Quantile-quantile plots of cold tolerance tested in four environments.

<p>Yellow, green, blue and red are for XD2013, YX2013, XD2014 and SM2014, respectively.</p

Principal component analysis of the IB population and its parents.

<p>The first and the second principal components (PC) are shown as x- and y-axis, respectively. Percentages in brackets denote the variance explained by the respective PC. Donors and IB lines are color-coded based on donor’s geographical origins.</p

The physical location of <i>qCT-3-2</i>.

<p>The black colored strip represents chromosome 3 while the grey and white strips indicated the homozygous genotypes of the donor and recurrent parent, respectively. Allele frequency indicated percentage of the alleles derived from HHZ comparing with the entire genome. The phenotypic differences between seven lines were statistically tested using the multiple t-test with Bonferroni adjustment.</p

Manhattan plot of mixed linear model analysis for cold tolerance.

<p>The letters A, B, C and D indicated XD2013, YX2014, XD2014 and SM2014, respectively.</p

Histogram depicting distribution of spikelet fertilities (SF) of the main panicles IB population and the recurrent parent (HHZ) in four cold stress environments.

<p>SF of HHZ is shown with black arrows pointing to the environments.</p

Validation of the major QTL for Al toxicity tolerance by linkage analysis with 11 KASP SNP markers (a), genotype of 93 extremely Al toxicity tolerance (b) and sensitive (c) individuals by SNP1661173, the last three sites were NTC, PR and PS.

<p>Validation of the major QTL for Al toxicity tolerance by linkage analysis with 11 KASP SNP markers (a), genotype of 93 extremely Al toxicity tolerance (b) and sensitive (c) individuals by SNP1661173, the last three sites were NTC, PR and PS.</p

Manhattan plots of QTL for aluminum toxicity tolerance in the whole genome.

<p>Significant SNPs from different conditions are displayed in different colors: control is green, aluminum stress is grey, the ratio of stress to control is red. The associated traits are represented by different symbols: shoot height = triangle up, root length = triangle down, shoot fresh weight = ×, shoot dry weight = square, root dry weight = circle, shoot water content = star.</p

Performance of the two parents and F₂ population after treatment of Al stress.

<p>(a) Phenotypic difference of two parents under control and Al stress conditions. (b-c) Frequency distribution of root length (RL) and shoot height (SH) in the F₂ population derived from the two parents under Al stress condition.</p

QTL identified with significant association to Al toxicity tolerance related traits.

<p>QTL identified with significant association to Al toxicity tolerance related traits.</p

Haplotype analysis in the region of <i>Nrat1</i>.

<p>(a) Haplotypes of <i>Nrat1</i> observed in 327 accessions using 32M SNP data. (b) The performance of root ratio between Al stress to control condition in seven haplotypes.</p