Genome-Wide Association Study Using a Multiparent Advanced Generation Intercross (MAGIC) Population Identified QTLs and Candidate Genes to Predict Shoot and Grain Zinc Contents in Rice

Shilei Liu, Wenli Zou, Xiang Lu, Jianmin Bian, Haohua He, Jingguang Chen and Guoyou Ye
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Shilei Liu: Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
Wenli Zou: Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
Xiang Lu: CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
Jianmin Bian: Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
Haohua He: Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
Jingguang Chen: CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
Guoyou Ye: CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China

Agriculture, 2021, vol. 11, issue 1, 1-14

Abstract: Zinc (Zn) is an essential trace element for the growth and development of both humans and plants. Increasing the accumulation of Zn in rice grains is important for the world’s nutrition and health. In this study, we used a multiparent advanced generation intercross (MAGIC) population constructed using four parental lines and genotyped using a 55 K rice SNP array to identify QTLs related to Zn 2+ concentrations in shoots at the seedling stage and grains at the mature stage. Five QTLs were detected as being associated with shoot Zn 2+ concentration at the seedling stage, which explained 3.7–5.7% of the phenotypic variation. Six QTLs were detected as associated with grain Zn 2+ concentration at the mature stage, which explained 5.5–8.9% of the phenotypic variation. Among the QTLs, qSZn2-1/qGZn2 and qSZn3/qGZn3 were identified as being associated with both the shoot and grain contents. Based on gene annotation and literature information, 16 candidate genes were chosen in the regions of qSZn1 , qSZn2-1/qGZn2 , qSZn3/qGZn3 , qGZn7 , and qGZn8 . Analysis of candidate genes through qRT-PCR, complementation assay using the yeast Zn-uptake-deficient double-mutant ZHY3, and sequencing of the four parental lines suggested that LOC_Os02g06010 may play an important role in Zn 2+ accumulation in indica rice.

Keywords: Zn 2+ content; genome-wide association analysis; quantitative trait loci (QTL); MAGIC population; rice (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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