Publications by authors named "Piergiorgio Stevanato"

34 Publications

Novel Effects of Leonardite-Based Applications on Sugar Beet.

Front Plant Sci 2021 18;12:646025. Epub 2021 Mar 18.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy.

The present study aimed to explore the effects of foliar application of a leonardite-based product on sugar beet ( L.) plants grown in the field. The approach concerned the evaluation of the community compositional structure of plant endophytic bacteria through a metabarcoding approach, the expression level of a gene panel related to hormonal metabolism and signaling, and the main sugar beet productivity traits. Results indicated that plants treated with leonardite (dosage of 2,000 ml ha, dilution 1:125, 4 mg C l) compared with untreated ones had a significant increase ( < 0.05) in (i) the abundance of spp., recognized to be an endophyte bacterial genus with plant growth-promoting activity; (ii) the expression level of gene, coding for auxin transport proteins; and (iii) sugar yield. This study represents a step forward to advance our understanding of the changes induced by leonardite-based biostimulant in sugar beet.
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http://dx.doi.org/10.3389/fpls.2021.646025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8013720PMC
March 2021

Quantification of rhizomania virus by automated RNA isolation and PCR based methods in sugar beet.

Virusdisease 2021 Mar 19:1-6. Epub 2021 Mar 19.

DAFNAE, Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università Degli Studi Di Padova, Viale dell'Università 16, 35020 Legnaro, PD Italy.

Rhizomania is a grave disease affecting sugar beet ( L.). It is caused by the Beet Necrotic Yellow Vein Virus (BNYVV), an RNA virus transmitted by the plasmodiophorid vector . Genetic resistance to the virus has been accomplished mostly using phenotype-genotype association studies. As yet, the most convenient method to ascertain plant resistance has been the quantification of viral titer in roots through the ELISA test. This method is particularly time-consuming and clashes with the necessities of modern plant breeding. Here, we propose an alternative and successful phenotyping method based on the automatic extraction of the viral RNA from sugar beet roots and its relative and absolute quantification by quantitative real-time PCR (qRT-PCR) and digital PCR (dPCR), respectively. Such a method enables an improved standardization of the study, as well as an accurate quantification of the virus also in those samples presenting low virus titer, with respect to the ELISA test.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-021-00674-7.
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http://dx.doi.org/10.1007/s13337-021-00674-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7976688PMC
March 2021

Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity.

Microorganisms 2021 Feb 16;9(2). Epub 2021 Feb 16.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy.

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.
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http://dx.doi.org/10.3390/microorganisms9020407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920277PMC
February 2021

Green walls to treat kitchen greywater in urban areas: Performance from a pilot-scale experiment.

Sci Total Environ 2021 Feb 4;757:144189. Epub 2020 Dec 4.

Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy.

An increase in water use in urban areas is forcing scientists and policy makers to find alternative solutions for freshwater management, aimed at attaining integrated water resources management. Here, we tested in a 2-year experiment (June 2017-April 2019) the treatment performance of an innovative wall cascade constructed wetland (WCCW) system. The aim was to combine the multifunctional benefits of green walls (e.g. aesthetic, surface area requirements) with those of constructed wetland systems (e.g. high pollutants removal efficiencies, water recycling) to treat kitchen greywaters. The WCCW was a terraced system of six phytoremediation lines, each of which was composed of three plastic tanks (3 × 0.04 m), filled with lightweight porous media, and vegetated with different ornamental species, namely Mentha aquatica L., Oenanthe javanica (Blume) DC., and Lysimachia nummularia L. Physicochemical (temperature, pH, electrical conductivity, dissolved oxygen, turbidity) and chemical parameters (chemical oxygen demand, biochemical oxygen demand, anionic surfactants, Kjeldahl, ammonium and nitric nitrogen, total orthophosphate) were monitored at a frequency of at least 15 days, depending on the season and WCCW management. Results showed that the WCCW significantly reduced the main water pollutants (e.g. organic compounds, nutrients), suggesting its potential application in urban environments for water recycling in the context of green infrastructures and ecological sanitation. A culture-independent taxonomic assessment of suspended bacterial communities before and after the treatment showed clear treatment-related shifts, being the functional ecology attributes changed according to changes in greywater chemical parameters. Future research should attempt to optimize the WCCW system management by regulating the nutrients balance to avoid macronutrients deficiency, and setting the most suitable water flow dynamics (hydraulic retention time, saturation-desaturation cycles) to improve the greywater treatment.
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http://dx.doi.org/10.1016/j.scitotenv.2020.144189DOI Listing
February 2021

Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, .

Front Plant Sci 2020 11;11:579529. Epub 2020 Nov 11.

Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India.

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Toward this end, our lab had initiated sequencing the genome of (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman (A.hyp.V.2.1). The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly . A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.
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http://dx.doi.org/10.3389/fpls.2020.579529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686145PMC
November 2020

Physiological and Transcriptome Analysis of Sugar Beet Reveals Different Mechanisms of Response to Neutral Salt and Alkaline Salt Stresses.

Front Plant Sci 2020 19;11:571864. Epub 2020 Oct 19.

Heilongjiang Sugar Beet Center of Technology Innovation, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China.

