Fine mapping and molecular marker development of anthocyanin absent, a seedling morphological marker for the selection of male sterile 10 in tomato

Seedling morphology plays an important role in plant breeding via marker-assisted selection. The tomato ( Solanum lycopersicum ) mutant, anthocyanin absent ( aa ), presents a green hypocotyl during the seedling stage. This trait has been utilized in marker-assisted selection of male sterile 10 ( ms 10 ) at the seedling stage because their corresponding loci are closely linked on chromosome 2. However, the genetic basis of aa has not been ascertained to date. In the present study, aa was fine-mapped to a 96.3-kb region on chromosome 2 that contained 14 putative genes. Thereinto, Solyc02g081340 , which encodes a putative glutathione S-transferase, was thereby designated SlGSTAA . Phylogenetic analysis suggested that SlGSTAA was closely related to PhAN9, which is required for anthocyanin sequestration in petunia ( Petunia hybrida ). Real-time quantitative reverse transcription PCR analysis showed that the expression of the SlGSTAA gene was barely detected in aa mutants. Sequencing revealed that there was a 3.4-kb deletion in the aa region, where the SlGSTAA gene was apparently deleted. A codominant insertion/deletion marker was developed in line with the deletion to differentiate homozygous wild-type, heterozygous, and homozygous aa mutant genotypes. The findings of the present study may facilitate the functional analysis of the SlGSTAA gene and marker-assisted selection of aa and ms 10 in tomato.