The rankings, assessed by the private company Academic Analytics, are based on measurements of faculty productivity in terms of publications, federal-grant dollars awarded, and honors and awards.
Data from the 2005 rankings -- which are not without their share of controversy -- were published and explained in depth in The Chronicle of Higher Education (available by subscription here).
UC Berkeley doctoral programs from within CNR received impressive rankings:
Agricultural economics - 3
Botany and plant biology - 1
Microbiology - 3
Nutrition - 3
Toxicology - 2
Environmental Science - 4
A full list of UC Berkeley rankings is here.