Chromosome map.

<p>Chromosomes 9 and 10 are not pictured, as we found no QTL on these chromosomes. Chromosome number is indicated at the top of each chromosome. QTL positions and candidate gene positions from Truntzler <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145845#pone.0145845.ref039" target="_blank">39</a>] are indicated on the right side of each chromosome. QTL indicated as groups contained 4 or more individual QTL in the same region. Individual QTL contained within groups are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145845#pone.0145845.g002" target="_blank">Fig 2</a>. QTL names in <b><i>bold italics</i></b> indicate a higher area % value for the B73 allele, with regularly formatted text indicating a higher area % for the Mo17 allele.</p

Expanded chromosome map.

<p>Close up view of QTL Groups A through G. Group name from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145845#pone.0145845.g001" target="_blank">Fig 1</a> is shown at the top of the chromosome with the chromosome number indicated in parentheses. QTL names in <b><i>bold italics</i></b> indicate a higher area % value for the B73 allele, with regularly formatted text indicating a higher area % for the Mo17 allele.</p

IBM Data 20151011.xlsx

chromatogram data from Py/GC-MS measurement of IBM Syn4 maize population

Data from Mayer et.al 2017 TAG

This data package accompanies the following publication:<br><br>Mayer et al. 2017 (Theoretical and Applied Genetics)<br>Is there an optimum level of diversity in utilization of genetic resources?<div>doi:10.1007/s00122-017-2959-4<br><br>It contains a copy of the data files used in this paper as well as further accompanying files (see README.txt).<br></div

Distribution of genes in the maize seedling core and dispensable transcriptomes determined using a semi-qualitative approach.

<p>Reads were mapped to the 5b pseudomolecules (<a href="http://ftp.maizesequence.org/" target="_blank">http://ftp.maizesequence.org/</a>) using Bowtie version 0.12.7 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Langmead1" target="_blank">[50]</a> and TopHat version 1.2.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Trapnell1" target="_blank">[51]</a>, and fragments per kilobase of exon model per million fragments mapped (FPKM) were determined with Cufflinks version 0.9.3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Trapnell2" target="_blank">[56]</a> and the 5b annotation (<a href="http://ftp.maizesequence.org/" target="_blank">http://ftp.maizesequence.org/</a>).For each gene, a line was considered not expressed if the low confidence FPKM value was equal to zero, low expressed if the low confidence interval was greater than zero and the FPKM value was less than 5, medium expressed if the low confidence interval was greater than zero and the FPKM value was greater than or equal to 5 and less than or equal to 200, and high expressed if the low confidence interval was greater than zero and the FPKM value was greater than 200.</p

Read mapping, expression, and single nucleotide polymorphism (SNP) summary for 21 diverse maize lines.

<p>Reads were mapped requiring a unique hit for the SNPs and multiple hits for fragments per kilobase of exon model per million fragments mapped (FPKM) and mapping to the pseudomolecules plus the Velvet and Oases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Zerbino1" target="_blank">[45]</a> assembled transcripts. FPKM values were calculated using Cufflinks <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Trapnell2" target="_blank">[56]</a>. Genes with a FPKM 95% confidence interval lower boundary greater than zero were considered expressed. For each inbred line, a gene was considered to have SNP coverage if there was at least one polymorphic locus with coverage in the gene. SSS = Stiff Stalk Synthetic, NSS = Non-Stiff Stalk Synthetic, NA = Not applicable.</p

Neighbor-Joining tree of 21 diverse maize lines based on 351,710 single nucleotide polymorphisms (SNPs).

<p>Frequency based distances were calculated as pair-wise Rogers distances <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Rogers1" target="_blank">[53]</a>. PowerMarker version 3.25 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Liu2" target="_blank">[54]</a> was used to construct the tree.</p

Distribution of the number of single nucleotide polymorphisms (SNPs) and SNP density per gene.

<p>Reads were mapped against the 5b pseudomolecules (<a href="http://ftp.maizesequence.org/" target="_blank">http://ftp.maizesequence.org/</a>) with Bowtie version 0.12.7 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Langmead1" target="_blank">[50]</a> and TopHat version 1.2.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Trapnell1" target="_blank">[51]</a> requiring a unique hit for the SNP mapping. Gene assignment was determined based on the 5b annotation (<a href="http://ftp.maizesequence.org/" target="_blank">http://ftp.maizesequence.org/</a>), and not all SNPs identified were assigned to a gene model. (A) Distribution of the number of SNPs per gene. (B) Distribution of the average number of SNPs per 100 bp window per gene.</p

Frequency of novel <i>de novo</i> assembled transcripts across lines and heterotic groups.

<p>Reads were mapped to the 5b pseudomolecules plus assembled novel transcripts with Bowtie version 0.12.7 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Langmead1" target="_blank">[50]</a> and TopHat version 1.2.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Trapnell1" target="_blank">[51]</a>. Novel transcripts from unmapped reads were assembled using Velvet version 1.0.17 and Oases version 0.1.18 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033071#pone.0033071-Zerbino1" target="_blank">[45]</a>. (A) Distribution of the number of inbred lines with read support for each novel <i>de novo</i> assembled transcript requiring unique alignments and allowing for multiple mapping. (B) Venn diagram of shared and group specific novel <i>de novo</i> assembled transcripts. (C) Venn diagram of shared and group specific novel <i>de novo</i> assembled transcripts and transcripts from the 5b annotated genes (<a href="http://ftp.maizesequence.org/" target="_blank">http://ftp.maizesequence.org/</a>).</p

Comparison of RNA-Seq and microarray co-expression networks.

<p>(A) The density of Fisher-transformed and normalized edge weights are shown for both the microarray (y-axis) and RNA-Seq (x-axis) co-expression networks. (B) The frequency of correlation coefficient (R) values for a series of 1000 random co-expression networks is plotted relative to the observed value (red arrow). The random co-expression networks were generated by selecting a mixture of RNA-Seq and microarray data for each of the two networks.</p