Coexpression gene network analysis of cold-tolerant Solanum commersonii reveals new insights in response to low temperatures

AbstractAmong abiotic stressors, cold is one of the most harmful for the cultivated potato (Solanum tuberosum L.), a frost‐sensitive crop. RNA sequencing (RNA‐seq) profiling of two different clones of wild potato (S. commersonii Dun.) contrasting in their capacity to withstand low temperatures revealed a higher number of differentially expressed genes (DEGs) under nonacclimated conditions (NAC) in tolerant clone cmm1T vs. the susceptible cmm6‐6 (1,002 and 8,055 DEGs, respectively). By contrast, the number of DEGs was much more comparable when both genotypes were under acclimated conditions (AC). Indeed, a total of 5,650 and 8,936 DEGs were detected in the tolerant genotype vs. the susceptible. Gene ontology (GO) classification under NAC showed a significant role for transcription regulation, lignin catabolic genes, and regulation of plant type secondary cell wall in the cold‐tolerant genotypes, suggesting an important role in conferring tolerance response. By contrast, response to stress and response to stimuli were enriched GO categories in both clones under AC. Unsigned weighted correlation networks analysis (WGCNA) allowed identification of coexpressed hub genes with possible main regulatory functions and major impacts on the phenotype. Among those identified, we clarified the role of CBF4. This gene showed contrasting expression profiles in the two clones under NAC, being induced in cold‐tolerant cmm1T but suppressed in susceptible cmm6‐6. By contrast, under AC, CBF4 was upregulated in both clones. Our study provides a global understanding of mechanisms involved following exposure to NAC and AC in S. commersonii. The mechanisms described here will inform future investigations for detailed validation in studies regarding cold tolerance in plants

Changes in Disease Resistance Phenotypes Associated With Plant Physiological Age Are Not Caused by Variation in R Gene Transcript Abundance

Foliar late blight is one of the most important diseases of potato. Foliar blight resistance has been shown to change as a plant ages. In other pathosystems, resistance (R) gene transcript levels appear to be correlated to disease resistance. The cloning of the broad-spectrum, foliar blight resistance gene RB provided the opportunity to explore how foliar blight resistance and R-gene transcript levels vary with plant age. Plants of Solanum bulbocastanum PT29, from which RB, including the native promoter and other flanking regions, was cloned, and S. tuberosum cv. Dark Red Norland (nontransformed and RB-transformed) representing three different developmental stages were screened for resistance to late blight and RB transcript levels. Preflowering plants of all genotypes exhibited the highest levels of resistance, followed by postflowering and near-senescing plants. The RB transgene significantly affected resistance, enhancing resistance levels of all RB-containing lines, especially in younger plants. RB transgene transcripts were detected at all plant ages, despite weak correlation with disease resistance. Consistent transcript levels in plants of different physiological ages with variable levels of disease resistance demonstrate that changes in disease-resistance phenotypes associated with plant age cannot be attributed to changes in R-gene transcript abundance

Plant community richness and microbial interactions structure bacterial communities in soil

Abstract. Plant species, plant community diversity and microbial interactions can significantly impact soil microbial communities, yet there are few data on the interactive effects of plant species and plant community diversity on soil bacterial communities. We hypothesized that plant species and plant community diversity affect soil bacterial communities by setting the context in which bacterial interactions occur. Specifically, we examined soil bacterial community composition and diversity in relation to plant ''host'' species, plant community richness, bacterial antagonists, and soil edaphic characteristics. Soil bacterial communities associated with four different prairie plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, and Lupinus perennis) grown in plant communities of increasing species richness (1, 4, 8, and 16 species) were sequenced. Additionally, soils were evaluated for populations of antagonistic bacteria and edaphic characteristics. Plant species effects on soil bacterial community composition were small and depended on plant community richness. In contrast, increasing plant community richness significantly altered soil bacterial community composition and was negatively correlated with bacterial diversity. Concentrations of soil carbon, organic matter, nitrogen, phosphorus, and potassium were similarly negatively correlated with bacterial diversity, whereas the proportion of antagonistic bacteria was positively correlated with soil bacterial diversity. Results suggest that plant species influences on soil bacterial communities depend on plant community diversity and are mediated through the effects of plant-derived resources on antagonistic soil microbes

Higher copy numbers of the potato RB transgene correspond to enhanced transcript and late blight resistance levels.

Late blight of potato ranks among the costliest of crop diseases worldwide. Host resistance offers the best means for controlling late blight, but previously deployed single resistance genes have been short-lived in their effectiveness. The foliar blight resistance gene RB, previously cloned from the wild potato Solanum bulbocastanum, has proven effective in greenhouse tests of transgenic cultivated potato. In this study, we examined the effects of the RB transgene on foliar late blight resistance in transgenic cultivated potato under field production conditions. In a two-year replicated trial, the RB transgene, under the control of its endogenous promoter, provided effective disease resistance in various genetic backgrounds, including commercially prominent potato cultivars, without fungicides. RB copy numbers and transcript levels were estimated with transgene-specific assays. Disease resistance was enhanced as copy numbers and transcript levels increased. The RB gene, like many other disease resistance genes, is constitutively transcribed at low levels. Transgenic potato lines with an estimated 15 copies of the RB transgene maintain high RB transcript levels and were ranked among the most resistant of 57 lines tested. We conclude that even in these ultra–high copy number lines, innate RNA silencing mechanisms have not been fully activated. Our findings suggest resistance-gene transcript levels may have to surpass a threshold before triggering RNA silencing. Strategies for the deployment of RB are discussed in light of the current research

Mapping a Novel Black Spot Resistance Locus in the Climbing Rose Brite Eyes™ (‘RADbrite’)

