Genetic distance

Relationship between progeny growth performance and molecular marker-based genetic distances in Eucommia ulmoides parental genotypes

Y. Li, Wei, Y. C., Li, Z. Q., Wang, S. H., and Chang, L., “Relationship between progeny growth performance and molecular marker-based genetic distances in Eucommia ulmoides parental genotypes”, vol. 13, pp. 4736-4746, 2014.

Progeny performances, variations and combining abilities for growth traits were evaluated in a factorial mating design of Eucommia ulmoides. Three marker systems, sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat, were used to determine genetic distances between parents. Correlations of genetic distances with progeny performances, within-family coefficients of variation and specific-combining abilities were established for height and basal diameter traits.

Genetic distances and phylogenetic trees of different Awassi sheep populations based on DNA sequencing

R. M. Al-Atiyat and Aljumaah, R. S., “Genetic distances and phylogenetic trees of different Awassi sheep populations based on DNA sequencing”, vol. 13, pp. 6557-6568, 2014.

This study aimed to estimate evolutionary distances and to reconstruct phylogeny trees between different Awassi sheep populations. Thirty-two sheep individuals from three different geographical areas of Jordan and the Kingdom of Saudi Arabia (KSA) were randomly sampled. DNA was extracted from the tissue samples and sequenced using the T7 promoter universal primer. Different phylogenetic trees were reconstructed from 0.64-kb DNA sequences using the MEGA software with the best general time reverse distance model. Three methods of distance estimation were then used.

Genetic and biochemical differentiation in Vitis vinifera (Kabarcik) populations grown at different altitudes in Coruh Valley

G. Agar, Yildirim, N., and Ercisli, S., “Genetic and biochemical differentiation in Vitis vinifera (Kabarcik) populations grown at different altitudes in Coruh Valley”, vol. 11, pp. 211-220, 2012.

We examined genetic differences of four Vitis vinifera populations (A, B, C, D) including local Kabarcik cultivar grown along an altitude gradient of 800, 900, 1000, and 1150 m above sea level in the Coruh Valley (800 m: A population; 900 m: B population; 1000 m: C population; 1150 m: D population). Leaf samples were used for both RAPD and fatty acid analysis. A total of 60 individuals with 15 individuals per population were included in this study. RAPD analyses showed various band sizes, which ranged from 250 to 3000 bp.

Analysis of genetic distance by SSR in waxy maize

R. H. Yu, Wang, Y. L., Sun, Y., and Liu, B., “Analysis of genetic distance by SSR in waxy maize”, vol. 11, pp. 254-260, 2012.

We examined the genetic diversity of 80 inbred waxy maize lines using 22 SSR molecular markers that could be used to achieve heterosis in waxy maize. Eighty inbred waxy maize lines with different phenotypes, 40 yellow, 25 white, 13 black, and two red lines were analyzed by SSR molecular marker fingerprint and cluster analysis. Using a standard genetic distance of 0.55, the 80 waxy maize inbred lines were clustered into nine groups.

Significance of linkage disequilibrium heterogeneous patterns in the 21q22.3 region for mapping 21 trisomy individuals

Y. Valle, Padilla-Gutiérrez, J. R., Quintero-Ramos, A., García-González, I. J., and Rivas, F., “Significance of linkage disequilibrium heterogeneous patterns in the 21q22.3 region for mapping 21 trisomy individuals”, vol. 12. pp. 2821-2828, 2013.

Recombination patterns can be indirectly inferred by means of linkage disequilibrium (LD) estimates, since LD is negatively correlated with genetic distance. However, LD does not necessarily have absolute correspondence with genetic distance. We estimated LD at 5 loci located in the 21q22.3 region. These STRs (D21S1440, D21S168, D21S1260, D21S1446, and D21S1411) covered 8.81 Mb of the 21q22.3 region. They were genotyped by conventional PCR. Similar size samples previously validated by sequencing were used as a genotyping control.

