A major locus for chloride accumulation on chromosome 5A in bread wheat.

Chloride (Cl-) is an essential micronutrient for plant growth, but can be toxic at high concentrations resulting in reduced growth and yield. Although saline soils are generally dominated by both sodium (Na+) and Cl- ions, compared to Na+ toxicity, very little is known about physiological and genetic control mechanisms of tolerance to Cl- toxicity. In hydroponics and field studies, a bread wheat mapping population was tested to examine the relationships between physiological traits [Na+, potassium (K+) and Cl- concentration] involved in salinity tolerance (ST) and seedling growth or grain yield, and to elucidate the genetic control mechanism of plant Cl- accumulation using a quantitative trait loci (QTL) analysis approach. Plant Na+ or Cl- concentration were moderately correlated (genetically) with seedling biomass in hydroponics, but showed no correlations with grain yield in the field, indicating little value in selecting for ion concentration to improve ST. In accordance with phenotypic responses, QTL controlling Cl- accumulation differed entirely between hydroponics and field locations, and few were detected in two or more environments, demonstrating substantial QTL-by-environment interactions. The presence of several QTL for Cl- concentration indicated that uptake and accumulation was a polygenic trait. A major Cl- concentration QTL (5A; barc56/gwm186) was identified in three field environments, and accounted for 27-32% of the total genetic variance. Alignment between the 5A QTL interval and its corresponding physical genome regions in wheat and other grasses has enabled the search for candidate genes involved in Cl- transport, which is discussed

A major locus for chloride accumulation on chromosome 5A in bread wheat.

Chloride (Cl-) is an essential micronutrient for plant growth, but can be toxic at high concentrations resulting in reduced growth and yield. Although saline soils are generally dominated by both sodium (Na+) and Cl- ions, compared to Na+ toxicity, very little is known about physiological and genetic control mechanisms of tolerance to Cl- toxicity. In hydroponics and field studies, a bread wheat mapping population was tested to examine the relationships between physiological traits [Na+, potassium (K+) and Cl- concentration] involved in salinity tolerance (ST) and seedling growth or grain yield, and to elucidate the genetic control mechanism of plant Cl- accumulation using a quantitative trait loci (QTL) analysis approach. Plant Na+ or Cl- concentration were moderately correlated (genetically) with seedling biomass in hydroponics, but showed no correlations with grain yield in the field, indicating little value in selecting for ion concentration to improve ST. In accordance with phenotypic responses, QTL controlling Cl- accumulation differed entirely between hydroponics and field locations, and few were detected in two or more environments, demonstrating substantial QTL-by-environment interactions. The presence of several QTL for Cl- concentration indicated that uptake and accumulation was a polygenic trait. A major Cl- concentration QTL (5A; barc56/gwm186) was identified in three field environments, and accounted for 27-32% of the total genetic variance. Alignment between the 5A QTL interval and its corresponding physical genome regions in wheat and other grasses has enabled the search for candidate genes involved in Cl- transport, which is discussed

<b>Estimated genetic correlations extracted from the fitted multi-environment model for individual traits.</b>

<p><b>Estimated genetic correlations extracted from the fitted multi-environment model for individual traits.</b></p

Location of Cl⁻ concentration QTL (<i>barc56</i>/<i>gwm186</i>) on chromosome 5A detected in field trials (Balaklava, Georgetown and Roseworthy) with varying salinity levels.

<p>The outlier statistics represent LOD scores (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098845#pone-0098845-t004" target="_blank">Table 4</a>).</p

<b>Estimated genetic correlations between shoot DW (hydroponics), grain yield (field) Na⁺, K⁺, and Cl⁻ (field and hydroponics) extracted from the fitted multi-trait model at each environment.</b>

<p><b>Estimated genetic correlations between shoot DW (hydroponics), grain yield (field) Na⁺, K⁺, and Cl⁻ (field and hydroponics) extracted from the fitted multi-trait model at each environment.</b></p

<b>Parental means, population mean and range for Na⁺, Cl⁻, K⁺, Ca²⁺ and Mg²⁺ concentrations (mmol kg¹ DW) in penultimate leaves (field trials) and whole shoots (hydroponics), seedling biomass [shoot DW (g plant¹)] and grain yield (t ha¹) in Berkut/Krichauff DH population tested for ST in hydroponics and field trials (Roseworthy, Balaklava and Georgetown).</b>

<p>The means represent predicted values from MET (Na⁺, Cl⁻, K⁺) and single environment (Ca²⁺ and Mg²⁺) analysis of each trait. Broad-sense heritability is also given for individual traits at each environment.</p

<b>Candidate genes underlying the physical interval of the Cl⁻ QTL on chromosome 5A.</b>

a<p>according to MSU Rice Genome Annotation Project release 7, Ensembl Plants release 22 or NCBI;</p>b<p>Genome Zipper v5.</p

<b>QTL associated with Ca²⁺ and Mg²⁺ concentrations in hydroponics and in a field trial (Balaklava) under varying degrees of salinity stress.</b>

<p>Only those intervals with <i>P</i> values ≤0.01 and LOD>2.0 are presented. Balaklava location was classified as moderate salinity. Please see Genc et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098845#pone.0098845-Genc2" target="_blank">[24]</a> for soil salinity classification.</p><p>*Positive and negative values indicate that Berkut and Krichauff alleles increased the phenotypic values, respectively. QTL names with letter C indicate several co-locating markers at those loci.</p

Additional file 8: Table S5. of Diversity in boron toxicity tolerance of Australian barley (Hordeum vulgare L.) genotypes

Barley genotypes included in each (a) HvBot1 allele class and (b) HvNIP2;1 haplotype class, for gene expression analyses data presented in Figs. 1b and 3b, respectively (PDF 301 kb

Additional file 5: Table S3. of Diversity in boron toxicity tolerance of Australian barley (Hordeum vulgare L.) genotypes

Primers, PCR markers and probes used in this study (PDF 350 kb