title: Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice.
abstract: The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5DEL1+IN1, and GSE5DEL2) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5DEL1+IN1haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5DEL2haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
authors.forename: Penggen
authors.initials: P
authors.lastname: Duan
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
authors.forename: Jinsong
authors.initials: J
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Dali
authors.initials: D
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
authors.forename: Baolan
authors.initials: B
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China.
authors.forename: Mufan
authors.initials: M
authors.lastname: Geng
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China.
authors.forename: Guozheng
authors.initials: G
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China.
authors.forename: Ke
authors.initials: K
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China.
authors.forename: Luojiang
authors.initials: L
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
authors.forename: Ran
authors.initials: R
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China.
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China. Electronic address: yhli@genetics.ac.cn.
authors.forename: Yunhai
authors.initials: Y
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D049109:Cell Proliferation / Q000235:genetics; D018744:DNA, Plant; D002523:Edible Grain / Q000033:anatomy & histology / Q000166:cytology / Q000235:genetics*; D019143:Evolution, Molecular; D015870:Gene Expression; D017343:Genes, Plant; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D008565:Membrane Proteins / Q000235:genetics; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic; D000072417:Protein Domains; D017384:Sequence Deletion
chemical_list: D018744:DNA, Plant; D008565:Membrane Proteins; D010940:Plant Proteins
keywords: GSE5; cell proliferation; grain size; natural variation; rice