DNA profiling of sugarcane genotypes using randomly amplified polymorphic DNA

S. Tabasum, Khan, F. A., Nawaz, S., Iqbal, M. Z., and Saeed, A., “DNA profiling of sugarcane genotypes using randomly amplified polymorphic DNA”, vol. 9, pp. 471-483, 2010.

DNA profiles of 40 sugarcane genotypes were constructed with 30 RAPD markers. Sugarcane genotypes of both Saccharum officinarum and S. barberi were included in this study. Multiple alleles were detected from each RAPD; there was a high level of polymorphism. On average, 7.93 alleles were produced per primer, giving a total of 238 alleles. The genetic distances between these genotypes were assessed with the POPGENE DNA sequence analysis software. A dendrogram was constructed from these data; cultivated species of sugarcane formed clusters with S.

Genetic studies of “noble cane” for identification and exploitation of genetic markers

S. Nawaz, Khan, F. A., Tabasum, S., Iqbal, M. Z., and Saeed, A., “Genetic studies of “noble cane” for identification and exploitation of genetic markers”, vol. 9, pp. 1011-1022, 2010.

Forty genotypes (clones) of sugarcane, including elite lines, commercial cultivars of Saccharum officinarum and clones of S. barberi were fingerprinted with 50 SSR markers using a PCR-based marker assay. Nei’s genetic distances for SSR data were determined and relationships between accessions were portrayed graphically in the form of a dendrogram. Genetic distance values ranging from 0.60 to 1.11 were observed among the 40 sugarcane accessions. The shortest genetic distance of 0.60 was seen between genotypes US-804 and US-130.

Phylogenetic relationships among Saccharum clones in Pakistan revealed by RAPD markers

S. Nawaz, Khan, F. A., Tabasum, S., Zakria, M., Saeed, A., and Iqbal, M. Z., “Phylogenetic relationships among Saccharum clones in Pakistan revealed by RAPD markers”, vol. 9, pp. 1673-1682, 2010.

Forty sugarcane genotypes (clones), including elite lines, commercial cultivars of Saccharum officinarum and S. barberi clones, were fingerprinted with 30 RAPD markers, using a PCR-based marker assay. The genetic distance for RAPD data was determined according to Nei, and relationships between accessions were graphed in a dendrogram. Genetic distance values ranging from 16.2 to 86.3% were observed among the 40 sugarcane accessions. The lowest genetic distance was found between genotypes US-406 and US-186.

Estimation of genetic distance based on RAPDs between 11 cotton accessions varying in heat tolerance

A. I. Khan, Khan, I. A., Awan, F. S., Sadaqat, H. A., and Bahadur, S., “Estimation of genetic distance based on RAPDs between 11 cotton accessions varying in heat tolerance”, vol. 10, pp. 96-101, 2011.

The genetic distance of 11 cotton genotypes varying in heat tolerance was studied using RAPD markers. Fifty-three random decamer primers were used for the estimation of genetic distance. Among the 53 RAPD primers, which were custom synthesized by GeneLink Inc., UK, 32 were polymorphic and 21 were monomorphic. The 32 polymorphic primers produced 273 fragments, with a mean of 8.3 fragments per primer. The number of polymorphic bands produced in the 11 cotton accessions ranged from 1 to 31.

Molecular characterization and RAPD analysis of Juniperus species from Iran

J. Kasaian, Behravan, J., Hassany, M., Emami, S. A., Shahriari, F., and Khayyat, M. H., “Molecular characterization and RAPD analysis of Juniperus species from Iran”, vol. 10, pp. 1069-1074, 2011.

The genus Juniperus L. (Cupressaceae), an aromatic evergreen plant, consists of up to 68 species around the world. We classified five species of Juniperus found in Iran using molecular markers to provide a means for molecular identification of Iranian species. Plants were collected (three samples of each species) from two different provinces of Iran (Golestan and East Azarbayejan). The DNA was extracted from the leaves using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using 18 ten-mer RAPD primers.

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