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Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data

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Abstract:

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 (x ¯ = 7.36) and PIC values ranged from 0.34 to 0.86 (x ¯ = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 (x ¯ = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (p < 0.001) r 2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.

Keywords: DArT; SSR; barley; coefficient de parenté; distance génétique; déséquilibre de liaison (LD); genetic distance; kinship coefficient; linkage disequilibrium (LD); orge

Document Type: Research Article

DOI: https://doi.org/10.1139/gen-2013-0048

Affiliations: 1: Département de Phytologie, Université Laval, 1243 Marchand Building, Québec, QC G1K 7P4, Canada. 2: Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.

Publication date: 2013-01-01

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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