cluster analysis

Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species

Y. Yang, Jing, Z. B., Ruan, X. F., and Cheng, J. M., “Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species”, vol. 14, pp. 609-618, 2015.

Persimmon (Diospyros L.) is an economically important fruit in the world, and it has been recognized as a healthy nutrient supply for human consumption. In this study, 14 microsatellite markers were developed from an AG/TC and AC/TG-enriched genomic library of Chinese persimmon Mopanshi. Twelve polymorphic markers were selected in 4 related species; these markers showed transferability to the 4 related persimmon species. In addition, 10 simple sequence repeat (SSR) markers were used to detect the genetic diversity among 51 persimmon accessions from China, Japan, and Korea.

Assessment of the genetic diversity of tomato yellow leaf curl virus

H. J. Wan, Yuan, W., Wang, R. Q., Ye, Q. J., Ruan, M. Y., Li, Z. M., Zhou, G. Z., Yao, Z. P., and Yang, Y. J., “Assessment of the genetic diversity of tomato yellow leaf curl virus”, vol. 14, pp. 529-537, 2015.

The objective of the present study was to analyze the genetic diversity of tomato yellow leaf curl virus (TYLCV). Representative TYLCV sequences were searched in the National Center for Biotechnology Information database. Comprehensive analysis of TYLCV was performed using bioinformatics by examining gene structure, sequence alignments, phylogeny, GC content, and homology. Forty-eight representative TYLCV sequences were selected from 48 regions in 29 countries.

Analysis of synonymous codon usage in FAD7 genes from different plant species

Q. P. Ma, Li, C., Wang, J., Wang, Y., and Ding, Z. T., “Analysis of synonymous codon usage in FAD7 genes from different plant species”, vol. 14, pp. 1414-1422, 2015.

In this study, the codon bias of the FAD7 genes among 10 different plant species was analyzed to identify general patterns of codon usage in the FAD7 genes. Our results showed that U-ended or A-ended codons were preferentially used in FAD7 for dicots, whereas G-ended or C-ended codons were preferentially used in FAD7 for monocots. An ENC-plot showed that some other factors may influence the codon usage of FAD7, except mutation bias in plant species.

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.

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.

Genotype by environment interaction for post-weaning weight gain, scrotal circumference, and muscling score of composite beef cattle in different regions of Brazil

M. L. Santana, Jr., Eler, J. P., Cardoso, F. F., Albuquerque, L. G., Balieiro, J. C. C., Pereira, R. J., and Ferraz, J. B. S., “Genotype by environment interaction for post-weaning weight gain, scrotal circumference, and muscling score of composite beef cattle in different regions of Brazil”, vol. 13, pp. 3048-3059, 2014.

The objectives of this study were to characterize and define homogenous production environments of composite beef cattle in Brazil in terms of climatic and geographic variables by using multivariate exploratory techniques; to evaluate the presence of genotype by environment interaction (GxE) for post-weaning weight gain (PWG), yearling scrotal circumference (SC), and yearling muscling (MUS). Hierarchical and nonhierarchical cluster analysis was used to group farms located in regions with similar environmental variables into clusters. Six clusters of farms were formed.

Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers

X. Y. Liang, Zhang, X. Q., Bai, S. Q., Huang, L. K., Luo, X. M., Ji, Y., and Jiang, L. F., “Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers”, vol. 13, pp. 7736-7746, 2014.

Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701).

Correlation of genetic variation among wild Trigonella foenum-graecum L. accessions with their antioxidant potential status

E. A. Haliem and Al-Huqail, A. A., “Correlation of genetic variation among wild Trigonella foenum-graecum L. accessions with their antioxidant potential status”, vol. 13, pp. 10464-10481, 2014.

In this study, we analyzed the correlation between genetic variation based on random amplified polymorphic DNA (RAPD), acid phosphatase, and glutamate-oxaloacetate transaminase isozymes, and amino acid composition with the antioxidant potential status of 7 wild Trigonella foenum-graecum L. accessions collected from diverse ecogeographical regions. RAPD revealed that 90 DNA products had highly polymorphism value (94.12%) based on band numbers, with sizes ranging from 50-2100 base pairs, and band intensity.

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.

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.

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