Using prokaryote proteomes to identify temperature-sensitive amino acid residues

Presentation of poster 1867A at TAGC 2020 Online. Files include a PDF of the poster (Jensen_TAGC_virtual_poster.pdf) and a 7-minute video walkthrough of the poster material (Jensen_TAGC_posterExplanation.mp3).</div

Quantitative Genetics of the Maize Phyllosphere

Bioinfromatic scripts and key intermediate files for analysis of the maize Phyllosphere from ~300 diverse inbred maize lines grown in Aurora, New York in the summer of 2014. Support dataset for Wallace et al. 2018, "Quantitative genetics of the maize leaf microbiome."Note: v1.1 added scripts used for a simulation analysis requested in revisions.</div

Pearson correlation coefficient between multiple traits.

<p>No clear pattern can be observed between correlation between traits and its association to the 6 bp and 18 bp deletions in <i>d8</i>.</p

Effect estimates in days for NAM subpopulations carrying QTL in the region of <i>d8</i>, <i>p</i>-value<0.05.

<p>Light gray bar shows QTL effect estimate at marker position 116 (RefGen_v2 position: Chr. 1; 231,701,106–231,703,173 bp) (137.6 cM) on the NAM map. Dark gray bar shows QTL effect estimate at marker position 155 (181.3 cM). <i>d8</i> is located closest to marker 135 (RefGen_v2 position: Chr. 1; 269,321,476–269,322,794 bp), (RefGen_v2 position: Chr. 1; 286,977,415–287,063,457 bp), (162.2 cM). * indicates taxa with the 6 bp deletion in <i>d8</i>.</p

LD on chromosome 1 for the subpopulations, Northern Flint (red), stiff stalk (blue), non-stiff stalk (green), tropical (yellow), of the 282 association panel.

<p>White dot indicates median R² for each bin. This graph shows that there is more extended LD in Northern Flint than in other subpopulations.</p

Genetic variance explained by respective model used for the association study.

<p>Genetic variance explained by respective model used for the association study.</p

Genome-wide association results for flowering time.

<p>A. GWAS results for flowering time (days to silking) in the 282 association panel using genotyping by sequencing (GBS) and 55k SNPs. The Q+K mixed linear model was fitted at each SNP to account for population structure (Q) and kinship (K). Genome-wide association results using the naïve model and Q model in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003246#pgen.1003246.s001" target="_blank">Figures S1</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003246#pgen.1003246.s002" target="_blank">S2</a>. B. GWAS results for flowering time (days to silking) using three models in the chromosomal region surrounding <i>tb1</i> (Chr. 1; 265,745,979–265,747,712 bp) and <i>d8</i> (Chr. 1; 266,094,769–266,097,836 bp). All GBS and 55K SNPs between 255 Mb and 270 Mb on Chr. 1 are included in the figure. Brown lines indicate results from naïve model, red lines indicate results from Q model, and blue lines indicate results from Q+K model. C. GWAS results for flowering time (days to silking) using three models in the chromosomal region surrounding <i>tb1</i> (Chr. 1; 265,745,979–265,747,712 bp) and <i>d8</i> (Chr. 1; 266,094,769–266,097,836 bp). All GBS and 55K SNPs between 265 Mb and 267 Mb on Chr. 1 are included in the figure. Black markers on the right are significant SNPs located within <i>d8</i>. Black markers on the left are significant SNPs located within <i>tb1</i>. Triangles indicate results from naïve model, squares indicate results from Q model, and diamonds indicate results from Q+K model.</p

Results from association study between polymorphisms within <i>d8</i> and a range of traits using MLM (Q+K).

<p>Results from association study between polymorphisms within <i>d8</i> and a range of traits using MLM (Q+K).</p

Association between polymorphisms at the <i>d8</i> locus and variation in flowering time in the 92 and 282 association panel, and association between polymorphisms in the region between <i>d8</i> and <i>tb1</i> (<i>d8</i>/<i>tb1</i>) and variation in flowering time in the 282 line association panel.

a<p>A general linear model not controlling for population structure.</p>b<p>A mixed linear model controlling for kinship but not population structure.</p>c<p>A general linear model controlling for population structure (<i>k</i> = 5).</p>d<p>A mixed linear model controlling for both population structure (<i>k</i> = 5) and kinship.</p

R² between the 6 bp indel in <i>d8</i> and all the other sites on chromosome 1.

<p>Blue dots indicate results from 13,815 GBS SNPs present in 200 or more of the 282 lines. Red dots indicate results from 7,695 55K SNPs present in 200 or more of the 282 lines.</p