Analysis of Genetic Diversity in Barley Cultivars Reveals Incongruence Between S-SAP,SNP and Pedigree Data |
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Authors: | V. D. Soleimani B. R. Baum D. A. Johnson |
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Affiliation: | (1) Agriculture and Agri-Food Canada, K. W. Neatby Building, 960 Carling Avenue, K1A 0C6 Ottawa, Ont., Canada;(2) Ottawa-Carleton Institute of Biology, University of Ottawa, 150 Louis Pasteur, P.O. Box 450, Station A, K1N 6N5 Ottawa, Ont., Canada |
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Abstract: | Accurate assessment of genetic similarity is important for plant breeding, germplasm enhancement and conservation of plant genetic resources. A comparative analysis of genome diversity among a group of six-rowed spring barley (Hordeum vulgare L.) cultivars was carried out using sequence-specific amplified polymorphism (S-SAP) and single nucleotide polymorphism (SNP), with the results compared to the kinship coefficients derived from the pedigree data. Mean pair-wise GS values were estimated to be 0.0957 ± 0.144 (Kinship), 0.491 ± 0.189 (SNPs), and 0.602 ± 0.098 (S-SAPs). S-SAP and SNP-based genetic similarity (GS) values were normally distributed but kinship values had a non-normal and skewed distribution. Pair-wise correlation of GS values were lowest for the S-SAP and the SNP matrices (r =; 0.040, p<0.230) and highest for the SNP and pedigree matrices (r =; 0.240, p < 0.001). Analysis of molecular variance (AMOVA) attributed about 90.4% of observed variation to the cultivars within each of the malting and feed groups. Variance component between malting and feed groups was 6.6% for both SNP and S-SAP data suggesting lack of a significant genetic differentiation along this agronomic division. The remaining 3% of variation was attributed to genetic diversity within cultivars. Although both DNA-based marker systems were able to differentiate all barley cultivars, significant difference were observed in the pattern of genetic relationships obtained by the two marker systems and the pedigree data. |
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Keywords: | Barley Genetic similarity Genome evolution Hordeum vulgare Kinship coefficient SNP S-SAP |
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