Identification of genes related to root shape in radish (Raphanus sativus) using suppression subtractive hybridization

Abstract

Radish is an important vegetable, and displays a wide variation in root shape. To understand the mechanisms controlling development and/or inheritance of different root shapes, we attempted to identify the genes expressed differentially in roots of two cultivars with different root shapes; long and thick type (Lt) cv. Taibyousoubutori and skinny type (St) cv. Kosena. Morphological studies revealed that significant differences in thickness of roots began at 4 weeks after sowing. By suppression subtractive hybridization using roots at this stage, 140 and 70 non-redundant ESTs were identified from subtraction of St (tester) × Lt (driver) and reverse subtraction, respectively. Of these ESTs, 102 and 52 showed high similarity to previously identified genes, and the remaining 38 and 18 showed no matches to known genes. Quantitative RT-PCR analysis for selected eleven genes demonstrated that they are differentially expressed in roots of two radish cultivars according to the direction of subtraction. These results will contribute to a better understanding of the mechanisms and inheritance of radish root shape.