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Table 2 Sequence variations in brt-2 compared to other tomato species in the 1.9 Mbp mapping region

From: Missense mutation of a class B heat shock factor is responsible for the tomato bushy root-2 phenotype

Position in SL2.50

SNP/InDel

region

gene

AA change

unique variation

KASP marker

linkage to brt-2

62,760,651

G/A

intergenic

n/a

n/a

yes

yes

90%

62,869,990

G/A

intron

Solyc04g078000

n/a

no

no

n/a

63,083,160

G/GC

intergenic

n/a

n/a

no

no

n/a

63,443,492

A/T

exon

Solyc04g078770

Ser to Cys

yes

yes

100%

63,565,771

G/T

intergenic

n/a

n/a

no

yes

99%

64,082,367

T/A

intergenic

n/a

n/a

no

no

n/a

64,309,622

T/A

intron

Solyc04g080010

n/a

no

no

n/a

64,313,709

T/−

promoter

Solyc04g080020

n/a

no

no

n/a

64,381,246

G/T

exon

Solyc04g080120

Pro to His

no

no

n/a

64,623,394

A/G

intergenic

n/a

n/a

no

yes

84%

  1. Unique variants are not present in the re-sequenced lines of SGN database. KASP marker accessibility and the linkage to the brt-2 phenotype are marked. The proposed causative gene for brt-2 is in bold