Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq

Payá‐Milans, Miriam; Nunez, Gerardo H.; Olmstead, James W.; Rinehart, Timothy A.; Staton, Margaret

doi:10.1186/s12864-017-3967-0

Cited by 20 publications

(20 citation statements)

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“…The statistical dispersion of the data in sand was much greater than in CF. These results can be justified by the recent results published by Pay a- Milans et al (2017), who indicated there are wild species of Vaccinium arboreum that are capable of adapting to a wider range of soil pH. As our data are only from one cultivar, it would be advisable to perform these same studies in several cultivars of blueberry species.…”

Section: Expt 2: Ph Of the Nutrient Solution/ Parameters Of Fertigatmentioning

confidence: 61%

Effect of pH and Silicon in the Fertigation Solution on Vegetative Growth of Blueberry Plants in Organic Agriculture

Gallegos-Cedillo¹,

Álvaro²,

Capatos³

et al. 2018

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The effect of pH and silicon (Si) in the nutrient solution on the vegetative development of 2-year-old blueberry plants (Vaccinium corymbosum L. cv. Ventura) was studied. Two independent experiments were performed on coir fiber (CF) and sand as substrates. In experiment 1, Si was applied in the nutrient solution at a dose of 0.0, 0.3, 0.6, and 1.2 mM. In experiment 2, plants were treated with nutrient solution at pH 4.00, 4.75, 5.50, and 6.25, using two sources of acidification: nitric acid and citric acid. The parameters of plant growth, foliar surface, and stem biomass were measured. With the application of 1.2 mM Si to CF, plant height registered a significant increase of 8%, and shoot dry and fresh biomass increased by 21% and 25%, respectively. The results of experiment 1 indicated that the application of Si benefits the vegetative growth of blueberry plants in CF, but no effect was observed in the sand substrate. In the results of experiment 2, the pH level of 6.25 in CF decreased the dry weight of stems and leaves by 21% and 18%, respectively. A significant increase in the pH range of 4.00 to 5.50 was recorded in both the citric acid and nitric acid treatments, but these significant effects were not found in sand. Citric acid presented a similar behavior to nitric acid, which indicates that it can be a good source of acidification in organic and ecologically friendly crops.

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Section: Expt 2: Ph Of the Nutrient Solution/ Parameters Of Fertigatmentioning

confidence: 61%

Effect of pH and Silicon in the Fertigation Solution on Vegetative Growth of Blueberry Plants in Organic Agriculture

Gallegos-Cedillo¹,

Álvaro²,

Capatos³

et al. 2018

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“…Preparation of RNA-seq libraries from root tissue of diploid V. arboreum cultivar FL148 and tetraploid V. corymbosum “Emerald” blueberry species are previously described [ 25 ] and available in NCBI as bioproject PRJNA353989. Briefly, eight plants per species were acclimated to growth in hydroponic systems at either pH 4.5 or pH 6.5 for 8 weeks, after which roots were collected and flash frozen.…”

Section: Methodsmentioning

confidence: 99%

“…The sequencing data used in this work is 270 million Illumina paired-end reads (2*101 bp long) for diploid VA and 582 million reads for tetraploid VC, originating from eight plants each [ 25 ] and sequenced on duplicate lanes. Libraries were prepared from RNA collected from roots of plants of similar age after eight weeks of growth in hydroponic systems under either stressful (pH 6.5) or control (pH 4.5) conditions.…”

Section: Data Descriptionmentioning

confidence: 99%

“…When using a distant genome, sequence divergence between reads and the reference genome may compromise results; nucleotide mismatches are more likely to decrease the number of mapped reads, while indels are usually better tolerated with gapped alignments [ 2 ]. One benefit from the utilization of a distant genome is a direct comparison of gene expression results from multiple related species [ 25 ]. On the other hand, utilization of de novo assemblies avoids the mapping issues to a distant genome and also captures divergent and novel genes useful for species-specific discovery of new functions.…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

et al. 2018

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BackgroundThe usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis.FindingsAt the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads could be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality, and completeness of de novo assemblies and with number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP.ConclusionsThe selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.

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“…Plants in family Ericaceae (i.e., acid-loving plants) thrive in acidic soils (pH 4.2-5.5) where NH 4 + is the most abundant form of N (Marrs and Bannister, 1978). When acid-loving plants are grown in neutral or high-pH soils, they exhibit stress, nutritional deficiencies, stunted growth, and low survival (Finn et al, 1993;Marrs and Bannister, 1978;Paya-Milans et al, 2017;Tsuda et al, 2014). Acidic soils are rare in agricultural and landscape settings.…”

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confidence: 99%

Ammonium Uptake Is the Main Driver of Rhizosphere pH in Southern Highbush Blueberry

Imler¹,

Arzola²,

Nunez³

2019

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Unlike most horticultural crops, blueberry (Vaccinium spp. section cyanococcus) prefers low-pH (4.2–5.5) soils. Other plants can acidify their rhizosphere to create a hospitable microenvironment. Southern highbush blueberry (SHB; Vaccinium corymbosum interspecific hybrids) plants do not acidify their rhizosphere in response to Fe deficiency, but other factors that affect rhizosphere pH have not been elucidated. We report results from two hydroponic experiments exploring N uptake effects on the rhizosphere pH of ‘Emerald’ SHB. Ammonium (NH4+) uptake led to rhizosphere acidification, whereas nitrate (NO3–) uptake led to rhizosphere alkalization. When grown in a split-root hydroponic system, roots that took up NH4+ acidified the rhizosphere to a greater extent that roots not exposed to NH4+. Rhizosphere acidification was observed even in a nontreated control. These results suggest that NH4+ uptake is the main driver of rhizosphere pH in SHB. N form effects suggest that fertilization with NO3– might lead to undesirable rhizosphere alkalization.

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Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq

Cited by 20 publications

References 84 publications

Effect of pH and Silicon in the Fertigation Solution on Vegetative Growth of Blueberry Plants in Organic Agriculture

Effect of pH and Silicon in the Fertigation Solution on Vegetative Growth of Blueberry Plants in Organic Agriculture

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

Ammonium Uptake Is the Main Driver of Rhizosphere pH in Southern Highbush Blueberry

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