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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #370635

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: Rice seedling cold stress QTL revealed by genome-wide association mapping and biparental mapping

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

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/3/2019
Publication Date: 12/16/2019
Citation: Eizenga, G.C., Shimoyama, N.S., Jackson, A.K., Edwards, J., Jessel, A.R., Schlappi, M.R. 2019. Rice seedling cold stress QTL revealed by genome-wide association mapping and biparental mapping. Abstract, Plant and Animal Genome Conference XXVIII, San Diego, California, January 11-15, 2020.

Interpretive Summary:

Technical Abstract: Improved seedling cold stress tolerance would allow rice to be planted earlier in the growing season in the USA, thus increasing yield. To identify genes controlling seedling cold tolerance, the USDA Rice Minicore (RMC) and Rice Diversity Panel 1 (RDP1) association mapping panels were phenotyped for cold stress traits designed to mimic the natural environment, including low temperature seeding survivability (LTSS) and electrolyte leakage (EL). Genome-wide association (GWA) mapping was conducted with genotypes derived from 3,200K SNPs for the RMC and 700K SNPs for the RDP1. For RDP1, 40 GWA-QTL were discovered and six Multiple Chilling Phenotype (MP)-QTL, qMP3-1, qMP6-2, qMP9-4, qMP10-1, qMP10-4 and qMP11-2 overlapped with previously reported RMC GWA-QTL. Database searches revealed eleven candidate genes near MP3-1, MP6-2, MP9-4 and MP10-4. To further validate these GWA-QTL, both recombinant (RIL) and backcross (BIL) inbred line mapping populations were developed from three RMC accessions, Krasnodarskij 3352, Wir911 and Carolino 164. The two populations were genotyped with 7K SNPs and phenotyped for LTSS and EL. For the RILs, six LTSS-QTL and one EL-QTL were found on chromosomes 3, 4, 6, 8 and 9. Only qLTSS6 did not have an overlapping GWA-QTL. Four putative candidate genes associated with various stress tolerances, were identified in four of the QTL regions. Only qEL6 was specifically associated with cold stress. For the BILs, three possible QTL, qLTSS1, qLTSS8 and qEL8 were found, but only qLTSS8 was near a GWA-QTL. The next steps will be to validate selected candidate genes and develop markers for breeding.