Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

Authors: SCHLAPPI, MICHAEL - Marquette University; JESSEL, AVERY - Marquette University; Jackson, Aaron; PHAN, HUY - Marquette University; Jia, Melissa; Edwards, Jeremy; Eizenga, Georgia

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2023
Publication Date: 12/14/2023
Citation: Schlappi, M.R., Jessel, A.R., Jackson, A.K., Phan, H., Jia, M.H., Edwards, J., Eizenga, G.C. 2023. Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1303651.
DOI: https://doi.org/10.3389/fpls.2023.1303651

Interpretive Summary: Global climate change resulting in extreme temperature fluctuations including cooler temperatures, has made it imperative to explore the natural variation for chilling tolerance at the seedling stage in rice. Discovering new sources of seedling cold tolerance will facilitate the development of new climate resilient, cold tolerant rice varieties. Often rice seedlings struggle to survive when the seedlings experience cold temperatures because they lack chilling tolerance which limits how early rice can be planted in many rice growing regions of the world including the USA. Previous studies documented rice varieties differ in their level of seedling cold tolerance. Determining which genes are responsible for the cold tolerance would enable these cold tolerance genes to be incorporated into rice varieties adapted to the US growing environment. This study was conducted to discover genes associated with cold tolerance at the seedling stage by crossing selected cold tolerant and cold susceptible varieties and 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, 25 potential genes affecting cold tolerance at the seedling stage were discovered. Future studies will focus on validating the function of these 25 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 would be more resilient to climate change because they would 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. Mid-South due to the earlier planting.

Technical Abstract: Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate breeding of climate resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two 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 four EL QTL and 12 LTSS QTL, with all but one overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold tolerance candidate genes were identified based on genomic differences between the cold tolerant and cold sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes had deleterious nucleotide variants in the cold sensitive parent, which might contribute to its cold sensitive phenotype.