterases were obtained from 37 isolates of Saccharum spp, which clustered into five endophyte groups.

Genetic variability in accessions of the acerola germplasm bank of Universidade Federal Rural de Pernambuco, Brazil

R. M. Moraes Filho, Martins, L. S. S., Musser, R. S., Montarroyos, A. V. V., and Silva, E. F., Genetic variability in accessions of the acerola germplasm bank of Universidade Federal Rural de Pernambuco, Brazil, vol. 12, pp. 5145-5151, 2013.

Brazil is the world’s largest producer of acerola, Malpighia emarginata (Malpighiaceae); the Northeast is responsible for 60% of the national production. The culture of acerola in Brazil has great genetic variability; plantings have high phenotypic diversity and are not very productive, often originating from propagation by seed. We evaluated the genetic diversity of 42 accessions from the Acerola Active Germplasm Bank of Universidade Federal de Pernambuco. Using 15 RAPD primers, 182 markers were obtained, of which 166 were polymorphic and 16 were monomorphic.

Isolation and characterization of polymorphic microsatellite loci in the swimming crab Portunus trituberculatus (Portunidae)

L. P. Ren, Qin, Y., Li, X. C., Sun, Y. N., and Wang, R. X., Isolation and characterization of polymorphic microsatellite loci in the swimming crab Portunus trituberculatus (Portunidae), vol. 12, pp. 5911-5915, 2013.

The Swimming crab Portunus trituberculatus (Portunidae) is an important economically food species. To provide molecular markers for P. trituberculatus, we isolated and characterized polymorphic microsatellite markers. We developed a 5'-anchored genomic library of P. trituberculatus DNA, and derived 45 positive clones. We designed 30 pairs of primers from the sequences of these clones, and 10 of which were polymorphic. The loci were screened in 31 P. trituberculatus individuals; the number of alleles ranged from 2 to 5.

Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

I. A. Arif, Khan, H. A., Shobrak, M., Homaidan, A. A. Al, M. Sadoon, A., Farhan, A. H. Al, and Bahkali, A. H., Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx, vol. 9, pp. 259-265, 2010.

Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx.

Prediction of maize single-cross performance by mixed linear models with microsatellite marker information

M. Balestre, Von Pinho, R. G., and Souza, J. C., Prediction of maize single-cross performance by mixed linear models with microsatellite marker information, vol. 9, pp. 1054-1068, 2010.

We evaluated the potential of the best linear unbiased predictor (BLUP) along with the relationship coefficient for predicting the performance of untested maize single-cross hybrids. Ninety S0:2 progenies arising from three single-cross hybrids were used. The 90 progenies were genotyped with 25 microsatellite markers, with nine markers linked to quantitative trait loci for grain yield. Based on genetic similarities, 17 partial inbred lines were selected and crossed in a partial diallel design.

Morphological, pathological and molecular variability in Botryodiplodia theobromae (Botryosphaeriaceae) isolates associated with die-back and bark canker of pear trees in Punjab, India

M. D. Shah, Verma, K. S., Singh, K., and Kaur, R., Morphological, pathological and molecular variability in Botryodiplodia theobromae (Botryosphaeriaceae) isolates associated with die-back and bark canker of pear trees in Punjab, India, vol. 9, pp. 1217-1228, 2010.

Thirteen isolates of Botryodiplodia theobromae collected from pear varieties grown in various regions of Punjab were studied for morphological, pathological and molecular characterization. The mycelial growth of B. theobromae isolates was classified as fluffy or depressed, uniform to irregular and cottony white turning to black. Colony growth rate varied from 19.1 to 24.9 mm per day. Pycnidia were produced either on the edge, centered or scattered on Petri dishes after 20 to 34 days of incubation.

Molecular identification of Greek olive (Olea europaea) cultivars based on microsatellite loci

K. Roubos, Moustakas, M., and Aravanopoulos, F. A., Molecular identification of Greek olive (Olea europaea) cultivars based on microsatellite loci, vol. 9, pp. 1865-1876, 2010.

Olea europaea is one of the oldest species of domesticated trees. We used microsatellite markers for fingerprinting and for evaluation of genetic similarity and structure of 26 Greek olive cultivars, which cover most of the olive cultivation regions of Greece, including previously undescribed denominations from northern Greece. Eighty-one alleles were revealed with six SSR loci that were selected as most informative of 10 SSR primers that were initially investigated. The number of alleles per locus varied from 7 to 20 (mean, 13.5).

Genetic characterization of heat tolerant tomato (Solanum lycopersicon) genotypes by SRAP and RAPD markers

N. Comlekcioglu, Simsek, O., Boncuk, M., and Aka-Kacar, Y., Genetic characterization of heat tolerant tomato (Solanum lycopersicon) genotypes by SRAP and RAPD markers, vol. 9, pp. 2263-2274, 2010.

We employed RAPD and sequence-related amplified polymorphism (SRAP) markers to evaluate polymorphisms in 15 tomato (Solanum lycopersicon) genotypes that were obtained from a tomato breeding program. Four local tomato genotypes selected from the Sanliurfa province (Southeastern Anatolia Region of Turkey), 10 heat-tolerant tomato genotypes, received from the Asian Vegetable Research and Development Center, and a sample of S. pimpinellifolium were genotyped with RAPD and SRAP markers. Eleven SRAP primer combinations were used and 66 bands were scored.

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp)

S. A. L. Garcia, Van der Lee, T. A. J., Ferreira, C. F., B. Hekkert, T. Lintel, Zapater, M. - F., Goodwin, S. B., Guzmán, M., Kema, G. H. J., and Souza, Jr., M. T., Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp), vol. 9, pp. 2207-2212, 2010.

We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units.

Prediction of maize double-cross hybrids using the best linear unbiased prediction with microsatellite marker information

M. Balestre, Von Pinho, R. G., and Souza, J. C., Prediction of maize double-cross hybrids using the best linear unbiased prediction with microsatellite marker information, vol. 10, pp. 25-35, 2011.

We examined the usefulness of the best linear unbiased prediction associated with molecular markers for prediction of untested maize double-cross hybrids. Ten single-cross hybrids from different commercial backgrounds were crossed using a complete diallel design. These 10 single-cross hybrids were genotyped with 20 microsatellite markers.

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