Rose black spot, caused by Diplocarpon rosae, is one of the most devastating foliar diseases of cultivated roses (Rosa spp.). The globally distributed pathogen has the potential to cause large economic losses in the outdoor cultivation of roses. Fungicides are the primary method to manage the disease, but are often viewed unfavorably by home gardeners due to potential environmental and health impacts. As such, rose cultivars with genetic resistance to black spot are highly desired. The tetraploid climbing rose Brite EyesTM (‘RADbrite’) is known for its resistance to black spot. To better characterize the resistance present in Brite EyesTM, phenotyping was conducted on a 94 individual F1 population developed by crossing Brite EyesTM to the susceptible tetraploid rose ‘Morden Blush’. Brite EyesTM was resistant to all D. rosae races evaluated except for race 12. The progeny were either resistant or susceptible to all races (2, 3, 8, 9, 10, 11, and 13) evaluated. The segregation ratio was 1:1 (χ2 = 0.3830, P = 0.5360) suggesting resistance is conferred by a single locus. The roses were genotyped with the WagRhSNP 68K Axiom array and the ‘polymapR’ package was used to construct a map. A single resistance locus (Rdr4) was identified on the long arm of chromosome 5 homoeolog 4. Three resistance loci have been previously identified (Rdr1, Rdr2, and Rdr3). Both Rdr1 and Rdr2 are located on a chromosome 1 homoeolog. The chromosomal location of Rdr3 is unknown, however, races 3 and 9 are virulent on Rdr3. Rdr4 is either a novel gene or an allele of Rdr3 as it provides resistance to races 3 and 9. Due to its broad resistance, Rdr4 is an excellent gene to introgress into new rose cultivars

Apple skin patterning is associated with differential expression of MYB10

Background: Some apple (Malus × domestica Borkh.) varieties have attractive striping patterns, a quality attribute that is important for determining apple fruit market acceptance. Most apple cultivars (e.g. ‘Royal Gala’) produce fruit with a defined fruit pigment pattern, but in the case of ‘Honeycrisp’ apple, trees can produce fruits of two different kinds: striped and blushed. The causes of this phenomenon are unknown. Results: Here we show that striped areas of ‘Honeycrisp’ and ‘Royal Gala’ are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, nucleotide changes in the promoter and coding sequence of MYB10 do not correlate with skin pattern in ‘Honeycrisp’ and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MYB10 and a 2.5 Kb region 5’ of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Cytosine methylation was present in all three contexts, with higher methylation levels observed for CHH and CHG (where H is A, C or T) than for CG. Comparisons of methylation levels of the MYB10 promoter in ‘Honeycrisp’ red and green stripes indicated that they correlate with peel phenotypes, with an enrichment of methylation observed in green stripes. Conclusions: Differences in anthocyanin levels between red and green stripes can be explained by differential transcript accumulation of MYB10. Different levels of MYB10 transcript in red versus green stripes are inversely associated with methylation levels in the promoter region. Although observed methylation differences are modest, trends are consistent across years and differences are statistically significant. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in ‘Honeycrisp’. We suggest that methylation in the MYB10 promoter is more variable in ‘Honeycrisp’ than in ‘Royal Gala’, leading to more variable color patterns in the peel of this cultivar.https://doi.org/10.1186/1471-2229-11-9

Foliage of the +<i>RB</i> line has a higher frequency of DE genes 24 hpi with <i>Phytophthora infestans</i>.

<p>Foliage samples collected 0, 6, and 24 hpi were subjected to RNA-seq, revealing a total of 475 DE genes between water- and <i>P</i>. <i>infestans-</i>inoculated comparisons within the same genotype and the same time point. (A) All 475 DE genes were analyzed using the “Venn count” function in the limma package of R [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159969#pone.0159969.ref022" target="_blank">22</a>] and results were summarized as a Venn diagram. Red: WT 6 hpi; orange: +<i>RB</i> 6 hpi; blue: WT 24 hpi; green: +<i>RB</i> 24 hpi. The results show that the <i>+RB</i> line is the main contributor of DE genes during water- vs. <i>P</i>. <i>infestans</i>-inoculated comparisons. (B) All 475 DE genes were also assigned to a MapMan ontology based on the Mercator mapping file (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159969#sec002" target="_blank">methods</a>), and subjected to Fisher’s exact test. As described previously [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159969#pone.0159969.ref008" target="_blank">8</a>], bins in red were significantly up-regulated; bins in blue were significantly down-regulated; transcription of bins in white did not change significantly. The results indicate that ontology bins encompassing ET metabolism and stress are enriched for DE genes in <i>+RB</i> but not in WT at 24 hpi.</p

Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen <i>Phytophthora infestans</i>

<div><p>The late blight pathogen <i>Phytophthora infestans</i> can attack both potato foliage and tubers. When inoculated with <i>P</i>. <i>infestans</i>, foliage of nontransformed ‘Russet Burbank’ (WT) develops late blight disease while that of transgenic ‘Russet Burbank’ line SP2211 (+<i>RB</i>) does not. We compared the foliar transcriptome responses of these two lines to <i>P</i>. <i>infestans</i> inoculation using an RNA-seq approach. A total of 515 million paired end RNA-seq reads were generated, representing the transcription of 29,970 genes. We also compared the differences and similarities of defense mechanisms against <i>P</i>. <i>infestans</i> in potato foliage and tubers. Differentially expressed genes, gene groups and ontology bins were identified to show similarities and differences in foliage and tuber defense mechanisms. Our results suggest that <i>R</i> gene dosage and shared biochemical pathways (such as ethylene and stress bins) contribute to <i>RB</i>-mediated incompatible potato-<i>P</i>. <i>infestans</i> interactions in both the foliage and tubers. Certain ontology bins such as cell wall and lipid metabolisms are potentially organ-specific.</p></div