Identification of candidate genes contributing to grain filling in rice through genomic neighborhood mining

Abstract

Grain filling is an important process that determines grain yield in rice. Genes associated with grain filling primarily belong to carbohydrate metabolism like sucrose biosynthesis and transport as well as starch biosynthesis and storage. The knowledge on the network and interplay of proteins in regulating various pathways associated with grain filling is still sparce. In this study we have surveyed the genomic neighbourhood of grain filling associated genes viz. Alpha-amylase, Starch synthase, Sucrose phosphate synthase, Glucose transporter, Sucrose transporter, Triose phosphate translocator and identified several genes coding for transcription factors, enzymes and other proteins. The identified neighbourhood genes constitute a prudent set of candidate genes for functional validation to establish their direct or indirect involvement in grain filling related pathways. A subset of the identified neighbourhood genes is expected to co-express with the known grain filling related genes. It was found that stress tolerance genes were present in the neighbourhoods of all the grain filling related enzymes selected for this study implicating their involvement in stress tolerance during reproductive phase