Correlation coefficients for the leaf widths at each position above the uppermost ear in the four RIL populations.

<p>FirLW, width of the first leaf above the uppermost ear; SecLW, width of the second leaf above the uppermost ear; ThiLW, width of the third leaf above the uppermost ear; ForLW, width of the fourth leaf above the uppermost ear. The correlation coefficients above the diagonal line in each quadrant of the table are for the Yu82 × Shen137 and Yu537 × Shen137 recombinant inbred lines, and the correlation coefficients below the diagonal line are for the Yu82 × Yu87-1 and Yu82 × Shen137 recombinant inbred lines.</p><p>*Significant at P = 0.05;</p><p>**significant at P = 0.01.</p><p>Correlation coefficients for the leaf widths at each position above the uppermost ear in the four RIL populations.</p

Meta-QTLs (mQTLs) for leaf-width traits in the four recombinant inbred line (RIL) populations across the three environments.

<p>Meta-QTLs (mQTLs) for leaf-width traits in the four recombinant inbred line (RIL) populations across the three environments.</p

Phenotypic performance of leaf width in five parental lines and four recombinant inbred lines (RILs) across three environments.

<p>Phenotypic performance of leaf width in five parental lines and four recombinant inbred lines (RILs) across three environments.</p

Distribution of single nucleotide polymorphism (SNP) markers in the integrated molecular genetic linkage map.

<p>Distribution of single nucleotide polymorphism (SNP) markers in the integrated molecular genetic linkage map.</p

Genome-Wide Identification and Expression Profiling Analysis of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> Auxin Transporter Gene Families in Maize (<i>Zea mays</i> L.) under Various Abiotic Stresses

<div><p>The auxin influx carriers auxin resistant 1/like aux 1 (AUX/LAX), efflux carriers pin-formed (PIN) (together with PIN-like proteins) and efflux/conditional P-glycoprotein (ABCB) are major protein families involved in auxin polar transport. However, how they function in responses to exogenous auxin and abiotic stresses in maize is largely unknown. In this work, the latest updated maize (<i>Zea mays</i> L.) reference genome sequence was used to characterize and analyze the <i>ZmLAX</i>, <i>ZmPIN</i>, <i>ZmPILS</i> and <i>ZmABCB</i> family genes from maize. The results showed that five <i>ZmLAXs</i>, fifteen <i>ZmPINs</i>, nine <i>ZmPILSs</i> and thirty-five <i>ZmABCBs</i> were mapped on all ten maize chromosomes. Highly diversified gene structures, nonconservative transmembrane helices and tissue-specific expression patterns suggested the possibility of function diversification for these genes. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the expression patterns of <i>ZmLAX</i>, <i>ZmPIN</i>, <i>ZmPILS</i> and <i>ZmABCB</i> genes under exogenous auxin and different environmental stresses. The expression levels of most <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> genes were induced in shoots and were reduced in roots by various abiotic stresses (drought, salt and cold stresses). The opposite expression response patterns indicated the dynamic auxin transport between shoots and roots under abiotic stresses. Analysis of the expression patterns of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> genes under drought, salt and cold treatment may help us to understand the possible roles of maize auxin transporter genes in responses and tolerance to environmental stresses.</p></div

Expression levels of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> gene families in response to cold.

<p>Expression levels of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> genes were analyzed by qRT-PCR in both shoot (A) and roots (B) of 14-day-old seedlings, which were treated with cold (4°C) for 48 hours. The relative expression levels were normalized to a value of 1 in mock seedlings. Error bars represent SD from five biological replicates.</p

Phylogenetic relationship analysis of auxin transporter family between maize, <i>Arabidopsis</i> and rice.

<p>Bootstrap values are presented for all branches. (A) LAX protein family: inventory of AtLAX and OsLAX families is based on TAIR and TIGR rice databases. (B) PIN protein family: sequence data on AtPIN and OsPIN families is based on TAIR annotation and Shen’s publish. (C) PILS protein families: inventory of AtPILS and OsPILS families is listed at <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118751#pone.0118751.s003" target="_blank">S1 Table</a>. (D) ABCB protein family: inventory of AtABCB and OsABCB families is based on the ABC superfamily review by Verrier <i>et al</i>. Different colors indicated different subfamilies. The ortholog genes between maize and <i>Arabidopsis</i> or rice were indicated by green dotted boxes. The paralog genes within maize were indicated by red dotted boxes.</p

Chromosomal distribution and expansion patterns of maize auxin transporter encoding genes.

<p>(A) The genome visualization tool SyMAP Synteny Browser was employed (<a href="http://www.symapdb.org/" target="_blank">http://www.symapdb.org/</a>) to analyze the maize genome. Maize chromosomes were arranged in blocks. Fifteen <i>ZmPIN</i> genes, nine <i>ZmPILS</i> genes, five <i>ZmLAX</i> genes and thirty-five <i>ZmABCB</i> genes were among ten chromosomes. <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX and ZmABCB</i> family genes are mapped by locus and the gene clusters were indicated by red boxes. (B) Gene segmental duplications were showed with dotted arrows.</p

Expression levels of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> gene families in response to salt.

<p>Expression levels of <i>ZmPIN</i>, <i>ZmPILS</i>, <i>ZmLAX</i> and <i>ZmABCB</i> genes were analyzed by qRT-PCR in both shoot (A) and roots (B) of 14-day-old seedlings, which were treated with 150 mM NaCl (salt) for 48 hours. The relative expression levels were normalized to a value of 1 in mock seedlings. Error bars represent SD from five biological replicates.</p

Real-time quantitative RT-PCR (qRT-PCR) analysis of <i>ZmLAX</i>, <i>ZmPIN</i>, <i>ZmPILS</i> and <i>ZmABCB</i> genes in plants under IAA treatment in both shoots (A) and roots (B).

<p>Total RNA was extracted from the seedlings shoots and roots of maize for expression analysis. The histogram shows the relative expression levels of <i>ZmLAX</i>, <i>ZmPIN</i>, <i>ZmPILS</i> and <i>ZmABCB</i> genes under IAA treatment (10 μM, 48 hours) compared to the mock expression level. Untreated seedlings were used as mock seedlings. The relative mRNA level of individual genes was normalized with respect to the <i>ZmACTIN</i> gene (defines as 1). The data were analyzed by five independent repeats, and standard deviations were shown with error bars.</p