title: Copy number variation at the GL7 locus contributes to grain size diversity in rice.
abstract: Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits. Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.
authors.affiliation: 1] State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China. [2] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [3] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yuexing
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [3] Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Xiong
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Hu
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Jiang
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Yunxia
authors.initials: Y
authors.lastname: Fang
authors.affiliation: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Longjun
authors.initials: L
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Erbo
authors.initials: E
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Weijun
authors.initials: W
authors.lastname: Ye
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiangbing
authors.initials: X
authors.lastname: Meng
authors.affiliation: 1] State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China. [2] Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Ruifang
authors.initials: R
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Hongqi
authors.initials: H
authors.lastname: Chen
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Jing
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Xudong
authors.initials: X
authors.lastname: Zhu
authors.affiliation: 1] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jiayang
authors.identifier: 0000000204876574
authors.initials: J
authors.lastname: Li
authors.affiliation: 1] State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China. [2] Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D056915:DNA Copy Number Variations; D002523:Edible Grain / Q000235:genetics*; D056625:Endosperm / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci / Q000235:genetics; D008855:Microscopy, Electron, Scanning; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D030821:Plants, Genetically Modified; D040641:Quantitative Trait Loci / Q000235:genetics; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013213:Starch / Q000378:metabolism / Q000648:ultrastructure
chemical_list: D010940:Plant Proteins; D013213:Starch