Comparative proteomic analysis of indica and japonica rice varieties

Abstract

Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93-11 and Nipponbare). In all, 47 proteins that differed significantly between 93-11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93-11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.

Keywords: indica and japonica rice; molecular marker; proteomics; quantitative real-time PCR; unique proteins.

Figure 1

The proteomic profiles of Nipponbare and 93-11. The protein spots 1 to 47 were identified by MS and database searches. The upward and downward pointing arrows indicate up-regulated and down-regulated proteins in 93-11, respectively. Protein spots unique in this 2-D gel are identified with a plus symbol (+). NPB – Nipponbare.

Figure 2

The unique protein spots in Nipponbare and 93-11. NPB – Nipponbare.

Figure 3

Functional classifications of the identified proteins (Bevan et al., 1998).

Figure 4

Gene ontology (GO) categories of the identified differentially expressed proteins in 93-11 and Nipponbare. These proteins were divided into three main categories and 21 subcategories (Ye et al., 2006).

Figure 5

Relative expression levels of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, L-ascorbate peroxidase 1, chlorophyll A-B binding protein and harpin binding protein 1 in 93-11 and Nipponbare. The X-axis shows the protein spot number and the Y-axis shows the relative expression level of each protein.

Figure 6

Enlarged views of the unique proteins (spots 8, 13, 37, 39 and 42) in indica and japonica rice varieties. Indica rice varieties: 93-11, NJ11 – Nanjing 11, MH63 – Minghui 63. Japonica rice varieties: NPB – Nipponbare, WYJ3 – Wuyujing 3 and WYJ7 – Wuyunjing 7.