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GWAS with a PCA uncovers candidate genes for accumulations of microelements in maize seedlings
Author(s) -
Ma Langlang,
Qing Chunyan,
Zhang Minyan,
Zou Chaoying,
Pan Guangtang,
Shen Yaou
Publication year - 2021
Publication title -
physiologia plantarum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.351
H-Index - 146
eISSN - 1399-3054
pISSN - 0031-9317
DOI - 10.1111/ppl.13466
Subject(s) - single nucleotide polymorphism , quantitative trait locus , biology , allele , candidate gene , gene , shoot , zinc , genetics , genome wide association study , phenotype , plant genetics , inbred strain , botany , genotype , chemistry , genome , organic chemistry
Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation‐related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome‐wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly ( P < .05) associated with Zn‐PC1, Zn‐PC2, Cu‐PC1, and Mn‐PC2, respectively, with 11 genes closely linked ( r 2 > 0.8) to these SNPs. Of them, GRMZM2G142870 , GRMZM2G045531 , and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more “higher‐accumulation” alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker‐assisted selection of microelement accumulations in maize.