Single nucleotide polymorphism markers linked to root elongation rate in sugar beet

Abstract

The aim of this study was to identify single nucleotide polymorphism (SNP) markers genetically linked to root elongation rate (RER) in sugar beet (Beta vulgaris L.). A population of 244 F3 individuals, obtained from the cross between lines L01 (a low RER) and L18 (a high RER), was phenotyped by measuring RER of 11-d-old seedlings grown in a hydroponic culture. Two DNA bulks of 50 F3 individuals with extreme phenotypes were used for bulk segregant analysis by restriction-associated DNA sequencing. A total of 20 376 SNPs were identified. Single nucleotide polymorphisms were filtered to reduce the number of the false positive and mapped on candidate chromosomal regions of the B. vulgaris reference genome. One of the total of SNPs selected, SNP10139, was strongly linked to RER (P < 0.01). The pattern of association between the SNP10139 genotype and RER was also evaluated on a breeding line panel comprising 40 low and 40 high RER individuals with different allele frequencies between groups (P < 0.01). The SNP10139 sequence was mapped on the B. vulgaris peptide transporter (PTR) gene, a carrier that influences root elongation in Arabidopsis thaliana. Our results suggest that SNP10139 influence RER in sugar beet, and sequence information can be used in marker-assisted selection programs.

Keywords

• abiotic stresses
• beta vulgaris
• bulk segregant analysis
• restriction-associated dna sequencing