The salinization and alkalization of soil are widespread environmental problems. Sugar beet ( L.) is a moderately salt tolerant glycophyte, but little is known about the different mechanisms of sugar beet response to salt and alkaline stresses. The aim of this study was to investigate the influence of neutral salt (NaCl:NaSO, 1:1) and alkaline salt (NaCO) treatment on physiological and transcriptome changes in sugar beet. We found that a low level of neutral salt (NaCl:NaSO; 1:1, Na 25 mM) or alkaline salt (NaCO, Na 25 mM) significantly enhanced total biomass, leaf area and photosynthesis indictors in sugar beet. Under a high concentration of alkaline salt (NaCO, Na 100 mM), the growth of plants was not significantly affected compared with the control. But a high level of neutral salt (NaCl: NaSO; 1:1, Na 100 mM) significantly inhibited plant growth and photosynthesis. Furthermore, sugar beet tends to synthesize higher levels of soluble sugar and reducing sugar to cope with high neutral salt stress, and more drastic changes in indole acetic acid (IAA) and abscisic acid (ABA) contents were detected. We used next-generation RNA-Seq technique to analyze transcriptional changes under neutral salt and alkaline salt treatment in sugar beet. Overall, 4,773 and 2,251 differentially expressed genes (DEGs) were identified in leaves and roots, respectively. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that genes involving cutin, suberine and wax biosynthesis, sesquiterpenoid and triterpenoid biosynthesis and flavonoid biosynthesis had simultaneously changed expression under low neutral salt or alkaline salt, so these genes may be related to stimulating sugar beet growth in both low salt treatments. Genes enriched in monoterpenoid biosynthesis, amino acids metabolism and starch and sucrose metabolism were specifically regulated to respond to the high alkaline salt. Meanwhile, compared with high alkaline salt, high neutral salt induced the expression change of genes involved in DNA replication, and decreased the expression of genes participating in cutin, suberine and wax biosynthesis, and linoleic acid metabolism. These results indicate the presence of different mechanisms responsible for sugar beet responses to neutral salt and alkaline salt stresses.
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http://dx.doi.org/10.3389/fpls.2020.571864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7604294PMC
October 2020

Effect of Microalgal Extracts from and on Germination of Seeds.

Plants (Basel) 2020 May 26;9(6). Epub 2020 May 26.

Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.

Sugar beet ( subsp. ) is a commercially important biennial root crop, providing about 20% of the world's annual sugar production. Seed quality is crucial for adequate plant growth and production. The productivity of sugar beet is often limited by heterogeneous germination in the field. In order to improve the sugar beet germination process, the effect of different concentrations of microalgal extracts from or was investigated by calculating several indices useful to evaluate the germination performance. Moreover, root morphological analysis was performed by using WinRHIZO software. seeds were soaked with five different concentrations (from 0.1 to 10 mg C/L) of the microalgal extracts, considering the amount of organic carbon (C) in each extract. Our results show that these microalgal extracts exert a positive effect on sugar beet germination, by increasing efficiency and regularity of this critical process for seeds. The best results, in terms of germination indices as well as root morphological traits, were reached by using extract at the concentrations C2 (1 mg C/L) and C3 (2 mg C/L).
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http://dx.doi.org/10.3390/plants9060675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355607PMC
May 2020

The hidden layers of microbial community structure: extracting the concealed diversity dimensions from our sequencing data.

FEMS Microbiol Lett 2020 06;367(11)

Department of Agronomy, Animals, Food, Natural Resources and Environment DAFNAE, University of Padova, Viale dell'Università, 16, 35020 Legnaro, PD, Italy.

Microbial metabarcoding is the standard approach to assess communities' diversity. However reports are often limited to simple OTU abundances for each phylum, giving rather one-dimensional views of microbial assemblages, overlooking other accessible aspects. The first is masked by databases incompleteness; OTU picking involves clustering at 97% (near-species) sequence identity, but different OTUs regularly end up under a same taxon name. When expressing diversity as number of obtained taxonomical names, a large portion of the real diversity lying within the data remains underestimated. Using the 16S sequencing results of an environmental transect across a gradient of 17 coastal habitats we first extracted the number of OTUs hidden under the same name. Further, we observed which was the deepest rank yielded by annotation, revealing for which microbial groups are we missing most knowledge. Data were then used to infer an evolutionary aspect: what is, in each phylum the success of the present time individuals (abundances for each OTU) in relation to their prior evolutionary success in differentiation (number of OTUs). This information reveals whether the past speciation/diversification force is matched by the present competitiveness in reproduction/persistence. The final layer explored is functional diversity, i.e. abundances of groups involved in specific environmental processes.
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http://dx.doi.org/10.1093/femsle/fnaa086DOI Listing
June 2020

Germination Data Analysis by Time-to-Event Approaches.

Plants (Basel) 2020 May 12;9(5). Epub 2020 May 12.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy.

