Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat

Frontiers in Plant Science
Yanchun PengWei Chen

Abstract

Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annot...Continue Reading

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Citations

Nov 2, 2019·International Journal of Molecular Sciences·Vijay JoshiUmesh K Reddy
Sep 3, 2019·Frontiers in Plant Science·Chuanying FangShouchuang Wang
Jan 22, 2019·Frontiers in Plant Science·Mingwei GuanCunmin Qu

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Methods Mentioned

BETA
dissection

Software Mentioned

mGWAS
MEGA
MEGA5
FASTmrEMMA
pKWmEB
FaST
BLASTx
FASTmrMLM
SigmaPlot
pLARmEB

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