Genetic mapping of tomato mutants using InDel markers between S. pimpinellifolium and two S. lycopersicum cultivars

Abstract

Genetic mapping is essential for identifying mutations linked to phenotype in crops. Recent approaches combining marker-based rough mapping and mapping-by-sequencing have proven cost-effective for accelerating mutation identification in forward genetics. In this study, we identified genome-wide insertion–deletion (InDel) variations by comparing whole-genome re-sequencing data of S. pimpinellifolium with S. lycopersicum cultivars, Heinz and M82, as well as Micro-Tom. Compared to the 60 InDel marker between S. pimpinellifolium and Heinz, Heinz inherited 46 InDels with cultivar M82 (76.67%) and 48 InDels with Micro-Tom (80%), which we successfully validated by PCR, and at least two InDel markers were identified on each chromosome. Using these markers for rough mapping, we located and mapped lazy mutant to an interval on chromosome 5 from 5 to 61 Mb in M82. The wiry leaf mutant was mapped to chromosome 1, revealing a mutation causing a premature stop codon in the AGO7 in Micro-Tom. These InDel markers offer a simple tool for marker-based rough mapping and can be applied in molecular breeding for trait mapping in tomato cultivars.