Germination data are analyzed by several methods, which can be mainly classified as germination indexes and traditional regression techniques to fit non-linear parametric functions to the temporal sequence of cumulative germination. However, due to the nature of germination data, often different from other biological data, the abovementioned methods may present some limits, especially when ungerminated seeds are present at the end of an experiment. A class of methods that could allow addressing these issues is represented by the so-called "time-to-event analysis", better known in other scientific fields as "survival analysis" or "reliability analysis". There is relatively little literature about the application of these methods to germination data, and some reviews dealt only with parts of the possible approaches such as either non-parametric and semi-parametric or parametric ones. The present study aims to give a contribution to the knowledge about the reliability of these methods by assessing all the main approaches to the same germination data provided by sugar beet ( L.) seeds cohorts. The results obtained confirmed that although the different approaches present advantages and disadvantages, they could generally represent a valuable tool to analyze germination data providing parameters whose usefulness depends on the purpose of the research.
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http://dx.doi.org/10.3390/plants9050617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285257PMC
May 2020

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive ( L.).

Genes (Basel) 2020 04 23;11(4). Epub 2020 Apr 23.

Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro PD, Italy.

The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive ( L.) breeding lines, 18 from var. (escarole) and 14 from var. (curly), using heterologous -derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce ( L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of , subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.
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http://dx.doi.org/10.3390/genes11040462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231076PMC
April 2020

Weed Seed Decay in No-Till Field and Planted Riparian Buffer Zone.

Plants (Basel) 2020 Mar 1;9(3). Epub 2020 Mar 1.

Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35020 Legnaro (PD), Italy.

Field management practices can alter the physical and chemical properties of the soil, also causing changes to the seed bank. Alterations can also occur to the soil microbial community, which in turn can increase or diminish the process of weed seed decay. In this research, the issue of seed degradation was studied in an undisturbed and a no-till soil, trying not only to uncover where seeds are more degraded, but also to investigate the microbial activities that could be involved in this process. Six different weed species, commonly found in northern Italy, were used: and . Seed decay was tested in two different sites, a no-till field and the adjacent buffer zone. Soil microbial activity was also measured using the Fertimetro, an approach based on the degradation of cotton and silk threads buried in the soil for one week. Degradation of the buried seeds was higher in the no-till field soil than in the buffer strip for all the studied species as was the microbial cellulolytic activity. Even though the buffer strip soil is an undisturbed habitat and resulted as having higher organic matter, the no-till soil conditions appeared more unfavourable to seed viability. Our findings suggest that no-till management can improve weed seed suppression in the soil. Moreover, cellulolytic microorganisms play an important role in seedbank longevity, so cellulolytic activity surveys could be used as an early monitoring bioindicator for weed seed suppression in soil.
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http://dx.doi.org/10.3390/plants9030293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154824PMC
March 2020

Transcriptome Analysis of Salt-Sensitive and Tolerant Genotypes Reveals Salt-Tolerance Metabolic Pathways in Sugar Beet.

Int J Mol Sci 2019 Nov 25;20(23). Epub 2019 Nov 25.

Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Crop Academy of Heilongjiang University, Heilongjiang University, Harbin 150080, China.

Soil salinization is a common environmental problem that seriously affects the yield and quality of crops. Sugar beet ( L.), one of the main sugar crops in the world, shows a strong tolerance to salt stress. To decipher the molecular mechanism of sugar beet under salt stress, we conducted transcriptomic analyses of two contrasting sugar beet genotypes. To the best of our knowledge, this is the first comparison of salt-response transcriptomes in sugar beet with contrasting genotypes. Compared to the salt-sensitive cultivar (S710), the salt-tolerant one (T710MU) showed better growth and exhibited a higher chlorophyll content, higher antioxidant enzyme activity, and increased levels of osmotic adjustment molecules. Based on a high-throughput experimental system, 1714 differentially expressed genes were identified in the leaves of the salt-sensitive genotype, and 2912 in the salt-tolerant one. Many of the differentially expressed genes were involved in stress and defense responses, metabolic processes, signal transduction, transport processes, and cell wall synthesis. Moreover, expression patterns of several genes differed between the two cultivars in response to salt stress, and several key pathways involved in determining the salt tolerance of sugar beet, were identified. Our results revealed the mechanism of salt tolerance in sugar beet and provided potential metabolic pathways and gene markers for growing salt-tolerant cultivars.
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http://dx.doi.org/10.3390/ijms20235910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928841PMC
November 2019

Expression Profiling of Candidate Genes in Sugar Beet Leaves Treated with Leonardite-Based Biostimulant.

High Throughput 2019 Oct 11;8(4). Epub 2019 Oct 11.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro (PD), Italy.

Leonardite-based biostimulants are a large class of compounds, including humic acid substances. Foliar application of biostimulants at field level improves plant growth, yield and quality through metabolic changes and stimulation of plant proton pumps. The present study aimed at identifying optimum dosage of BLACKJAK, a humic acid-based substance, which is able to modify genes involved in sugar beet growth. Thirty-three genes belonging to various biochemical pathway categories were tested in leaves of treated sugar beet ( L.) samples to assess gene expression profiling in response to BLACKJAK. Seedlings of a diploid and multigerm variety were grown in plastic pots and sprayed with two dilutions of BLACKJAK (dilution 1:500-1.0 mg C L and dilution 1:1000-0.5 mg C L). Leaf samples were collected after 24, 48, and 72 h treatment with BLACKJAK for each dilution. RNA was extracted and the quantification of gene expression was performed while using an OpenArray platform. Results of analysis of variance demonstrated that, 15 genes out of a total of 33 genes tested with OpenArray qPCR were significantly affected by treatment and exposure time. Analysis for annotation of gene products and pathways revealed that genes belonging to the mitochondrial respiratory pathways, nitrogen and hormone metabolisms, and nutrient uptake were up-regulated in the BLACKJAK treated samples. Among the up-regulated genes, Bv_PHT2;1 and Bv_GLN1 expression exerted a 2-fold change in 1:1000 and 1:500 BLACKJAK concentrations. Overall, the gene expression data in the BLACKJAK treated leaves demonstrated the induction of plant growth-related genes that were contributed almost to amino acid and nitrogen metabolism, plant defense system, and plant growth.
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http://dx.doi.org/10.3390/ht8040018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6970231PMC
October 2019

