Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

Abstract

Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance, RAR1 encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties.

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)

“…The black triangles in the LD heatmap represent the haploblocks. QTL was also found to with QTLs associated with SPAD ratio (Kaewcheenchai et al, 2021) and SDW and RDW (Dufey et al, 2015). Of the 16 genes annotated for qFe5.2, only the gene LOC_Os05g16670 was found to contain different haplotypes based on nonsynonymous SNPs of this gene.…”

“…However, this trait showed little difference at the vegetative stage and no significance at the reproductive stage. SDW was previously used as a parameter to identify QTLs associated with Fe toxicity tolerance at the seedling stage ( Kaewcheenchai et al, 2021 ). For the other traits, the median difference is less than 30% at all stages.…”

“…Twenty-eight QTLs in 18 different chromosomal regions associated with morphological and physiological traits have been obtained from a population of 220 BC 3 DH of O. sativa (Caiapo)/ O. glaberrima (MG12)/ O. sativa (Caiapo) tested under hydroponic conditions for Fe 2+ 250 mg L −1 ( Dufey et al, 2015 ). Genome-wide association studies (GWAS) have also been applied to identify QTLs/genes associated with Fe toxicity-related traits in rice ( Matthus et al, 2015 ; Zhang et al, 2017 ; Diop et al, 2020 ; Melandri et al, 2020 ; Kaewcheenchai et al, 2021 ).…”

“…sativa (Caiapo) tested under hydroponic conditions for Fe 2+ 250 mg L −1 (Dufey et al, 2015). Genome-wide association studies (GWAS) have also been applied to identify QTLs/genes associated with Fe toxicity-related traits in rice (Matthus et al, 2015;Zhang et al, 2017;Diop et al, 2020;Melandri et al, 2020;Kaewcheenchai et al, 2021).…”

Field Evaluation of Rice Lines Derived from Suakoko 8 X Bao Thai for Iron Tolerance in the South Saharan African Farming System

“…Rice intra-specific and inter-specific mapping populations have been used in a number of studies to try and discover quantitative trait loci (QTLs) or genes linked with Fe 2+ toxicity [ 19 , 20 , 21 ]. The identification of QTLs and genes linked to Fe 2+ toxicity-related depictions in rice has also been performed using genome-wide association studies [ 21 , 22 , 23 ].…”