Copy number variation at the GL7 locus contributes to grain size diversity in rice

Nature Genetics

Volumn 47, Issue 8, 2015, Pages 944-948

  Wang, Yuexing ^a,b   Xiong, Guosheng ^b,c   Hu, Jiang ^a   Jiang, Liang ^b   Yu, Hong ^b   Xu, Jie ^a   Fang, Yunxia ^a   Zeng, Longjun ^c   Xu, Erbo ^a   Xu, Jing ^a   Ye, Weijun ^a   Meng, Xiangbing ^b   Liu, Ruifang ^a,c   Chen, Hongqi ^a   Jing, Yanhui ^b   Wang, Yonghong ^b   Zhu, Xudong ^a   Li, Jiayang ^b   Qian, Qian ^a,c  

^a CHINA NATIONAL RICE RESEARCH INSTITUTE   (China)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 7; CONTROLLED STUDY; COPY NUMBER VARIATION; DOWN REGULATION; GENE LOCUS; GENETIC REGULATION; GENETIC VARIABILITY; GRAIN; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT BREEDING; PLANT CHROMOSOME; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; TANDEM REPEAT; UPREGULATION; AMINO ACID SEQUENCE; CEREAL; CHROMOSOME MAP; CLASSIFICATION; DNA SEQUENCE; ENDOSPERM; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; PHYLOGENY; PLANT SEED; QUANTITATIVE TRAIT LOCUS; SCANNING ELECTRON MICROSCOPY; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TRANSGENIC PLANT; ULTRASTRUCTURE;

ARABIDOPSIS THALIANA; ORYZA SATIVA;

STARCH; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; BASE SEQUENCE; CEREALS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CLONING, MOLECULAR; DNA COPY NUMBER VARIATIONS; ENDOSPERM; GENE EXPRESSION REGULATION, PLANT; GENETIC LOCI; MICROSCOPY, ELECTRON, SCANNING; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; QUANTITATIVE TRAIT LOCI; SEEDS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; STARCH;

EID: 84938287602     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3346     Document Type: Article

References (27)

1. Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853 (2007).
2. Tang, Y.C. & Amon, A. Gene copy-number alterations: A cost-benefit analysis. Cell 152, 394-405 (2013).
3. Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J.O. Phenotypic impact of genomic structural variation: Insights from and for human disease. Nat. Rev. Genet. 14, 125-138 (2013).
4. McHale, L.K. et al. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 159, 1295-1308 (2012).
5. Cook, D.E. et al. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338, 1206-1209 (2012).
6. Yu, P. et al. Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genomics 12, 372 (2011).
7. Yu, P. et al. Genome-wide copy number variations in Oryza sativa L. BMC Genomics 14, 649 (2013).
8. Fitzgerald, M.A., McCouch, S.R. & Hall, R.D. Not just a grain of rice: The quest for quality. Trends Plant Sci. 14, 133-139 (2009).
9. Fan, C. et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164-1171 (2006).
10. Zhang, X. et al. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc. Natl. Acad. Sci. USA 109, 21534-21539 (2012).
11. Song, X.J., Huang, W., Shi, M., Zhu, M.Z. & Lin, H.X.A. QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39, 623-630 (2007).
12. Shomura, A. et al. Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40, 1023-1028 (2008).
13. Li, Y. et al. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat. Genet. 43, 1266-1269 (2011).
14. Ishimaru, K. et al. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat. Genet. 45, 707-711 (2013).
15. Qi, P. et al. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Res. 22, 1666-1680 (2012).
16. Wang, S. et al. Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet. 44, 950-954 (2012).
17. Li, Y. et al. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat. Genet. 46, 398-404 (2014).
18. Zuo, J. & Li, J. Molecular genetic dissection of quantitative trait loci regulating rice grain size. Annu. Rev. Genet. 48, 99-118 (2014).
19. Qiu, X., Gong, R., Tan, Y. & Yu, S. Mapping and characterization of the major quantitative trait locus qSS7 associated with increased length and decreased width of rice seeds. Theor. Appl. Genet. 125, 1717-1726 (2012).
20. Shao, G. et al. Allelic variation for a candidate gene for GS7, responsible for grain shape in rice. Theor. Appl. Genet. 125, 1303-1312 (2012).
21. Lee, Y.K. et al. LONGIFOLIA1 and LONGIFOLIA2, two homologous genes, regulate longitudinal cell elongation in Arabidopsis. Development 133, 4305-4314 (2006).
22. Drevensek, S. et al. The Arabidopsis TRM1-TON1 interaction reveals a recruitment network common to plant cortical microtubule arrays and eukaryotic centrosomes. Plant Cell 24, 178-191 (2012).
23. Imbe, T. et al. Development of a multipurpose high yielding rice variety "Takanari". Bull. Natl. Inst. Crop Sci. 5, 35-51 (2004).
24. Cheng, J., Li, C., Wu, Y., Zheng, H. & Liang, S. Features and properties of indica rice sterile line Yuefeng A with high quality and its utilization. Guangdong Agr. Sci. 4, 5-6 (2002).
25. Wang, Z. et al. A practical vector for efficient knockdown of gene expression in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 22, 409-417 (2004).
26. Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6, 271-282 (1994).
27. Walter, M. et al. Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J. 40, 428-438 (2004).