QuantStudio 12K Flex OpenArray System as a Tool for High-Throughput Genotyping and Gene Expression Analysis.

Methods Mol Biol 2020 ;2065:199-208

DAFNAE, Università Degli Studi di Padova, Legnaro (PD), Italy.

Real time technology provides great advancements over PCR-based methods for a broad range of applications. With the increased availability of sequencing information, there is a need for the development and application of high-throughput real time PCR genotyping and gene expression methods that significantly broaden the current screening capabilities. Thermo Fisher Scientific (USA) has released a platform (QuantStudio™ 12K Flex system coupled with OpenArray technology) with key elements required for high-throughput SNP genotyping and gene expression analysis. This allows for a rapid screening of large numbers of TaqMan assays (up to 256) in many samples (up to 480) per run. This advanced real-time method involves the use of an array composed of 3,000 through-holes running on the QuantStudio™ 12K with OpenArray block. The aim of this chapter is to outline the OpenArray approach while providing a comprehensive in-depth review of the scientific literature on this topic. In agreement with a large number of independent studies, we conclude that the use of OpenArray technology is a rapid and accurate method for high-throughput and large-scale systems biology studies with high specificity and sensitivity.
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http://dx.doi.org/10.1007/978-1-4939-9833-3_15DOI Listing
December 2020

Identification and validation of SNP markers linked to seed toxicity in Jatropha curcas L.

Sci Rep 2019 07 15;9(1):10220. Epub 2019 Jul 15.

DAFNAE, Università degli Studi di Padova, Legnaro, Italy.

Edible/non-toxic varieties of Jatropha curcas L. are gaining increasing attention, providing both oil as biofuel feedstock or even as edible oil and the seed kernel meal as animal feed ingredient. They are a viable alternative to the limitation posed by the presence of phorbol esters in toxic varieties. Accurate genotyping of toxic/non-toxic accessions is critical to breeding management. The aim of this study was to identify SNP markers linked to seed toxicity in J. curcas. For SNP discovery, NGS technology was used to sequence the whole genomes of a toxic and non-toxic parent along with a bulk of 51 toxic and 30 non-toxic F plants. To ascertain the association between SNP markers and seed toxicity trait, candidate SNPs were genotyped on 672 individuals segregating for seed toxicity and two collections of J. curcas composed of 96 individuals each. In silico SNP discovery approaches led to the identification of 64 candidate SNPs discriminating non-toxic and toxic samples. These SNPs were mapped on Chromosome 8 within the Linkage Group 8 previously identified as a genomic region important for phorbol ester biosynthesis. The association study identified two new SNPs, SNP_J22 and SNP_J24 significantly linked to low toxicity with R values of 0.75 and 0.54, respectively. Our study released two valuable SNP markers for high-throughput, marker-assisted breeding of seed toxicity in J. curcas.
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http://dx.doi.org/10.1038/s41598-019-46698-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629616PMC
July 2019

Molecular and Morphological Changes Induced by Leonardite-based Biostimulant in L.

Plants (Basel) 2019 Jun 18;8(6). Epub 2019 Jun 18.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.

Humic substances extracted from leonardite are widely considered to be bioactive compounds, influencing the whole-plant physiology and the crop yield. The aim of this work was to evaluate the effect of a new formulate based on leonardite in the early stage of growth of sugar beet ( L.). A commercial preparation of leonardite (BLACKJAK) was characterized by ionomic analysis, solid-state C MAS NMR spectroscopy. Seedlings of sugar beet were grown in Hoagland's solution under controlled conditions. After five days of growth, an aliquot of the concentrated BLACKJAK was added to the solution to obtain a final dilution of 1:1000 (0.5 mg C L). The sugar beet response in the early stage of growth was determined by evaluating root morphological traits as well as the changes in the expression of 53 genes related to key morphophysiological processes. Root morphological traits, such as total root length, fine root length (average diameter < 0.5 mm), and number of root tips, were significantly < 0.001) increased in plants treated with BLACKJAK, compared to the untreated plants at all sampling times. At the molecular level, BLACKJAK treatment upregulated many of the evaluated genes. Moreover, both Real Time PCR and digital PCR showed that genes involved in hormonal response, such as PIN, ARF3, LOGL 10, GID1, and BRI1, were significantly 0.05) upregulated by treatment with BLACKJAK. Our study provides essential information to understand the effect of a leonardite-based formulate on plant growth hormone metabolism, although the molecular and physiological basis for these complicated regulatory mechanisms deserve further investigations.
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http://dx.doi.org/10.3390/plants8060181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630732PMC
June 2019

Comparative Physiological and Proteomic Analysis of Two Sugar Beet Genotypes with Contrasting Salt Tolerance.

