Principal  Component Analysis-based Genome-wide Association Study for Detecting Candidate Genes Associated with Various Traits in Rice

J. K. Lee; S. G. Hwang

doi:10.22698/jales.20200036

All Issue

2020 Vol.32, Issue 3 Preview Page Next Page

Research Article

Principal Component Analysis-based Genome-wide Association Study for Detecting Candidate Genes Associated with Various Traits in Rice 다양한 형질 관련 후보유전자 동정을 위한 주성분 분석 기반 GWAS

31 December 2020. pp. 417-424

PDF XML

Abstract

In this study, we attempted to identify candidate single-nucleotide polymorphisms (SNPs) corresponding to agronomic traits via a genome-wide association study (GWAS) using principal component analysis (PCA). We confirmed the normally distributed traits in each PC, suggesting that the PCs were suitable for GWAS. We found 2,527,855 SNPs and 381,681 indels among 26 rice varieties. The PC1 was showed 22 significant missense SNPs associated with three traits (leaf blight disease, rice stripe disease, and gains per panicle). Especially, three of 22 missense SNPs had the highest significance in GWAS for each trait. The 06g0587200 gene associated with gain per panicle belongs to two QTLs: qtl1-5 corresponding to the length and width of grains and Tgw6.1 corresponding to the thousand-grain weight. The two candidate genes (Os01g0858000 implicated in rice stripe disease and Os03g0165000 implicated in leaf blight disease) were newly detected in this study. However, further studies are required to confirm the exact function of these two genes. Thus, GWAS based on PCA can be used to find a key gene corresponding to various traits.

Keywords

GWAS

Indel

PCA

Rice, SNP

References

Ayana, G. T., Ali, S., Sidhu, J. S., Gonzalez Hernandez, J. L., Turnipseed, B., Sehgal, S. K. (2018) Genome-wide association study for spot blotch resistance in hard winter wheat. Front Plant Sci 9:926. 10.3389/fpls.2018.0092630034404PMC6043670

Bush, W. S., Moore, J. H. (2012) Chapter 11: Genome-Wide Association Studies. PLoS Comput Biol 8:e1002822. 10.1371/journal.pcbi.100282223300413PMC3531285

Cubry, P., Pidon, H., Kim, N. T., Christine, T. D., Thuillet, A. C., Holzinger, M., Adam, H., Kam, H., Chrestin, H., Ghesquiere, A., Sabot, O. F., Vigouroux, T., Alvar, L., Jouannic, S. (2020) Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima. Rice 7:897298. 10.1101/2020.01.07.897298

Daovongdeuan, S., Kim, M. Y., Jeong, H., Lee, S. H. (2017) Genome-wide association study for seed size and color in mungbean (Vigna radiata (L.) Wilczek). The Korean Society of Crop Science 274-274 Seoul national University. Seoul, Korea.

Gao, H., Zhang, T., Wu, Y., Jiang, L,. Zhan, J,. Yang, R. (2014) Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix. Heredity 113:526-532. 10.1038/hdy.2014.5724984606PMC4274615

Garg, R., Patel, R. K., Tyagi, A. K., Jain, M. (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53-63. 10.1093/dnares/dsq02821217129PMC3041503

Guo, C., McDowell, I. C., Nodzenski, M., Scholtens, D. M., Allen, A. S., Lowe, W. L., Reddy, T. E. (2017) Transverions have large regulatory effects than transitions. BMC Genomics 18:394. 10.1186/s12864-017-3785-428525990PMC5438547

Kruglyak, L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-44. 10.1038/964210369254

Lee, T. H., Guo, H., Wang, X., Kim, C., Paterson, A. H. (2014) SNPhylo : a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15:162. 10.1186/1471-2164-15-16224571581PMC3945939

Lekklar, C., Suriya-arunroj, D., Pongpanich, M., Comai, L., Kositsup, B., Chadchawan, S., Buaboocha, T. (2019) Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress. Genes 10:562. 10.3390/genes1008056231349693PMC6722916

McDowell, E. T., Kapteyn, J., Schmidt, A., Li, C., Kang, J. H., Descour, A., Shi, F., Larson, Matthew., Schilmiller, A., An, L., Jones, A. D., Pichersky, E., Soderlund, C. A., Gang, D. R. (2011) Comparative functional genomic analysis of Solanum glandular trichome types. Plant Physiol 155:524-539. 10.1104/pp.110.16711421098679PMC3075747

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., Cunningham, F. (2016) The Ensembl Variant Effect Predictor. Genome Biology 17:122. 10.1186/s13059-016-0974-427268795PMC4893825

Pearson, K. (1896) Mathematical contributions to the theory of evolution III. Regression, heredity, and panmixia. Philos Trans R Soc Lond Ser B Biol Sci 187:253-318. 10.1098/rsta.1896.0007

Seck, P. A., Diagne, A., Mohanty, S. Marco, C. S. W. (2012) Crops that feed the world 7: Rice. Food Sec 4:7-24. 10.1007/s12571-012-0168-1

Sloan, D. B., Keller, S. R., Berardi, A. E., Sanderson, B. J., Karpovich, J. F., Taylor, D. R. (2012) De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Molecular Ecology Resources 12:333-343. 10.1111/j.1755-0998.2011.03079.x21999839

Yan, Wj., Liu, H., Zhou, X., Li, Q., Zhang, J., Lu, L., Liu, T., Liu, H., Zhang, C., Zhang, Z., Shen, G., Yao, W., Chen, H., Yu, S., Xie, W., Xing, Y. (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969-971. 10.1038/cr.2013.4323507971PMC3698629

Yano, K., Morinaka, Y., Wang, F., Huang, P., Takehara, S., Hirai, T., Ito, A., Koketsu, E., Kawamura, M., Kotake, K. (2019) GWAS with principal component analysis identifes a gene comprehensively controlling rice architecture. Proc Natl Acad Sci USA 116:21262-21267. 10.1073/pnas.190496411631570620PMC6800328

Information

Publisher :Agriculture and Life Sciences Research Institute, Kangwon National University
Publisher(Ko) :강원대학교 농업생명과학대학 농업생명과학연구원
Journal Title :Journal of Agricultural, Life and Environmental Sciences
Journal Title(Ko) :농업생명환경연구
Volume : 32
No :3
Pages :417-424
Received Date : 2020-11-19
Revised Date : 2020-12-10
Accepted Date : 2020-12-16
DOI :https://doi.org/10.22698/jales.20200036

Journal of Agricultural, Life and Environmental Sciences ISSN:2233-8322(Print) 2508-870X(Online) 농업생명환경연구

All Issue