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.

Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

“…indica . The japonica varieties are adapted to more temperate climates, whereas most indica varieties are generally adapted to tropical lowland cultivation [2]. The distinction between the two rice subspecies has been recognized in China since at least the Han dynasty [3].…”

Proteomic and transcriptomic approaches to identify resistance and susceptibility related proteins in contrasting rice genotypes infected with fungal pathogen Rhizoctonia solani

“…The expression pattern of majority of these genes at the transcript level showed consistency with the protein expression, confirming their differential expression during R. solani infection. Earlier study in rice showed consistency of genes expression with proteomic analysis (Yang et al, 2014). Few genes did not show the desired consistency with protein expression level which might be due to several regulatory processes of these genes such as mRNA stability, splicing, post-transcriptional gene regulation, translational regulation, and protein degradation, as reported earlier by Liao et al (2013).…”

Comparative analysis of nine different small heat shock protein gene promoters in Oryza sativa L. subsp. indica

“…japonica is mainly found in temperate regions with high latitudes, whereas subsp. indica is mostly cultivated in tropical and subtropical rice planting regions (Yang et al 2014). The fast development of whole genome sequencing technology and the application of bioinformatics have made it possible to explore genetic differentiation between Indica and Japonica rice.…”