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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #367377
Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: The genetic basis of cold stress tolerance in rice at the seedling stage identified in two independent high resolution genome-wide association mapping studies

Author
item Eizenga, Georgia
item SHIMOYAMA, NAOKI - Marquette University
item Jackson, Aaron
item Edwards, Jeremy
item SCHLAPPI, MICHAEL - Marquette University

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 8/29/2019
Publication Date: 8/30/2019
Citation: Eizenga, G.C., Shimoyama, N., Jackson, A.K., Edwards, J., Schlappi, M.R. 2019. The genetic basis of cold stress tolerance in rice at the seedling stage identified in two independent high resolution genome-wide association mapping studies. Abstract, ASA-CSSA-SSSA Annual Meeting, San Antonio, Texas, November 10-13, 2019.

Interpretive Summary:

Technical Abstract: Improved cold stress tolerance at the early growth stages is necessary when rice (Oryza sativa L.) is grown in temperate climates or at high altitudes. To identify new sources of cold tolerance and the potential underlying candidate genes, 173 diverse accessions from the USDA Rice Minicore (RMC) collection were evaluated for five traits designed to mimic cold stress at the early growth stages and about 400 accessions from the Rice Diversity Panel 1 (RDP1) were evaluated for low temperature seeding survival (LTSS) and electrolyte leakage (EL). RMC genome-wide association (GWA) mapping was conducted using genotypes based on 3.2 million SNPs, and RDP1 GWA mapping was conducted with genotypes based on 700,000 SNPs. Comparing the GWA-QTL from these studies, peak SNPs of 17 RMC GWA-QTL were near RDP1 GWA-QTL peak SNPs. The closest GWA-QTL peak SNPs were located on chromosome (chr.) 3 (21.06-22.47 Mb), chr. 9 (15.29-15.75 Mb) and chr. 10 (14.97-18.27 Mb). Database searches revealed three candidate genes for cold stress tolerance near the chr. 3 RMC peak SNP, four genes near the chr. 9 RMC peak SNP, and five genes near the three chr. 10 RMC peak SNPs. Currently, two biparental recombinant inbred line (RIL) populations developed from three RMC accessions, are being evaluated for LTSS and EL. Once the QTL mapping is complete, peak RIL-QTL SNPs near peak GWA-QTL SNPs will further validate the GWA peak SNPs and underlying gene(s). Ultimately, SNPs will be selected for marker development and utilization in marker assisted selection.