Navigating rice seedling cold resilience in the Aus and Tropical Japonica Subpopulations: QTL Mapping and the search for genes

Authors: Eizenga, Georgia; SANTAMARIA, YAMI - Marquette University; Jackson, Aaron; PHAN, HUY - Marquette University; Jia, Melissa; Grunden, Quynh; Edwards, Jeremy; HIMELBLAU, ED - Marquette University; SCHLAPPI, MICHAEL - Marquette University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2025
Publication Date: 1/7/2026
Citation: Eizenga, G.C., Santamaria, Y., Jackson, A.K., Phan, H., Jia, M.H., Grunden, Q.P., Edwards, J., Himelblau, E., Schlappi, M.R. 2026. Navigating rice seedling cold resilience in the Aus and Tropical Japonica Subpopulations: QTL Mapping and the search for genes. Frontiers in Plant Science. 16:1716845. https://doi.org/10.3389/fpls.2025.1716845.
DOI: https://doi.org/10.3389/fpls.2025.1716845

Interpretive Summary: Low temperatures are a major problem for rice growing in 25 countries and yield losses as high as 80% have been reported. To enhance the ability of rice to adapt to a wide range of naturally occurring extreme temperature fluctuations and expand its production range to increase global food security, it is necessary to explore the natural genetic variation to facilitate rice breeding efforts to meet these challenges. In the U.S. Midsouth, improved rice seedling cold tolerance will allow the crop to be planted earlier in the growing season, thus taking advantage of the higher spring rainfall, expand the ratoon crop season and decrease exposure to high summer nighttime temperatures which decrease grain quality. Lastly, in regions like California, where cool temperatures occur during the growing season and cold irrigation water is used to water the crop, improved tolerance to cool temperatures would increase seedling survivability. Cultivated rice is divided into two main varietal groups, Indica and Japonica which have been recognized since ancient times. Crosses between these groups have few seeds produced, due to “sterility barriers”, thus identifying improved seedling cold tolerance within these varietal groups would avoid the problem of few seed being produced in other words, poor seed set. This study was conducted to discover genes associated with cold tolerance at the seedling stage in both the Indica and Japonica varietal groups by crossing a single cold tolerant and cold susceptible aus rice variety from the Indica varietal and single cold sensitive and cold tolerant tropical japonica variety from the Japonica varietal group and subsequently evaluating the progeny for cold tolerance using two different methods to find regions of the DNA associated with cold tolerance. Based on differences in the DNA in these targeted “cold tolerant” regions, 23 potential genes affecting cold tolerance at the seedling stage were discovered in the aus, Indica varietal group and 12 potential genes in the tropical japonica, Japonica varietal group. Future studies will focus on validating the function of these 35 genes to determine which genes would be most effective for improving rice seedling cold tolerance. Subsequently, the most effective “cold tolerance genes” will be transferred into adapted rice varieties so that new varieties will withstand cold more effectively during their early growth stages. This would allow farmers to sow rice earlier in the growing season, resulting in superior grain quality because the rice would mature before the intense heat of late summer. Also, it offers the option of extending the growing season for a secondary (ratoon) harvest in the U.S. MidSouth due to the earlier planting.

Technical Abstract: To enhance the ability of rice to adapt to a wide range of naturally occurring extreme temperature fluctuations and expand its production range to increase global food security, it is necessary to explore the natural genetic variation to facilitate rice breeding efforts to meet these challenges. Improved rice seedling cold tolerance will allow the crop to be planted earlier in the growing season, thus taking advantage of spring rainfall and decreasing exposure to high summer nighttime temperatures which decrease grain quality. To uncover genomic regions in rice involved in managing cold stress tolerance responses in the generally cold sensitive aus (AUS) and in the generally cold tolerant tropical japonica (TRJ) subpopulations and to identify associated cold tolerance genes underlying the cold tolerance mechanisms, AUS and TRJ inbred line populations developed from crosses between cold tolerant and cold sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after one week of cold exposure quantified as percent electrolyte leakage (EL), and percent low-temperature seedling survivability (LTSS) after one week of recovery growth. This revealed three EL QTL and four LTSS QTL in the AUS and two EL QTL and four LTSS in the TRJ subpopulations. Two AUS QTL overlap with QTL regions previously uncovered by our other biparental mapping approaches. Within the QTL regions, 35 cold-tolerant candidate genes, 23 genes in AUS and 12 in TRJ, were identified based on genomic differences between the cold-tolerant and cold-sensitive parents, and 80% had gene disruptive nucleotide variants in the sensitive parents, which might contribute to their reduced cold tolerance potential. Of the 35 genes, 29% coded for kinases and other components potentially involved in signal transducing cold stress tolerance responses, while 20% coded for ubiquitin and F-box type proteins and chaperones that might regulate protein integrity and/or protein homeostasis as a specific cold stress tolerance response mechanism.