Molecular tagging and candidate gene analysis of the high gamma-tocopherol trait in safflower (Carthamus tinctorius L.)

Genetic control of the synthesis of high gamma-tocopherol (gamma-T) content in the seed oil of safflower (Carthamus tinctorius L.) and development of highly reliable molecular markers for this trait were determined through molecular tagging and candidate gene approaches. An F2 population was developed by crossing the high gamma-T natural mutant IASC-1 with the CL-1 line (standard, high alpha-T profile). This population segregated for the partially recessive gene Tph2. Bulked segregant analysis with random amplified polymorphic DNA (RAPD) and microsatellite (SSR) markers revealed linkage of eight RAPD and one SSR marker loci to the Tph2 gene and allowed the construction of a Tph2 linkage map. RAPD fragments closest to the Tph2 gene were transformed into sequence-characterized amplified region markers. A gamma-T methyltransferase (gamma-TMT) locus was found to co-segregate with Tph2. The locus/band was isolated, cloned and sequenced and it was confirmed as a gamma-TMT gene. A longer partial genomic DNA sequence from this gene was obtained. IASC-1 and CL-1 sequence alignment showed one non-synonymous and two synonymous nucleotide mutations. Intron fragment length polymorphism and insertion-deletion markers based on the gamma-TMT sequence diagnostic for the Tph2 mutation were developed and tested across 22 safflower accessions, cultivars, and breeding lines. The results from this study provide strong support for the role of the gamma-TMT gene in determining high gamma-T content in safflower and will assist introgression of thp2 alleles into elite safflower lines to develop varieties with improved tocopherol composition for specific market niches.