Abstract
BackgroundDeveloping chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species.ResultsThe Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to “carbohydrate biosynthesis”, “carbohydrate transmembrane transport”, “small molecule protein modification”, and “plasma membrane” were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to “Golgi apparatus”, “stress response”, “transmembrane transport”, and “signal transduction”.ConclusionsTaken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.
Highlights
Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement
We show via genotype-based principal component analyses (PCA) combined with cold tolerance trait phenotyping analyses done at different temperatures that the Rice Diversity Panel 1 (RDP1) contains three distinct, mostly subpopulation-specific, clusters of accessions classified as chilling tolerant (Tolerant), intermediate chilling tolerant (Intermediate), and chilling sensitive (Sensitive)
Chilling Tolerance Trait Phenotyping of RDP1 Accessions To better understand the natural variation that allows the JAPONICA subspecies of rice to be more chilling tolerant than the INDICA subspecies, multiple phenotypic analyses on a subset of Rice Diversity Panel 1 (RDP1; Eizenga et al 2014) accessions were done at five different temperatures (4 °C, 8 °C, 10 °C, 12 °C, and 16 °C)
Summary
Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. Mechanisms underlying this complex trait are not fully understood. Every year, chilling stress causes major yield loss in the rice crop (da Cruz et al 2013). To eventually reduce such losses, our study aims to better understand cold stress tolerance response mechanisms in young seedlings, a critical stage for rice phenology
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