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Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.
Pubmed ID: 29237030
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Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes
View all literature mentionsSoftware package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)
View all literature mentionsSoftware tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate.
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