NSF NPGI Postdoctoral Fellowship in Biology FY 2012

Meyer Rachel S, New York NY

Investigators

Abstract

This action funds a National Plant Genome Initiative Postdoctoral Research Fellowship for FY 2012. The fellowship supports a research and training plan in a host laboratory for the Fellow to focus their studies in plant genomics with an emphasis on quantitative genetics, modern breeding approaches, and bioinformatics. The title of the research and training plan for this fellowship to Rachel S. Meyer is "Selection for Salt Tolerance in African Rice (Oryza Glaberrima) in Indigenous Riverine Agricultural Habitats of Western Africa". The host institution for the fellowship is New York University and the sponsoring scientist is Dr. Michael Purugganan. One major factor limiting worldwide crop production is high salinity, which affects 50% of global irrigated land area. Farmers in the Atlantic Coast region stretching from Senegal to Liberia plant indigenous crops that are tolerant to saline conditions. This project focuses on one such crop that is a major staple: African rice (Oryza glaberrima Steud.). O. glaberrima is irrigated by rivers with a conspicuous salinity gradient. Thus, the agricultural system developed for O. glaberrima implies that varieties have been arranged with matched fitness to local saline levels. However, farmers also practice agriculture in unique ways including dyking of mangrove swamps, soil overturning, and sometimes desalination, which spurs several critical questions. How has the O. glaberrima genome been modified to tolerate salinity? To what extent do specific agricultural practices play a role in the ability of O. glaberrima to be cultivated in saline environments? Is it geographic characteristics or cultural practices that guide selection for this crop? To address these questions, the genomes of 100 germplasm accessions from three agricultural river systems will be surveyed in order to build a SNP map for O. glaberrima and identify DNA regions that distinguish germplasm from saline coastal versus freshwater inland environments. Interviews will be conducted to gather information about land conditions, farming techniques, and community roles in seed trading along these rivers. DNA sequence data will be correlated with the salinity at collection locales, culturally specific agricultural practices, and salt injury tests. Results will connect aspects of human innovation to agroecology and selective crop breeding, while specifically addressing challenges faced by a need to practice agriculture on areas of high salinity. Training objectives include data management of entire genomes and population analyses, in-depth agroecological analysis, and cross-training between NYU and international institutions. Broader impacts include include capacity-building and advanced training for students from the United States to engage in interdisciplinary research in plant improvement and associated sciences such as physiology, quantitative genetics, and computational biology. Outreach activities include training workshops in West Africa and other countries to enhance utility of genome sequence generated and use of agroecological data to design tools to help farmers, and K-12 DNA barcoding mentoring.