Molecular markers

Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers

B. M. Zarroug, Baraket, G., Zourgui, L., Souid, S., and A. Hannachi, S., “Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers”, vol. 14, pp. 1423-1433, 2015.

Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm.

Genetic dissection of agronomic traits in Capsicum baccatum var. pendulum

M. M. Moulin, Rodrigues, R., Bento, C. S., Gonçalves, L. S. A., Santos, J. O., Sudré, C. P., and Viana, A. P., “Genetic dissection of agronomic traits in Capsicum baccatum var. pendulum”, vol. 14, pp. 2122-2132, 2015.

Genetic mapping is very useful for dissecting complex agronomic traits. Genetic mapping allows for identification of quantitative trait loci (QTL), provide knowledge on a gene position and its adjacent region, and enable prediction of evolutionary mechanisms, in addition to contributing to synteny studies. The aim of this study was to predict genetic values associated with different agronomic traits evaluated in an F2 population of Capsicum baccatum var. pendulum. Previously, a reference genetic map for C.

Construction of an integrated genetic map for Capsicum baccatum L.

M. M. Moulin, Rodrigues, R., Ramos, H. C. C., Bento, C. S., Sudré, C. P., Gonçalves, L. S. A., and Viana, A. P., “Construction of an integrated genetic map for Capsicum baccatum L.”, vol. 14, pp. 6683-6694, 2015.

Capsicum baccatum L. is one of the five Capsicum domesticated species and has multiple uses in the food, pharmaceutical and cosmetic industries. This species is also a valuable source of genes for chili pepper breeding, especially genes for disease resistance and fruit quality. However, knowledge of the genetic structure of C. baccatum is limited. A reference map for C.

Efficient identification of ornamental peach cultivars using RAPD markers with a manual cultivar identification diagram strategy

J. Han, Wang, W. Y., Leng, X. P., Guo, L., Yu, M. L., Jiang, W. B., and Ma, R. J., “Efficient identification of ornamental peach cultivars using RAPD markers with a manual cultivar identification diagram strategy”, vol. 13, pp. 32-42, 2014.

One of the most important uses of DNA markers is cultivar identification. However, no DNA fingerprint analysis strategy is available for making DNA markers helpful in practical plant cultivar identification, especially for the identification of a large number of cultivars. We developed a manual cultivar identification diagram strategy for efficient identification of plant cultivars, from which a cultivar identification diagram (CID) of genotyped plant individuals can be constructed manually.

Selfing rate estimation in sugarcane under unfavorable natural conditions of crossing by using microsatellite markers

M. L. G. Melloni, Scarpari, M. S., Pinto, L. R., Perecin, D., Xavier, M. A., and Landell, M. G. A., “Selfing rate estimation in sugarcane under unfavorable natural conditions of crossing by using microsatellite markers”, vol. 13, pp. 2278-2289, 2014.

The self-fertilization or selfing rate estimation using microsatellite markers and its impact on survival and selection rate were evaluated in families derived from polycrosses that involved parents that were widely used in sugarcane breeding in Brazil. These factors were evaluated under unfavorable natural conditions of flowering and crossing. After the germination test, the viable progeny were taken to the field for survival rate evaluation (4, 6, and 10 months) and phenotypic selection at plant cane.

Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata

L. R. G. Silva, Bajay, M. M., Monteiro, M., Mezette, T. F., Nascimento, W. F., Zucchi, M. I., Pinheiro, J. B., and Veasey, E. A., “Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata”, vol. 13, pp. 2766-2771, 2014.

Dioscorea cayenensis and Dioscorea rotundata are among the most important yam species for the humid and sub-humid tropics. We isolated nine polymorphic microsatellite markers using a microsatellite-enriched genomic library technique. The nine primer pairs were validated in 22 D. cayenensis accessions, and were tested for transferability in 26 D. rotundata accessions. The number of bands ranged from 2 to 4, with a mean of 3.11. D. cayenensis gave primer polymorphism information content values ranging from 0.37 to 0.62, while for D.

Genetic variations in the leptin gene associated with growth and carcass traits in Nellore cattle

D. B. S. Silva, Crispim, B. A., Silva, L. E., Oliveira, J. A., Siqueira, F., Seno, L. O., and Grisolia, A. B., “Genetic variations in the leptin gene associated with growth and carcass traits in Nellore cattle”, vol. 13, pp. 3002-3012, 2014.

The aim of the study was to detect polymorphisms in the leptin gene and to determine the association of these polymorphisms with growth and carcass traits in Nellore cattle. The single nucleotide polymorphisms (SNPs) -1457 (AJ571671:g.-1457A>G) and A59V (AF536174.1:g. 321C>T), as well as the microsatellite BM1500 (3.9 kb downstream), were genotyped. The measures of body weight and ultrasound examinations (rib eye area, back, and rump fat thickness) were performed in 3 different periods of animal management.

Genetic diversity and structure of natural Dactylis glomerata L. populations revealed by morphological and microsatellite-based (SSR/ISSR) markers

P. Madesis, Abraham, E. M., Kalivas, A., Ganopoulos, Ι., and Tsaftaris, A., “Genetic diversity and structure of natural Dactylis glomerata L. populations revealed by morphological and microsatellite-based (SSR/ISSR) markers”, vol. 13, pp. 4226-4240, 2014.

Dactylis glomerata L. is an important forage species in the Mediterranean region, and in other regions with a similar climate. Genetic material from 3 locations in north, central, and south Greece was studied, using morphological traits, SSR, and ISSR molecular markers. Morphological analysis revealed differences among the geographic locations studied for all morphological traits, except the number of reproductive tillers. Moreover, the highest phenotypic variation was observed on the accessions from south, while the lowest was observed on the accessions from the north.

Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection

M. M. Scaldaferri, Freitas, J. S., Vieira, J. G. P., Gonçalves, Z. S., Souza, A. M., and Cerqueira-Silva, C. B. M., “Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection”, vol. 13. pp. 5566-5573, 2014.

We investigated 10 similarity (and disimilarity) coefficients in a set of 40 wild genotypes of Croton linearifolius subjected to analyses using hierarchical grouping methods, grouping methods by optimization and data projection in two-dimensional space. Genotypes were characterized by analyzing DNA polymorphism with the use of 15 ISSR and 12 RAPD markers. The distance measurements were compared by the Spearman correlation test, projection in two-dimensional space and grouping efficiency evaluation.

Development of a cassava core collection based on single nucleotide polymorphism markers

E. J. Oliveira, Ferreira, C. F., Santos, V. S., and Oliveira, G. A. F., “Development of a cassava core collection based on single nucleotide polymorphism markers”, vol. 13, pp. 6472-6485, 2014.

Single nucleotide polymorphism (SNP) markers were used in the largest cassava (Manihot esculenta Crantz) germplasm collection from Brazil to develop core collections based on the maximization strategy. Subsets with 61, 64, 84, 128, 256, and 384 cassava accessions were selected and named PoHEU, MST64, PoRAN, MST128, MST256, and MST384, respectively. All the 798 alleles identified by 402 SNP markers in the entire collection were captured in all core collections.

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