Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)

BMC Genetics

Research Article

Hu Zhao¹  Risper Auma Magwa¹  Yongzhong Xing² 

[1]National Key Laboratory of Crop Genetic Improvement and National Center of Plant, Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China

[2]National Key Laboratory of Crop Genetic Improvement and National Center of Plant, Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China

[3]Hubei Collaborative Innovation Center for Grain Industry, Hubei, China

关键词: Seed dormancy;    Germination percentage;    After-ripening;    Association mapping;    Haplotype analysis;   

DOI  :  10.1186/s12863-016-0340-2

 received in 2015-11-12, accepted in 2016-01-21,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSeed dormancy is an adaptive trait employed by flowering plants to avoid harsh environmental conditions for the continuity of their next generations. In cereal crops, moderate seed dormancy could help prevent pre-harvest sprouting and improve grain yield and quality. We performed a genome wide association study (GWAS) for dormancy, based on seed germination percentage (GP) in freshly harvested seeds (FHS) and after-ripened seeds (ARS) in 350 worldwide accessions that were characterized with strong population structure of indica, japonica and Aus subpopulations.ResultsThe germination tests revealed that Aus and indica rice had stronger seed dormancy than japonica rice in FHS. Association analysis revealed 16 loci significantly associated with GP in FHS and 38 in ARS. Three out of the 38 loci detected in ARS were also detected in FHS and 13 of the ARS loci were detected near previously mapped dormancy QTL. In FHS, three of the association loci were located within 100 kb around previously cloned GA/IAA inactivation genes such as GA2ox3, EUI1 and GH3-2 and one near dormancy gene, Sdr4. In ARS, an association signal was detected near ABA signaling gene ABI5. No association peaks were commonly detected among the sub-populations in FHS and only one association peak was detected in both indica and japonica populations in ARS. Sdr4 and GA2OX3 haplotype analysis showed that Aus and indica II (IndII) varieties had stronger dormancy alleles whereas indica I (IndI) and japonica had weak or non-dormancy alleles.ConclusionThe association study and haplotype analysis together, indicate an involvement of independent genes and alleles contributing towards regulation and natural variation of seed dormancy among the rice sub-populations.

【 授权许可】

CC BY   
© Magwa et al. 2016