Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (Oryza sativa L.)

Abstract

Zinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage within a rice core collection, named Ting's core collection, which showed extensive phenotypic variations in Zn toxicity with high-density single-nucleotide polymorphisms (SNPs). A total of 7 and 19 quantitative trait loci (QTL) were detected using root elongation (RE) and relative root elongation (RRE) under high Zn toxicity, respectively. Among them, 24 QTL were novel, and qRRE15 was located in the same region where 3 QTL were reported previously. In addition, qRE4 and qRRE9 were identical. Furthermore, we found eight candidate genes that are involved in abiotic and biotic stress, immunity, cell expansion, and phosphate transport in the loci of qRRE8, qRRE9, and qRRE15. Moreover, four candidate genes, i.e., Os01g0200700, Os06g0621900, Os06g0493600, and Os06g0622700, were verified correlating to Zn tolerance in rice by quantitative real time-PCR (qRT-PCR). Taken together, these results provide significant insight into the genetic basis for Zn toxicity tolerance and tolerant germplasm for developing rice tolerance to Zn toxicity and improving rice production in Zn-contaminated soils.

Keywords: GWAS; QTL; Ting’s core collection; Zn toxicity; rice.

Figure 1

GWAS of Zn tolerance by using EMMAX model. (a) Distribution of root elongation of Ting’s core collection growing under Zn toxicity (120 μM); (b) Manhattan plot of GWAS using root elongation under Zn toxicity (120 μM); (c) distribution of relative root elongation of Ting’s core collection growing under Zn toxicity (120 μM); and (d) Manhattan plot of GWAS using relative root elongation. Chromosomes are depicted in different colors. The horizontal green dashed line indicates the significance threshold (−log10(mBF) = 5.02). The black arrows represent the novel loci associated with Zn tolerance detected in the present study. The red arrow represents the loci, which were reported previously.

Figure 2

Effect analysis of allelic variations on root elongation under high Zn toxicity.

Figure 3

Effect analysis of allelic variations on relative root elongation under high Zn toxicity.

Figure 4

Local Manhattan plot (top panel) and LD heatmap (bottom panel) of the 13.65–13.85 Mb region of chromosome 3 (a), 17.08–17.28 Mb region of chromosome 6 (b), and 24.91–25.11 Mb region of chromosome 6 (c).

Figure 5

The gene expression of 8 candidate genes in representative varieties (the most sensitive variety in the present study, You zhan hong; the most tolerant variety in the present study, Nagabo) in control and high Zn conditions as measured by qRT-PCR. Error bars: S.D. The different letters indicate significant differences by one-way ANOVA analysis with Tukey’s HSD test (p < 0.05, n = 3).