Single-kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays)

Peer reviewedPublisher PD

Nuclear localised more sulphur accumulation1 epigenetically regulates sulphur homeostasis in Arabidopsis thaliana

Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over- accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation

Analysis of the NAM founders ionomic profiles from 2010 and 2011.

<p>Geno: p value for the genotype term in an ANOVA of a linear model with genotype and year and their interaction. Year: p value for the year term. GxY: p value for the genotype by year interaction. The significance cutoff for the first three columns was set at p<0.0005 to account for the multiple testing correction. NS: not significant. h2: the narrow sense heritability for each year and combined. Corr: the correlation between the line average from 2010 and 2011. The last two rows are the results from the jackknife analysis of 100 datasets with a single seed per plot. JK 5% p val: the 5% most significant p value for the genotype term in the two year model (i.e., 95% of the time the p value was more significant). JK 5% h2: the 5% highest heritability across two years.</p

Analysis of the sugary status on ionomic profiles.

<p>Line: p value for the genotype term in an ANOVA of a linear model with line and <i>sugary</i> genotype. Su: p value for the sugary term. The significance cutoff was set at p<0.0005 to account for the multiple testing correction. NS: not significant.</p

Alphabox plots of the effect of <i>su</i> on Ca and Zn accumulation.

<p>Five number summaries (median, 1^st and 3^rd quartiles, and 1.5 interquartile range) are shown of each seed type. Salmon denotes the values for the <i>su/su</i> (collapsed) seed, while teal denotes the values for <i>Su</i>/+ (plump) alleles. Outliers beyond 1.5 IQR are shown as black dots. Line names are the entry numbers in the Panzea database for the B73 x IL14H (Z011) population.</p

Correlation between 23 NAM parents across two years.

<p>The plot means of all 5 or 6 replicate plots for each NAM parent line (excluding Il14H, HP301 and P39) were averaged for each year.</p

Analysis of the seed position on the cob on B73 ionomic profiles.

<p>Dyn Range Cob: the average dynamic range of values (max accumulation of a position on a single cob/min accumulation on the same cob) from different positions on the cob. Dyn Range 2010 and 2011: the dynamic range in genotype values within that year (max accumulating genotype/min accumulating genotype). Farm p val: p value for the farm term in an ANOVA of a linear model with farm, field location, and location on cob. Field p val: p value for the field location term. Cob p val: p value for the location on cob term. The significance cutoff was set at p<0.0005 to account for the multiple testing correction. NS: not significant. Farm, Field and Cob SSperc are the percentage of the variance (sum of squares) accounted for by the various terms. Selenium was not measured in this experiment.</p

QTLs identified in the B73 x IL14H population.

<p>El: Element. Chm: Chromosome. Pos: Position of QTL in cM. LOD: LOD score. MI Start and Stop: the mapping intervals defining where the LOD trace crossed the 95% permutation threshold. R²: the fraction of variance accounted for by the QTL, Sum R²: The cumulative fraction of variance accounted for by all of the QTLs for the element. Add.eff: The additive effect of the QTL in PPM. PT: the 95% permutation threshold from 1000 permutations. CO: number of cofactors used in the model. Nearest Marker: The nearest marker.</p