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 F 3 individuals, obtained from the cross between lines L01 (low RER) and L18 (high RER), was phenotyped by measuring RER of 11-d-old seedlings grown in hydroponic culture. Two DNA bulks of 50 F 3 individuals with extremes phenotypes were used for bulk segregant analysis (BSA) by restriction-associated DNA (RAD) sequencing. A total of 20 376 SNP were identified. SNPs were filtered to reduce the number of false positive and mapped on candidate chromosomal regions the B. vulgaris reference genome. A total of SNPs were selected one of which, SNP10139, was strongly linked (P < 0.01) to RER. The pattern of association between 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 the B. vulgaris peptide transporter (PTR) gene, a carrier that influences root elongation in Arabidopsis thaliana. Our results suggest that SNP10139 influences RER in sugar beet and sequence information can be used in markerassisted selection programs.

Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms

“…The NRT/PTR family has been reported to transport nitrate, and many members have been shown to be essential for the development of lateral and primary roots. In a study aiming to identify SNPs linked to the root elongation rate (RER) in sugar beet, the SNP10139 sequence was mapped to the peptide transporter (PTR) gene, a carrier that influences root elongation [ 34 ]. In addition, MdNRT2.1 has a direct role in adventitious root formation and development [ 35 ].…”

“…Twenty-four nonbolting and 15 bolting beets of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq), and the single-nucleotide polymorphism (SNP) markers SNP_36780842 and SNP_48607347 were found to be associated with low bolting tendency by a genome-wide association study (GWAS) [ 12 ]. Two extreme phenotypes were used for bulk segregant analysis by RAD-seq, and the SNP10139 sequence was mapped to the B. vulgaris peptide transporter ( PTR ) gene, a carrier that influences root elongation [ 13 ]. Using pooled whole-genome sequencing (WGS) of the outcrossing sugar beet population EL57 (PI 663,212), which displays rhizoctonia resistance, a series of candidate genes were found to possibly function in plant disease resistance [ 14 ].…”