J Agric Food Chem 2019 May 16;67(21):6056-6073. Epub 2019 May 16.

DAFNAE, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente , Università degli Studi di Padova , Viale dell'Università 16 , Legnaro, Padova 35020 , Italy.

Soil salinity is one of the major constraints affecting agricultural production and crop yield. A detailed understanding of the underlying physiological and molecular mechanisms of the different genotypic salt tolerance response in crops under salinity is therefore a prerequisite for enhancing this tolerance. In this study, we explored the changes in physiological and proteome profiles of salt-sensitive (S210) and salt-tolerant (T510) sugar beet cultivars in response to salt stress. T510 showed better growth status, higher antioxidant enzymes activities and proline level, less Na accumulation, and lower P levels after salt-stress treatments. With iTRAQ-based comparative proteomics method, 47 and 56 differentially expressed proteins were identified in the roots and leaves of S210, respectively. In T510, 56 and 50 proteins changed significantly in the roots and leaves of T510, respectively. These proteins were found to be involved in multiple aspects of functions such as photosynthesis, metabolism, stress and defense, protein synthesis, and signal transduction. Our proteome results indicated that sensitive and tolerant sugar beet cultivars respond differently to salt stress. The proteins that were mapped to the protein modification, amino acid metabolism, tricarboxylic acid cycle, cell wall synthesis, and reactive oxygen species scavenging changed differently between the sensitive and tolerant cultivars, suggesting that these pathways may promote salt tolerance in the latter. This work leads to a better understanding of the salinity mechanism in sugar beet and provides a list of potential markers for the further engineering of salt tolerance in crops.
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http://dx.doi.org/10.1021/acs.jafc.9b00244DOI Listing
May 2019

HO Signature and Innate Antioxidative Profile Make the Difference Between Sensitivity and Tolerance to Salt in Rice Cells.

Front Plant Sci 2018 23;9:1549. Epub 2018 Oct 23.

Department of Biology, University of Padova, Padova, Italy.

Salt tolerance is a complex trait that varies between and within species. HO profiles as well as antioxidative systems have been investigated in the cultured cells of rice obtained from Italian rice varieties with different salt tolerance. Salt stress highlighted differences in extracellular and intracellular HO profiles in the two cell cultures. The tolerant variety had innate reactive oxygen species (ROS) scavenging systems that enabled ROS, in particular HO, to act as a signal molecule rather than a damaging one. Different intracellular HO profiles were also observed: in tolerant cells, an early and narrow peak was detected at 5 min; while in sensitive cells, a large peak was associated with cell death. Likewise, the transcription factor salt-responsive ethylene responsive factor 1 (TF SERF1), which is known for being regulated by HO, showed a different expression profile in the two cell lines. Notably, similar HO profiles and cell fates were also obtained when exogenous HO was produced by glucose/glucose oxidase (GOX) treatment. Under salt stress, the tolerant variety also exhibited rapid upregulation of K transporter genes in order to deal with K/Na impairment. This upregulation was not detected in the presence of oxidative stress alone. The importance of the innate antioxidative profile was confirmed by the protective effect of experimentally increased glutathione in salt-treated sensitive cells. Overall, these results underline the importance of specific HO signatures and innate antioxidative systems in modulating ionic and redox homeostasis for salt stress tolerance.
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http://dx.doi.org/10.3389/fpls.2018.01549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206305PMC
October 2018

Fast Regulation of Hormone Metabolism Contributes to Salt Tolerance in Rice ( spp. Japonica, L.) by Inducing Specific Morpho-Physiological Responses.

Plants (Basel) 2018 Sep 15;7(3). Epub 2018 Sep 15.

Department of Biology, University of Padova, 35131 Padua, Italy.

Clear evidence has highlighted a role for hormones in the plant stress response, including salt stress. Interplay and cross-talk among different hormonal pathways are of vital importance in abiotic stress tolerance. A genome-wide transcriptional analysis was performed on leaves and roots of three-day salt treated and untreated plants of two Italian rice varieties, Baldo and Vialone Nano, which differ in salt sensitivity. Genes correlated with hormonal pathways were identified and analyzed. The contents of abscisic acid, indoleacetic acid, cytokinins, and gibberellins were measured in roots, stems, and leaves of seedlings exposed for one and three days to salt stress. From the transcriptomic analysis, a huge number of genes emerged as being involved in hormone regulation in response to salt stress. The expression profile of genes involved in biosynthesis, signaling, response, catabolism, and conjugation of phytohormones was analyzed and integrated with the measurements of hormones in roots, stems, and leaves of seedlings. Significant changes in the hormone levels, along with differences in morphological responses, emerged between the two varieties. These results support the faster regulation of hormones metabolism in the tolerant variety that allows a prompt growth reprogramming and the setting up of an acclimation program, leading to specific morpho-physiological responses and growth recovery.
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http://dx.doi.org/10.3390/plants7030075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161274PMC
September 2018

Application of anaerobic dynamic membrane bioreactor (AnDMBR) for the successful enrichment of Anammox bacteria using mixed anaerobic and aerobic seed sludge.

