Overall resemblance of the F1 hybrids to <i>O</i>. <i>sativa</i> (maternal) or <i>O</i>. <i>alta</i> (paternal) parents, in 18 measured physiological or morphological traits under normal and N-limiting conditions.

<p>(<b>A</b>) Bar charts represent physiological or morphological traits, including (a) Cl^- concentration, (b) the ratio of the concentration K⁺ and Na⁺, (c) Chl (a+b) content, (d) whole plant fresh weight, the blue bars represent normal conditions and the orange bars represent N-limiting conditions. Different letters under same conditions represent significant difference among the samples. Capital and small letters denote for normal and N-limiting conditions, respectively. * and ** above the orange column refer to significant (<i>P</i> < 0.05) or extremely significant (<i>P</i> < 0.01) differences (based on LSD test) between the two conditions for a given physiological trait of each sample (i.e., comparisons between each pair of blue and orange columns). Error bars indicate s.d., n (replicates) = 3. (<b>B</b>) The similarities were depicted based on quantification of each of the 18 physiological or morphological traits as described by the methods of Yang et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172919#pone.0172919.ref036" target="_blank">36</a>].</p

Cytology and typical phenotypes of the F1 triploid hybrid plants between <i>Oryza sativa</i> ssp. <i>japonica</i> (<i>2n</i> = 2x = 24, genome AA) and <i>O</i>. <i>alta</i> (<i>2n</i> = 4x = 48, genome, CCDD) under both normal and N-limiting conditions.

<p>(<b>A</b>) Diagrams showing genesis of the F1 triploid rice hybrids; (<b>B</b>) Typical chromosomal constitution of the triploid hybrids based on multicolor GISH analysis (Bar = 10 μm). The pink-colored chromosomes belong to the A genome, green-colored chromosomes are the C genome and blue-colored chromosomes are the D genome; (<b>C</b>) Whole plant dry weight of parental plants (MPVs) and F1 hybrids under normal and N-limiting conditions, WPDW stands for whole plant dry weight. Different letters among genotypes of the same treatment denote statistical differences (based on the least significant difference or LSD test, <i>P</i> < 0.05). The capital and small letters refer to corresponding indices of normal and N-limiting conditions, respectively, Error bars indicate s.d., n (replicates) = 3 to 4; (<b>D-G</b>) The growth rates and whole plant fresh weight of parental plants (MPVs) and F1 hybrids under normal and N-limiting conditions after the treatment for 4 weeks, the blue-dotted lines represent normal conditions and the yellow-dotted lines N-limiting conditions, WPFW stands for whole plant fresh weight, error bars indicate s.d., n (replicates) = 3 to 4; (<b>H</b>) Whole plant phenotypic differences between normal and N-limiting conditions at the final seedling stage (Bar = 10 cm).</p

Hybrid weakness in a rice interspecific hybrid is nitrogen-dependent, and accompanied by changes in gene expression at both total transcript level and parental allele partitioning

<div><p>Background</p><p>Hybrid weakness, a phenomenon opposite to heterosis, refers to inferior growth and development in a hybrid relative to its pure-line parents. Little attention has been paid to the phenomenological or mechanistic aspect of hybrid weakness, probably due to its rare occurrence.</p><p>Methodology/Principal findings</p><p>Here, using a set of interspecific triploid F1 hybrids between <i>Oryza sativa</i>, ssp. <i>japonica</i> (genome AA) and a tetraploid wild rice species, <i>O</i>. <i>alta</i> (genome, CCDD), we investigated the phenotypic and physiological differences between the F1 hybrids and their parents under normal and nitrogen-limiting conditions. We quantified the expression levels of 21 key genes involved in three important pathways pertinent to the assayed phenotypic and physiological traits by real-time qRT-PCR. Further, we assayed expression partitioning of parental alleles for eight genes in the F1 hybrids relative to the <i>in silico</i> “hybrids” (parental cDNA mixture) under both normal and N-limiting conditions by using locus-specific cDNA pyrosequencing.</p><p>Conclusions/Significance</p><p>We report that the F1 hybrids showed weakness in several phenotypic traits at the final seedling-stage compared with their corresponding mid-parent values (MPVs). Nine of the 21 studied genes showed contrasted expression levels between hybrids and parents (MPVs) under normal vs. N-limiting conditions. Interestingly, under N-limiting conditions, the overtly enhanced partitioning of maternal allele expression in the hybrids for eight assayed genes echo their attenuated hybrid weakness in phenotypes, an observation further bolstered by more resemblance of hybrids to the maternal parent under N-limiting conditions compared to normal conditions in a suite of measured physiological traits. Our observations suggest that both overall expression level and differential partitioning of parental alleles of critical genes contribute to condition-specific hybrid weakness.</p></div

Number and percentage (%) of genes showing various expression patterns under normal and N-limiting conditions.

<p>Number and percentage (%) of genes showing various expression patterns under normal and N-limiting conditions.</p

Photosynthetic pigment content from hydrolyzed leaves in parental plants (MPVs), and F1 hybrids under normal and N-limiting conditions.

<p>Pigment contents including: <b>(A)</b> Chl a content, <b>(B)</b> Chl b content, <b>(C)</b> Car content and <b>(D)</b> Chl a/b. Bar charts showing mean values of all replicates in each genotype. Black and while bars represent normal and N-limiting conditions, respectively. Different letters among genotypes of the same treatment denote statistical differences (by least significant difference or LSD test, <i>P</i> < 0.05). The capital and small letters refer to corresponding indices of normal and N-limiting conditions, respectively. Statistical differences in photosynthetic pigment contents for a given genotype between normal and N-limiting conditions are denoted by double asterisks (<i>P</i> < 0.01), error bars indicate s.d., n (replicates) = 9 to 12. (<b>E-F</b>) leaf color difference between parents and F1 hybrids under normal and N-limiting conditions.</p

Density distribution plot showing parental allele expression partitioning for eight analyzed genes by cDNA-pyrosequencing in the F1 hybrids vs. <i>in silico</i> "hybrids" (parental cDNA mix) under normal and N-limiting conditions.

<p>Green and blue lines represent the density of in silico “hybrid” under normal and N-limiting conditions, respectively. Red and pink lines represent the density of F1 hybrid under normal and N-limiting conditions, respectively. X-axis is log₂ of expression ratio between paternal homeolog to maternal homeolog for each tested gene, “0” on x-axis stands for parental homeologs expressed equally. Gene number N = 8, the bandwidth stands for the standard deviation of the kernel and a measure of how closely you want the density to match the distribution, which means when the bandwidth is 0.59, the density curve will be smooth.</p

Number and percentage (%) of genes in the three pathways showing changes in expression pattern in N-limiting versus normal conditions.

<p>Number and percentage (%) of genes in the three pathways showing changes in expression pattern in N-limiting versus normal conditions.</p