Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #411379
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: CLIMtools: A web-based suite of tools for exploring genotype by environment (GxE) associations

Author
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item Ware, Doreen
item FERRERO-SERRAO, ANGEL - Pennsylvania State University
item ASSMANN, SARAH - Pennsylvania State University

Submitted to: Acarology International Congress Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: As agriculture faces the challenges of climate change, a key strategy involves finding climate related adaptations locked within the genomes of geographically diverse plants and crops. Gramene collaborators at Penn State University led two studies to identify such variants among genotyped wild Arabidopsis and domesticated rice landraces. An array of over 400 climate descriptors were obtained from satellite data for each variety’s geolocation for genome wide association analyses. The resulting datasets, now accessible at gramene.org/climtools, showcase a wealth of valuable information. In this workshop, we will demonstrate R-shiny apps developed to visualize and explore these datasets. The current tools let users answer questions such as “What are the climate variables associated with a landrace in rice?” and “Are there any environmental variables associated with my arabidopsis gene of interest?” Additionally, we will discuss plans for deeper integration into the Gramene resource. This work has been funded by Penn State and by National Science Foundation PGRP Grant IOS-2122357. Gramene is funded by USDA-ARS 8062-21000-041-00D.