Dr Upadhyaya's rice functional genomics project team produced rice insertion mutants as a resource for functional genomics. Several genes have been characterised using the insertion mutants by his group.

In collaboration with CSIRO Mathematical, Informatics and Statistics (CMIS) the team developed a web-based laboratory information management system called the Rice Gene Machine Information Management System (RGMIMS).

In collaboration with researchers at the New South Wales (NSW) Department of Primary Industries and Charles Sturt University, Wagga Wagga, NSW, Australia, Dr Upadhyaya conducted the first transgenic rice field trial in Australia for phenotyping of rice insertion lines and to study the horizontal gene transfer under Australian field conditions.

He has developed extensive international collaborations for mutant resource development and utilisation.

In previous projects he developed the T-DNA double right border vector technology for generating selectable marker-free transgenic plants.

Dr Upadhyaya has pioneered research into cloning and sequencing of Rice Ragged Stunt Oryzavirus (RRSV) genome and in producing RRSV genome based synthetic resistance gene constructs.