Czech Journal of Genetics and Plant Breeding - In Press
Assessment of the genetic diversity and population structure of almond germplasm in Van Province, Türkiye, using iPBS-retrotransposon-based markersOriginal Paper
Berna Sarman, Metin Koçak
The genetic characterisation of naturally grown almond genotypes can guide the selection of genetic resources to be used in the breeding program. Therefore, this study aims to assess the genetic diversity and population structure of almond germplasm comprising 50 accessions growing naturally in Van, Türkiye, and two commercial varieties (Pabuç and Dokuzoğuz). Thirteen inter-primer binding site (iPBS) retrotransposon markers produced a total of 102 bands, of which 95 were polymorphic. The average polymorphic band number per marker was 7.3, with a range of 5 to 13. A formula yielding a maximum of 0.5 resulted in polymorphic information content (PIC) values between 0.27 and 0.43, with a mean value of 0.36. Unweighted Pair Group Method Algorithm (UPGMA), Principal Coordinate Analysis (PCoA), and STRUCTURE analysis, based on Bayesian clustering analysis, yielded consistent results, indicating that local populations (Akdamar and Çarpanak) were distinctly grouped, while commercial accessions were classified alongside Çarpanak accessions. The diversity metrics and classification analysis utilising 13 iPBS-retrotransposon markers demonstrated that the iPBS-retrotransposon marker system possesses significant promise for evaluating the genetic variety and population structure of almonds.
Genetic diversity assessment of hydrocyanic acid, total carotenoid content, and dry matter content in biofortified cassava using trait-linked SNP markersOriginal Paper
Bismark Anokye, Peter Amoah, Bardee Wrojay Potter, Abdoul-Razak Oumarou Mahamane, Theophilus Adu-Gyamfi, Leviticus Dembure, Nezif Abajebal Abadura, Bunmi Olasanmi, Elizabeth Parkes
Assessment of genetic diversity is essential for identifying useful alleles for crop improvement. This study evaluated genetic diversity among two cassava breeding populations for total carotenoid content (TCC), dry matter content (DMC), and hydrogen cyanide (HCN) concentration using trait-linked single nucleotide polymorphism (SNP) markers. A total of 360 genotypes were analysed, including 261 from the IITA breeding program (Population 1), 23 progenitor lines, and 76 from the University of Ibadan Cassava (UIC) breeding program (Population 2). Minor allele frequency (MAF), gene diversity (GD), observed heterozygosity (He), and polymorphic information content (PIC) were computed. Principal component analysis (PCA) and hierarchical clustering were performed to examine genetic variation and population structure. Call rates were high (96–100%). MAF ranged from 0.00 to 0.50, with mean values of 0.28, 0.28, and 0.29 for Population 1, Population 2, and progenitors, respectively. GD averaged 0.36, 0.36, and 0.35 across the same groups. Observed heterozygosity was 0.42, 0.41, and 0.43, while PIC values averaged 0.29, 0.27, and 0.27 for Population 1, Population 2, and progenitors, respectively. PCA and clustering analyses grouped the genotypes into three clusters containing 257, 88, and 15 genotypes. The first two principal components explained 39.1% of the total genetic variation. The results indicate substantial genetic diversity among the studied genotypes, suggesting strong potential for allele pyramiding and demonstrating the informativeness of the SNP markers employed.