Copy number variation at the GL7 locus contributes to grain size diversity in rice 
Yuexing Wang^1-3,5, Guosheng Xiong^2-5, Jiang Hu^1,5, Liang Jiang^2,3, Hong Yu^2,3, Jie Xu¹, Yunxia Fang¹, Longjun Zeng⁴, Erbo Xu¹, Jing Xu¹, Weijun Ye¹, Xiangbing Meng^2,3, Ruifang Liu^1,4, Hongqi Chen¹, Yanhui Jing^2,3, Yonghong Wang^2,3, Xudong Zhu¹, Jiayang Li^2,3 & Qian Qian^1,4  

Nature Genetics 
Doi:10.1038/ng.3346 

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.