Simple sequence repeat

Genetic analysis of seed-shattering genes in rice using an F3:4 population derived from an Oryza sativa x Oryza rufipogon cross

S. - J. Kwon, Yu, J., Park, Y. J., Son, J. - H., Kim, N. - S., and Lee, J. K., Genetic analysis of seed-shattering genes in rice using an F3:4 population derived from an Oryza sativa x Oryza rufipogon cross, vol. 14, pp. 1347-1361, 2015.

Seed shattering of wild plant species is thought to be an adaptive trait to facilitate seed dispersal. For rice breeding, seed shatter­ing is an important trait for improving breeding strategies, particularly when developing lines use interspecific hybrids and introgression of genes from wild species. We developed F3:4 recombinant inbred lines from an interspecific cross between Oryza sativa cv. Ilpoombyeo and Oryza rufipogon. In this study, we genetically analyzed known shat­tering-related loci using the F3:4 population of O.

Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection

M. Ipek, Ipek, A., Seker, M., and Gul, M. K., Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection, vol. 14, pp. 2241-2252, 2015.

The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined.

Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya

C. T. Chiu, Wang, C. W., Chen, F. C., Chin, S. W., Liu, C. C., Lee, M. J., Chung, W. C., Chien, Y. W., Chang, H. J., and Lee, C. Y., Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya, vol. 14, pp. 2502-2511, 2015.

The papaya (Carica papaya L.) is one of the most important economic tropical fruits in the world, and the hermaphrodite is the preferred type in field cultures. We analyzed the sexual ratio of offspring from the cultivar ‘Taiwan Seed Station No. 7’ (T7) by a self-cross and its cross with Taichung Sunrise (TS). Female progeny from the T7 self-crossing were not observed. This finding may be caused by a lethal gene that is linked to females. In this study, we selected 192 simple sequence repeats (SSRs) to analyze the polymorphism between T7 and TS.

Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis

Y. J. Ye, Liu, Y., Cai, M., He, D., Shen, J. S., Ju, Y. Q., Bian, X. M., Pan, H. T., and Zhang, Q. X., Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis, vol. 14, pp. 4369-4380, 2015.

Plant height is one of the most important traits of plant architecture as it modulates both economic and ornamental values. Crape myrtle (Lagerstroemia indica L.) is a popular ornamental woody plant because of its long-lasting mid-summer bloom, rich colors, and diversified plant architecture. These traits also make it an ideal model of woody species for genetic analysis of many ornamental traits.

Isolation of microsatellite loci for Rhodiola alsia (Crassulaceae), an important ethno-medicinal herb endemic to the Qinghai-Tibetan plateau

F. Q. Zhang, Lei, S. Y., Gao, Q. B., Khan, G., Xing, R., Yang, H. L., and Chen, S. L., Isolation of microsatellite loci for Rhodiola alsia (Crassulaceae), an important ethno-medicinal herb endemic to the Qinghai-Tibetan plateau, vol. 14. pp. 5266-5269, 2015.

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeqTM 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau.

Assessment of apple core collections constructed using phenotypic and genotypic data

W. H. Yun, Ban, S. H., Kim, G. H., Kim, J. - H., Kwon, S. I., and Choi, C., Assessment of apple core collections constructed using phenotypic and genotypic data, vol. 14, pp. 6453-6464, 2015.

Several types of information can be used to select core collections, including passport data, agronomic data, and molecular data. However, little is known about the ability of core collections to retain the genetic diversity and structure of the whole collection for characters that were not considered during the selection, particularly when molecular markers are used.

Screening and characterization of novel polymorphic microsatellite markers from sea cucumber Holothuria leucospilota

J. B. Shangguan, Li, Z. B., Ning, Y. F., Huang, Y. S., Yuan, Y., Lu, J., Li, B. B., and Mao, X. Q., Screening and characterization of novel polymorphic microsatellite markers from sea cucumber Holothuria leucospilota, vol. 14, pp. 6555-6560, 2015.

The sea cucumber Holothuria leucospilota has high me­dicinal value and rich nutritional edible value, and thus is a commercially important aquatic product in China. Microsatellite loci were developed and screened using a fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. In this study, 16 novel polymorphic microsatellite markers in H. leucospilota were identified, and the relevant genetic variability index was assessed using 30 individu­als from a wild population.

Sequence divergence of microsatellites for phylogeographic assessment of Moroccan Medicago species

N. Zitouna, Marghali, S., Gharbi, M., Haddioui, A., and Trifi-Farah, N., Sequence divergence of microsatellites for phylogeographic assessment of Moroccan Medicago species, vol. 13, pp. 1548-1562, 2014.

Six Medicago species were investigated to characterize and valorize plant genetic resources of pastoral interest in Morocco. Samples were obtained from the core collection of the South Australian Research and Development Institute (SARDI). The transferability of single sequence repeat markers of Medicago truncatula was successful with 97.6% efficiency across the five species.

Limitation of high-resolution melting curve analysis for genotyping simple sequence repeats in sheep

M. Yang, Yue, Y. J., Guo, T. T., Han, J. L., Liu, J. B., Guo, J., Sun, X. P., Feng, R. L., Wu, Y. Y., Wang, C. F., Wang, L. P., and Yang, B. H., Limitation of high-resolution melting curve analysis for genotyping simple sequence repeats in sheep, vol. 13, pp. 2645-2653, 2014.

Variation in microsatellite or simple sequence repeat (SSR) loci has, until recently, relied heavily on the use of gel-based methods that can be both time consuming and difficult to genotype. Non gel-based systems are therefore important to increase simplicity and improve turn-around time without compromising assay sensitivity and accuracy. In this report, we assessed the latest of the non-gel-based methods, high-resolution melting (HRM) curve analysis.

Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species

Y. T. Liu, Chen, R. K., Lin, S. J., Chen, Y. C., Chin, S. W., Chen, F. C., and Lee, C. Y., Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species, vol. 13, pp. 2709-2717, 2014.

The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis.

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