Identification of SNP markers linked to Rf locus in carrot using GBS

Abstract

Commercial carrot production is based on the use of hybrid seed varieties worldwide. Cytoplasmic genetic male sterility (CGMS) mechanism has been widely used as the main method for hybrid carrot seed production. There is a significant demand for a rapid method for identification of fertility restorer gene (Rf) carrying individual plants in a carrot breeding population. The objective of this research was to identify SNP markers linked to Rf locus and develop a genetic map of Rf gene in carrot. For this purpose, a carrot F2 population segregating for male sterility was produced and segregating 10,425 SNP markers were discovered by using genotyping by sequencing (GBS). Association mapping analysis demonstrated that Rf was located on chromosome 9 in the carrot genome. A genetic map of chromosome 9 was constructed by using GBS based SNP markers. In order to confirm GBS-generated SNP markers, three markers closely linked to Rf locus were converted to simple probe markers (DcSNP-ch9_3342931, DcSNP-ch9_4822988 and DcSNP-ch9_6233708). Simple probe assay was able to distinguish the individuals of F2 population as homozygous male fertile (RfRf), heterozygous male fertile (Rfrf) and male sterile (rfrf). Simple probe assay confirmed the phenotypic observation in the population and a genetic map of Rf was constructed by using these markers. In conclusion, mapping of Rf in this work would be an efficient tool for future fine mapping and cloning studies of Rf gene in carrot. Thus, this research can help to accelerate the identification of maintainer lines for the development the new hybrid carrot varieties.