Journal article
Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. thermal stress and spikelet sterility
Journal of Experimental Botany, Vol.68(15), pp.4389-4406
2017
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Source: InCites
Abstract
<p>Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession <em>indica</em> rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at <em>P</em><1 × 10<sup>−5</sup> (33 at <em>P</em><1 × 10<sup>−4</sup>) were related to sterility effects of heat, cold, cold acclimation, or unexplained causes (baseline sterility). Nine annotated genes were found on average within the 50% linkage disequilibrium (LD) region. Among them, one to five plausible candidate genes per QTL were identified based on known expression profiles (organ, stage, stress factors) and function. Meiosis-, development- and flowering-related genes were frequent, as well a stress signaling kinases and transcription factors. Putative epigenetic factors such as DNA methylases or histone-related genes were frequent in cold-acclimation QTLs, and positive-effect alleles were frequent in cold-tolerant highland rice from Madagascar. The results indicate that epigenetic control of acclimation may be important in <em>indica</em> rice genotypes adapted to cool environments.</p>
Details
- Title
- Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. thermal stress and spikelet sterility
- Creators
- Michael Dingkhun - CIRAD, FranceRichard Pasco - International Rice Research Institute, PhilipinesJulie Mae Pasuquin - International Rice Research Institute, PhilipinesJean Damo - International Rice Research Institute, PhilipinesJean-Christophe Soulie - CIRAD, FranceLouis-Marie Raboin - CIRAD, FranceJulie Dusserre - CIRAD, FranceAbdoulaye Sow - Africa Rice Center, SenegalBaboucarr Manneh - Africa Rice Center, SenegalTobias Kretzschmar - International Rice Research Institute, PhilipinesSuchit Shrestha - International Rice Research Institute, Philipines
- Publication Details
- Journal of Experimental Botany, Vol.68(15), pp.4389-4406
- Identifiers
- 1984; 991012820806402368
- Academic Unit
- Southern Cross Plant Science; Science; Faculty of Science and Engineering
- Resource Type
- Journal article