Quantitative analysis of allelic differences in the grain proteome between the Wx g2 and Wx g3 alleles in rice ( Oryza sativa L.)

The Wx gene is the major gene controlling amylose synthesis in rice endosperm. In a previous study, we were able to separate the Wx a allele into two functional Wx alleles, Wx g2 and Wx g3 , according to their amylose phenotypes and a T/C nucleotide polymorphism in exon 10. Subsequent studies revealed that this Wx allelic variation also plays a vital role in regulating other important starch properties. However, the underlying molecular mechanisms related to the rice grain proteome have remained unclear. To elucidate this, we used two rice single-segment substitution lines harboring different Wx alleles, Wx g2 and Wx g3 , in comparative proteomic studies. On the basis of iTRAQ quantitative proteomics, we identified a total of 185 proteins as differentially accumulated between the Wx g2 and Wx g3 lines. Gene Ontology functional analysis revealed that a high proportion of differentially expressed proteins (DEPs) are involved in metabolic and cellular biological processes. Further functional and pathway enrichment analyses indicated that relevant functions of the DEPs on protein degradation and binding may play important roles in distinguishing the Wx g2 and Wx g3 alleles. The present results may provide comprehensive insights into the molecular regulatory mechanisms of starch biosynthesis as influenced by the Wx g2 and Wx g3 alleles in rice.