Bioresour Technol 2018 Oct 4;266:532-540. Epub 2018 Jul 4.

Laboratory of Technologies for Waste, Wastewater and Raw Materials Management, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), via M.M. Sole 4, 40129 Bologna, Italy.

This study investigated a novel bioreactor configuration coupled with a side-stream dynamic membrane (DM) for Anammox enrichment as an alternative for conventional membrane. Bioreactor was fed with synthetic feed and seeded with a mix of anaerobic and aerobic sludge. In situ mechanical cleaning was employed for DM cleaning. DM development and performance was analysed over two polyamide-nylon meshes (200 and 52 µm). Solid-liquid separation of 52 µm mesh outperformed 200 µm with an average effluent turbidity of 2.4 ± 0.1 NTU. The system was operated at a maximum nitrogen loading rate of 696 mg-N L d and achieved a maximum nitrogen removal rate of 611.6 mg-N L d. At steady state, the average ammonium, nitrite and total nitrogen removal efficiencies were 87 ± 0.6%, 98.5 ± 0.15% and 87.5 ± 0.56% respectively. Digital realtime PCRSequence analysis showed that Planctomycetales belonging to ascertained Anammox-specific genera progressively increased their presence in the reactor consistently with its nitrogen removal performance.
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http://dx.doi.org/10.1016/j.biortech.2018.06.100DOI Listing
October 2018

Comparison of three PCR-based assays for SNP genotyping in plants.

Plant Methods 2018 28;14:28. Epub 2018 Mar 28.

1DAFNAE, Università degli Studi di Padova, Legnaro, Italy.

Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved to increase genotyping efficiency. A new assay, rhAmp, based on RNase H2-dependent PCR (rhPCR) combined with a universal reporter system attempts to reduce error rates from primer/primer and primer/probe dimers while lowering costs compared to existing technologies. Before rhAmp can be widely adopted, more experimentation is required to validate its effectiveness versus established methods.

Results: The aim of this study was to compare the accuracy, sensitivity and costs of TaqMan, KASP, and rhAmp SNP genotyping methods in sugar beet ( L.). For each approach, assays were designed to genotype 33 SNPs in a set of 96 sugar beet individuals obtained from 12 parental lines. The assay sensitivity was tested using a series of dilutions from 100 to 0.1 ng per PCR reaction. PCR was carried out on the QuantStudio 12K Flex Real-Time PCR System (Thermo Fisher Scientific, USA). The call-rate, defined as the percentage of genotype calls relative to the possible number of calls, was 97.0, 97.6, and 98.1% for TaqMan, KASP, and rhAmp, respectively. For rhAmp SNP, 24 of the 33 SNPs demonstrated 100% concordance with other two technologies. The genotype concordance with either technologies for the other 9 targets was above 99% (99.34-99.89%).

Conclusion: The sensitivity test demonstrated that TaqMan and rhAmp were able to successfully determine SNP genotypes using as little as 0.2 ng DNA per reaction, while the KASP was unable to ascertain SNP states below 0.9 ng of DNA per reaction. Comparative cost per reaction was also analyzed with rhAmp SNP offering the lowest cost per reaction. In conclusion, rhAmp produced more calls than either TaqMan or KASP, higher signal to NTC data while offering the lowest cost per reaction.
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http://dx.doi.org/10.1186/s13007-018-0295-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872507PMC
March 2018

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses.

Front Plant Sci 2018 5;9:204. Epub 2018 Mar 5.

Department of Biology, University of Padova, Padova, Italy.

Salinity tolerance has been extensively investigated in recent years due to its agricultural importance. Several features, such as the regulation of ionic transporters and metabolic adjustments, have been identified as salt tolerance hallmarks. Nevertheless, due to the complexity of the trait, the results achieved to date have met with limited success in improving the salt tolerance of rice plants when tested in the field, thus suggesting that a better understanding of the tolerance mechanisms is still required. In this work, differences between two varieties of rice with contrasting salt sensitivities were revealed by the imaging of photosynthetic parameters, ion content analysis and a transcriptomic approach. The transcriptomic analysis conducted on tolerant plants supported the setting up of an adaptive program consisting of sodium distribution preferentially limited to the roots and older leaves, and in the activation of regulatory mechanisms of photosynthesis in the new leaves. As a result, plants resumed grow even under prolonged saline stress. In contrast, in the sensitive variety, RNA-seq analysis revealed a misleading response, ending in senescence and cell death. The physiological response at the cellular level was investigated by measuring the intracellular profile of HO in the roots, using a fluorescent probe. In the roots of tolerant plants, a quick response was observed with an increase in HO production within 5 min after salt treatment. The expression analysis of some of the genes involved in perception, signal transduction and salt stress response confirmed their early induction in the roots of tolerant plants compared to sensitive ones. By inhibiting the synthesis of apoplastic HO, a reduction in the expression of these genes was detected. Our results indicate that quick HO signaling in the roots is part of a coordinated response that leads to adaptation instead of senescence in salt-treated rice plants.
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http://dx.doi.org/10.3389/fpls.2018.00204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844958PMC
March 2018

Innovative Approaches to Evaluate Sugar Beet Responses to Changes in Sulfate Availability.

Front Plant Sci 2018 31;9:14. Epub 2018 Jan 31.

