Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus

Abstract

Background: The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon esculentum).

RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

“…The tomato ( Solanum lycopersicum ) cyclophilin DIAGEOTROPICA (DGT) has been linked to auxin-regulated development through identification of the gene affected by the diageotropica ( dgt ) mutation 1 , 2 . Tomato dgt mutants are auxin-resistant and display a pleiotropic phenotype that includes slow gravitropic response, lack of lateral root initiation, altered vascular development, reduced ethylene production in response to auxin, reduced apical dominance, impaired shoot and root growth, reduced fertility, and impaired fruit growth 3 – 11 .…”

Diageotropica and Lateral Rooting, the Rest of the Story

“…However, there is an additional complicating twist that has been all but ignored because of early attempts to discredit an initial hypothesis. The original mutant (diageotropica, dgt or dgt1-1 ) is a single gene point mutation resulting in an amino acid substitution (G 137 changed out) in a protein called a cyclophilin (Oh et al, 2002 , 2006 ). This mutation, though relatively simple, conditions a series of pleiotropic phenes (see Lynch and Brown, 2012 , for a definition of a phene) resulting in a complex phenotype: lack of lateral rooting, diageotropic growth habit of roots, and shoots, folded (curled) leaves and cotyledons, open hypocotyl hook, and modified vascular system (Zobel, 1973 , 1974 ; Madlung et al, 1999 ).…”

“…These conclusions attracted the attention of auxin researchers, especially the Lomax group (Hicks et al, 1989 ; Muday et al, 1995 ; Niebenfuhr et al, 2000 ; Oh et al, 2002 ; and additional), who, initially focused on auxin control of gravitropism. Except for the research of Madlung et al ( 1999 ), none of the research with dgt has investigated the response to low levels of ethylene, but has focused on the apparent specific auxin insensitive nature of the mutant, with a strong effort on the lateral rooting aspect (Ivanchenko et al, 2006 , 2015 ).…”