Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. (4th April 2013)

• Record Type: Journal Article
• Authors: Yano, Ryoichi; Takebayashi, Yumiko; Nambara, Eiji; Kamiya, Yuji; Seo, Mitsunori
• Is Part Of: Plant journal. Volume 74:Number 5(2013:Jun.)
• Page Start: 815
• Page End: 828
• Publication Date: 2013-04-04
• Subjects: Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.12167
• Languages: English
• ISSNs: 0960-7412

Abstract

<abstract abstract-type="main" xml:lang="en" id="tpj12167-abs-0001"> <title>Summary</title> <p>Seed dormancy is an important adaptive trait that enables germination at the proper time, thereby ensuring plant survival after germination. In Arabidopsis, considerable variation exists in the degree of seed dormancy among wild‐type accessions (ecotypes). In this paper, we identify a plant‐specific HD2 histone deacetylase gene, <italic>HD2B</italic> (<italic>At5g22650</italic>), as a genetic factor associated with seed dormancy. First, genome‐wide association mapping of 113 accessions was used to identify single nucleotide polymorphisms that possibly explain natural variation for seed dormancy. Integration of genome‐wide association mapping and transcriptome analysis during cold‐induced dormancy cycling identified <italic>HD2B</italic> as the most plausible candidate gene, and quantitative RT‐PCR analysis demonstrated that <italic>HD2B</italic> expression was up‐regulated by cold and after‐ripening (dry storage of mature seed), treatments that are known to break seed dormancy. Interestingly, quantitative RT‐PCR analysis in 106 accessions revealed that the expression of <italic>HD2B</italic> in imbibed seeds was significantly suppressed in most of the dormant accessions compared with less‐dormant accessions, suggesting that suppression of <italic>HD2B</italic> expression may be important to maintain seed dormancy in dormant accessions. In addition, transgenic seeds of a dormant Cvi‐0 accession that carried a 2.5 kb genomic DNA fragment of <italic>HD2B</italic> cloned from a less‐dormant Col‐0 accession (<sup><italic>Col</italic></sup><italic>HD2B</italic>/Cvi‐0) exhibited reduced seed dormancy accompanied by enhanced expression of <italic>HD2B</italic> when after‐ripened or cold‐imbibed. Endogenous levels of gibberellin were found to be increased in the imbibed seeds of after‐ripened <sup><italic>Col</italic></sup><italic>HD2B</italic>/Cvi‐0 compared with wild‐type Cvi‐0. These results suggest that <italic>HD2B</italic> plays a role in seed dormancy and/or germinability in <italic>Arabidopsis thaliana</italic>.</p> </abstract>