SNP Alleles Associated With Low Bolting Tendency in Sugar Beet

Abstract

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

“…As far as HRM is concerning, primer3 software version 4.0.0 (Whitehead Institute for Biomedical Research, Cambridge, MA; http://primer3.ut.ee ) was adopted to design primers. The HRM analyses were performed in 384 well plates on the QuantStudio 12 K Flex (Life Technologies, USA), following the procedure described by [ 93 ], whereas the rhAmp allelic discrimination assay was carried out following the procedure described by Broccanello et al [ 94 ] and Ravi et al [ 93 ]. Sequences of rhAmp assays are available upon request.…”

Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia solani AG-2-2-IIIB Resistance in Sugar Beet

“…Variant calling was performed individually on the two datasets from SBSI and Strube Research and adapted from the earlier published method [ 35 ]. The pipeline uses fastqc (version 0.11.5) for quality check of reads, bowtie2 (version 2.3.5.1) for mapping reads to the reference, samtools (version 1.9), Picard-tools (version 2.18.12), samtools (version 1.9) mpileup, and bcftools (version 1.9) to extract variants.…”

“…The HRM analyses were carried out in 384 well plates on the QuantStudio 12K Flex (Life Technologies, Carlsbad, CA, USA). Reactions were carried out according to a previously described method [ 35 ]. The melt curve profiles were analyzed using the HRM software.…”

“…The list of sequences was given as input to the stand-alone version of the Primer3 software (version 4.0) to design primers with suitable amplicon lengths. The reaction setup and PCR cycling conditions were adopted from an earlier study from our lab [ 35 ]. The amplicons were run on a 1.5% agarose gel to verify the amplification.…”

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

“…By using a modified method of mapping-by-sequencing (MBS), Capistrano-Gossmann et al identified the sugar beet resistance gene Rz2 in a crop wild relative (CWR) population of < 200 wild beets [ 11 ]. 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 ].…”