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy.

In this study, a system based on omics profiling was set-up for sugar beet ( L. subsp. ) evaluation after changes in sulfate availability. Seedlings were grown on sulfate-deprived Hoagland solution. Six days after germination, 100 μM MgSO was added to the solution. Root samples were collected 36 h after treatments. WinRHIZO root-scanning approach was used for the automated image analysis of plant root morphology. Inductively Coupled Plasma Spectrometry (ICP-OES) and quadrupole-time-of-flight mass spectrometry (Q-TOF) were used for ionomic and metabolic analysis, respectively. Nanofluidic real-time PCR (OpenArray system) was used for molecular profiling. OpenArray chips were designed with TaqMan probes for 53 sugar beet genes putatively involved in sulfate nutrition. At morphological level treated seedlings showed significantly higher values ( < 0.01) than untreated plants for root traits related to soil exploration and nutrient uptake, such as total root length, fine roots length and root tips number. ICP-OES, Q-TOF and transcriptomic data revealed changes due to sulfate availability in sugar beet samples. Two key results are highlighted in sulfate-supplied roots and leaves. Firstly, high expression levels of auxin efflux carrier component 1 (PIN) and 5-phosphoribosyl-anthranilate, precursor of tryptophan and auxin synthesis, were observed in roots. Secondly, high levels of 2-Cys peroxiredoxin BAS1, chloroplastic, thioredoxin reductase (NADPH) and cysteine synthase, chloroplastic/chromoplastic, acetylserine sulfhydrylase, involved in protection against oxidative stress and cysteine synthase activity, respectively, were observed in leaves. Based on our findings, the combination of evaluated omics approaches could become a key system for the evaluation of the nutritional status of sugar beet under different nutrient availability conditions.
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http://dx.doi.org/10.3389/fpls.2018.00014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797807PMC
January 2018

Targeted Next-Generation Sequencing Identification of Mutations in Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beets.

Genes (Basel) 2017 Oct 11;8(10). Epub 2017 Oct 11.

Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, 7144165186 Shiraz, Iran.

Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet ( L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples of ninety-six individuals from six sea beets ( L. subsp. ) and six sugar beet pollinators (eight individuals each) were used for the discovery of single-nucleotide polymorphisms (SNPs). Target amplicons of about 200 bp in length were designed with the Ion AmpliSeq Designer system in order to cover the DNA sequences of the RGAs. The number of SNPs ranged from 0 in four individuals to 278 in the pollinator R740 (which is resistant to rhizomania infection). Among different groups of beets, cytoplasmic male sterile lines had the highest number of SNPs (132) whereas the lowest number of SNPs belonged to O-types (95). The principal coordinates analysis (PCoA) showed that the polymorphisms inside the gene (including the CCCTCC sequence) can effectively differentiate wild from cultivated beets, pointing at a possible mutation associated to rhizomania resistance that originated directly from cultivated beets. This is unlike other resistance sources that are introgressed from wild beets. This gene belongs to the receptor-like kinase (RLK) class of RGAs, and is associated to a hypothetical protein. In conclusion, this first report of using Ion Torrent sequencing technology in beet germplasm suggests that the identified sequence CCCTCC can be used in marker-assisted programs to differentiate wild from domestic beets and to identify other unknown disease resistance genes in beet.
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http://dx.doi.org/10.3390/genes8100264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664114PMC
October 2017

Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island.

Sci Rep 2017 08 17;7(1):8511. Epub 2017 Aug 17.

Department of Agronomy, Animals, Natural Resources and Environment - DAFNAE, University of Padua, Viale dell'Università 16, 35020, Legnaro (Padova), Italy.

The unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.
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http://dx.doi.org/10.1038/s41598-017-08662-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561117PMC
August 2017

The physiological and metabolic changes in sugar beet seedlings under different levels of salt stress.

J Plant Res 2017 Nov 15;130(6):1079-1093. Epub 2017 Jul 15.

Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China.

Salinity stress is a major limitation to global crop production. Sugar beet, one of the world's leading sugar crops, has stronger salt tolerant characteristics than other crops. To investigate the response to different levels of salt stress, sugar beet was grown hydroponically under 3 (control), 70, 140, 210 and 280 mM NaCl conditions. We found no differences in dry weight of the aerial part and leaf area between 70 mM NaCl and control conditions, although dry weight of the root and whole plant treated with 70 mM NaCl was lower than control seedlings. As salt concentrations increased, degree of growth arrest became obvious In addition, under salt stress, the highest concentrations of Na and Cl were detected in the tissue of petioles and old leaves. N and K contents in the tissue of leave, petiole and root decreased rapidly with the increase of NaCl concentrations. P content showed an increasing pattern in these tissues. The activities of antioxidant enzymes such as superoxide dismutase, catalase, ascorbate peroxidase and glutathione peroxidase showed increasing patterns with increase in salt concentrations. Moreover, osmoprotectants such as free amino acids and betaine increased in concentration as the external salinity increased. Two organic acids (malate and citrate) involved in tricarboxylic acid (TCA)-cycle exhibited increasing contents under salt stress. Lastly, we found that Rubisco activity was inhibited under salt stress. The activity of NADP-malic enzyme, NADP-malate dehydrogenase and phosphoenolpyruvate carboxylase showed a trend that first increased and then decreased. Their activities were highest with salinity at 140 mM NaCl. Our study has contributed to the understanding of the sugar beet physiological and metabolic response mechanisms under different degrees of salt stress.
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http://dx.doi.org/10.1007/s10265-017-0964-yDOI Listing
November 2017

"Noisy beets": impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris.

