Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

Abstract

Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

“…Multiple comparison analysis was performed on parents following the least significant difference (LSD) post hoc test. Relative phenotypic value of morphological traits was determined for each line, that is, the phenotypic value obtained from the As treatment divided by the control value (Dasgupta et al 2004; Shrestha et al 2018). Pair-wise Pearson‘s correlation analysis was carried out among the As-related traits, in which P- value was two-tailed with two significant levels using P = 0.05 and P = 0.01, and a heat map was generated using corrplot package in R studio.…”

Genetic dissection of bread wheat diversity and identification of adaptive loci in response to elevated tropospheric ozone

“…The criteria [(mean of all genotypes) ± 3 standard deviations] were used to cut off extreme values (Ueda, Frimpong, et al, 2015). After removing SNPs with a minor allele frequency (MAF) of less than 5% (Shrestha et al, 2018), a total of 8,526 SNPs was left. Association mapping was conducted using TASSEL 5.2.54, which uses a mixed linear model (MLM) incorporating PCA with five principal components and kinship matrix data in default setting (P3D for variance component analysis and no compression level).…”

Genome Wide Association Analysis of Plant Height, Spike and Awn Length in Barley (Hordeum Vulgare L.) Exposed to Mn Stress

“…Only few studies have addressed genetic factors with Mn tolerance in plants (Wang et al, 2002;Kassem et al, 2004;Raman et al, 2017;Huang et al, 2018;Shrestha et al, 2018).…”

“…Only few studies reporting quantitative trait loci (QTL) for Mn toxicity in barley using bi-parental mapping population have been published till date. However, bi-parental populations do not cover the enormous diversity (Shrestha et al, 2018). Recently, association mapping based on the strength of linkage disequilibrium between markers and functional polymorphism across a set of diverse germplasm emerged as a powerful tool for gene tagging (Mackay and Powell, 2007;Zhu et al, 2008;Ahmadi et al, 2011).…”