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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #389663
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: Evaluation of seedling cold stress in the Krasnodarskij 3352 x Carolino 164 Recombinant Inbred Line population

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

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 11/12/2021
Publication Date: 11/12/2021
Citation: Eizenga, G.C., Shimoyama, N.S., Jia, M.H., Jackson, A.K., Edwards, J., Jessel, A.D., Schlappi, M.R. 2021. Evaluation of seedling cold stress in the Krasnodarskij 3352 x Carolino 164 Recombinant Inbred Line population. Abstract. ASA,CSSA,SSSA International Annual Meeting, Salt Lake City, Utah.

Interpretive Summary:

Technical Abstract: Improved seedling cold stress tolerance would allow rice (Oryza sativa L.) to be planted earlier in the growing season in the USA and ultimately increase yield. The USDA Rice Minicore (RMC) collection with 202 diverse rice accessions, was evaluated for cold stress at the seedling stage using three assays designed to mimic the natural environment, designated as Low Temperature Seeding Survivability (LTSS), Plumule Recovery Growth after Cold Exposure (PGC) and Low Temperature Survival (LTS). Of these, LTSS was the most reliable. Genome-wide association (GWA) mapping with RMC identified 39 GWA-QTL associated with cold stress. Subsequently, 354 O. sativa accessions from the Rice Diversity Panel 1 (RDP1) were assayed for LTSS and Electrolyte Leakage (EL) as a measure of cell membrane integrity. GWA mapping revealed 40 GWA-QTL classified as multiple trait QTLs, of which 18 overlapped with RMC GWA-QTL. To validate these QTL and associated candidate genes, a biparental recombinant inbred line (RIL) population was developed from RMC accessions, Krasnodarskij 3352, a cold tolerant, temperate japonica rice from Russia, and Carolino 164, a cold susceptible, aus rice from Chad. The resulting 140 F8 RILs were assayed for LTSS and EL and genotyped with 2,796 SNPs selected from the from the 7,000 SNPs included in on the Illumina Rice Array (C7AIR). Preliminary mapping with 93 RILs identified six LTSS-QTL and one EL-QTL of which six overlapped with RMC and/or RDP1 GWA-QTL. Candidate genes were found in four QTL regions with vacuolar H+-translocating inorganic pyrophosphatase1 (OVP1), associated with membrane transport and cold tolerance, in the qEL6 region being the most relevant. A Backcross Inbred Line (BIL) population was developed from RMC accession, Wir911, a cold tolerant, temperate japonica from Russia crossed with Carolino 164, as the recurrent parent. Preliminary QTL mapping of 93 BC1F5 BILs assayed for LTSS and EL and genotyped with 2,593 SNPs selected from the C7AIR SNPs, revealed three QTL qLTSS1, qLTSS8 and qEL8. Only qLTSS8 overlapped with RMC and RDP1 GWA-QTL but no candidate gene related to cold stress was previously reported in this region, thus this region may harbor a novel gene(s) associated with cold tolerance.