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Separating an allele associated with late flowering and slow maturation of Arabidopsis thaliana from population structure

By Yanjun Zan, Xiao Feng, Zheng Ning, Weilin Xu, Qianhui Wan, Dongyu Zeng, Ziyi Zeng, Yang Liu, Xia Shen

Posted 25 Sep 2017
bioRxiv DOI: 10.1101/193417

Genome-wide association analysis is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. A common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. We demonstrate the efficiency of multi-phenotype analysis to uncover hidden genetic loci masked by population structure. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.

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