Plant Methods 2016 18;12:36. Epub 2016 Jul 18.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.

Background: Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding.

Results: In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours-KNN, random forest-RF, ridge logistic regression-LR, and support vector machines with linear or radial basis function kernels) was investigated. A sugar beet population of 123 plants phenotyped for a binary trait and genotyped for 192 SNP (single nucleotide polymorphism) markers was used. Labels (0/1 phenotype) were randomly sampled to generate noise. From the base scenario without errors in the labels, increasing proportions of noisy labels-up to 50 %-were generated and introduced in the data.

Conclusions: Local classification methods-KNN and RF-showed higher tolerance to noisy labels compared to methods that leverage global data properties-LR and the two SVM models. In particular, KNN outperformed all other classifiers with AUC (area under the ROC curve) higher than 0.95 up to 20 % noisy labels. The runner-up method, RF, had an AUC of 0.941 with 20 % noise.
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http://dx.doi.org/10.1186/s13007-016-0136-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4949885PMC
July 2016

Proteomic changes induced by potassium deficiency and potassium substitution by sodium in sugar beet.

J Plant Res 2016 May 9;129(3):527-38. Epub 2016 Feb 9.

Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Room 410 Nongxue Building, Xuefu Road NO. 74, Nangang District, Harbin, 150080, Heilongjiang Province, China.

In this study, sugar beets (Beta vulgaris L.) were grown at different K(+)/Na(+) concentrations: mmol/L, 3/0 (control); 0.03/2.97 (K-Na replacement group; T(rep)); 0.03/0 (K deficiency group; T(def)) in order to investigate the effects of K(+) deficiency and replacement of K(+) by Na(+) on plant proteomics, and to explore the physiological processes influenced by Na(+) to compensate for a lack of K(+). After 22 days, fresh and dry weight as well as the Na(+) and K(+) concentration were measured and changes in proteomics were tested by 2D gel electrophoresis. Interestingly, Na(+) showed stimulation in growth of seedlings and hindrance of K(+) assimilation in T(rep). Significant changes were also observed in 27 protein spots among the treatments. These are proteins involved in photosynthesis, cellular respiration, protein folding and degradation, stress and defense, other metabolisms, transcription related, and protein synthesis. A wide range of physiological processes, including light reaction, CO2 assimilation, glycolysis, and tricaboxylic acid cycle, was impaired owing to K(+) starvation. Compensating for the effect of K(+) starvation, an increase in photosynthesis was also observed in T(rep). However, we also found a limitation of cellular respiration by Na(+). Na(+) is therefore in some ways able to recover damage due to K deficiency at protein level, but cannot functionally replace K as an essential nutrient.
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http://dx.doi.org/10.1007/s10265-016-0800-9DOI Listing
May 2016

Accuracy and responses of genomic selection on key traits in apple breeding.

Hortic Res 2015 23;2:15060. Epub 2015 Dec 23.

Biometris, Wageningen University and Research Center , Wageningen, The Netherlands.

The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.
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http://dx.doi.org/10.1038/hortres.2015.60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4688998PMC
January 2016

A new polymorphism on chromosome 6 associated with bolting tendency in sugar beet.

BMC Genet 2015 Dec 7;16:142. Epub 2015 Dec 7.

DAFNAE, Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università degli Studi di Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy.

Background: Premature flowering or bolting is an undesirable characteristic that causes severe sugar yield losses and interferes with harvesting. Vernalization is a prerequisite for the floral induction, achieved by exposure to low temperatures for 10-14 weeks. This process is also controlled by other environmental factors, such as long daylight photoperiods and a combination of genetic factors. The objective of this study was the identification of new genetic polymorphisms linked to bolting tendency in sugar beet.

Results: Two pollinators characterized by low and high bolting tendency were subjected to RAD-sequencing in order to detect discriminating SNPs between lines. 6,324 putative SNPs were identified. Of these, 192 were genotyped in a set of 19 pollinators, each comprising bolted and non-bolted individuals, for a total of 987 samples. Among the 192 candidate SNPs, the strongest overall association was found for SNP183 on chromosome 6 (p-value = 1.246 10(-13)). The association between SNP183 and bolting tendency was then confirmed in an independent population of 730 plants from 11 breeding lines (p-value = 0.0061). SNP183 is located in the intron of Bv_22330_orky, a sugar beet homolog of a matrix metalloproteinase (MMP) gene that could be implied in flowering in Arabidopsis thaliana.

Conclusion: Our data support a significant association between an intronic SNP in the MMP gene located on chromosome 6 and the regulation of bolting tendency in sugar beet. The newly identified locus supports the polygenic nature of flowering control. The associated marker can be used to design SNP panels for the discrimination of bolters and non-bolters, to be used in sugar beet breeding programs for the development of improved germplasm with low bolting tendency.
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http://dx.doi.org/10.1186/s12863-015-0300-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672520PMC
December 2015