engleski

SNP genotyping of croatian common bean landraces

Common bean (Phaseolus vulgaris L.) is economically the most important among five domesticated species from genus Phaseolus. In Croatia, common bean is a traditionally grown in low input production systems. The production is based on landraces displaying high levels of diversity. In order to assess the genetic diversity of Croatian common bean landraces, 174 accessions were analysed using a DArTseq method of SNP genotyping. Out of 17, 514 polymorphic markers, 8, 092 (46%) had high scoring reproducibility (>0.95), high call-rate (>0.90) and the minor-allele frequency higher than 5%. Genomic regions flanking SNPs were than aligned against the reference genome of P. vulgaris. From the 8, 092 SNP sequences, 6, 599 (82%) were aligned to 11 chromosomes of common bean. The average number of SNPs per chromosome was 599.91, ranging from 403 on chromosome 4 to 834 on chromosome 2. Mean number of SNPs per Mbp was 12.85 or on average one SNP every 77, 828 base pairs. The average expected heterozyogsity was 0.373, ranging from 0.096 to 0.500 while the polymorphism information content ranged from 0.091 to 0.373 with an average of 0.298. The model-based analysis of population structure was carried out using 923 SNPs in linkage equilibrium. The results were compared to those obtained by microsatellite markers. The SNP set will be used in genome- wide association studies (GWAS) concerning bioactive nutrient content.

DArTseq, Phaseolus vulgaris, SNP

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