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  • journal-article
    van Wesemael, Jelle;Hueber, Yann;Kissel, Ewaut;Campos, Nádia;Swennen, Rony;Carpentier, Sebastien; 2018. Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics. Scientific Reports ; 2018; Vol. 8; iss. 1
    LIRIAS1616490
    description
    The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.
    Publisher: Nature Publishing Group
    Published
  • presentation
    van Wesemael, Jelle;Hueber, Yeves;Campos, Nádia;Kissel, Ewaut;Swennen, Rony;Roux, N;Carpentier, Sebastien; 2018. Detection of variety specific alleles and correlation to their phenotype: a proof of principle in the Bioversity International collection.
    LIRIAS1718730
    description


    Published
  • journal-article
    Campos, Nádia;Swennen, Rony;Carpentier, Sebastien; 2018. The plantain proteome, a focus on allele specific proteins obtained from plantain fruits. Proteomics ; 2018; Vol. 18; iss. 3
    LIRIAS1634764
    description
    Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non-model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in-house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole-genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.
    Publisher: WILEY-VCH Verlag
    Published
  • journal-article
    Dazio de Souza, Kamila Rezende;Santos, Meline de Oliveira;Andrade, Cinthia Aparecida;da Silva, Dayane Meireles;Campos, Nadia Alves;Alves, Jose Donizeti; 2017. Aerenchyma formation in the initial development of maize roots under waterlogging. Theoretical And Experimental Plant Physiology; 2017; Vol. 29; iss. 4; pp. 165 - 175
    LIRIAS1611941
    description
    © 2017, Brazilian Society of Plant Physiology. We investigated the role of antioxidant and cell wall loosening enzymes in aerenchyma formation in roots of Saracura maize (Zea mays) from two different selection cycles with contrasting tolerance to waterlogging. Plantlets of Saracura maize from the 1st cycle (C1—sensitive) and 18th cycle (C18—tolerant) of selection were subjected to waterlogging for 0, 24, 48, 72, 96, and 120 h, and roots were collected for biochemical and anatomical analyses. Plantlets of cycle 18 exhibited higher aerenchyma formation, exodermis thickening, and higher activity of alcohol dehydrogenase, polygalacturonase, cellulase, and antioxidant enzymes than plantlets of cycle 1. Although these processes also occurred in C1 plantlets, they were independent of the waterlogging and therefore were initiated later. C18 plantlets exhibited biochemical and physiological characteristics that may have contributed to the higher water excess tolerance of Saracura maize plantlets from the later selection cycle. Higher aerenchyma formation in C18 plantlets is related to higher and early activity of cell wall loosening enzymes and higher activity of antioxidant enzymes than in C1 plantlets.
    Publisher: Springer (part of Springer Nature)
    Published
  • presentation
    van Wesemael, Jelle;Hueber, Y;Kissel, Ewaut;Campos, Nádia;Swennen, Rony;Carpentier, Sebastien; 2017. Quantification and identification of allele specific proteins for polyploid non-model crops: Proof of principle for 3 banana genotypes/phenotypes.
    LIRIAS1718708
    description


    Published
  • journal-article
    Campos, Nádia;Panis, Bart;Carpentier, Sebastien; 2017. Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities. Frontiers in Plant Science ; 2017; Vol. 8
    LIRIAS1389080
    description
    One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.
    Publisher: Frontiers Research Foundation
    Published
  • journal-article
    Therezan de Freitas, Rodrigo;Paiva, Renato;Campos, Nádia;Coutinho Silva, Luciano;Swennen, Rony;Panis, Bart; 2016. In vitro culture of Annona emarginata: A rootstock for commercial annonaceae species. Plant Cell Culture & Micropropagation ; 2016; Vol. 12; iss. 1; pp. 1 - 6
    LIRIAS1718673
    description

    Publisher: Editora UFLA
    Published
  • journal-article
    Campos, NA;Alves, JD;De Souza, KRD;Porto, BN;Magalhães, MM;Da Silva, GJ;Paiva, LV; 2016. Evolution of aerenchyma formation in a maize breeding program. Plant OMICS; 2016; Vol. 9; iss. 1; pp. 19 - 25
    LIRIAS1611943
    description
    Approximately 28 million hectares of intermittently flooded land with agricultural potential in Brazil could be used for rice crop rotation to increase production. Understanding the flood tolerance mechanisms in 'Saracura' is of paramount importance for maize and other crops. Thus, we evaluated the expression levels of the superoxide dismutase, ascorbate peroxidase, guaiacol peroxidase, and catalase antioxidant genes and cell wall loosening (XET) enzyme in maize roots under flooding as well as associated expression with the initiation of aerenchyma formation, which is the most important plant adaptation to flooding. We collected data on 'Saracura' at the beginning of the breeding program (cycle 1), a time considered more sensitive to flooding, and during the last selection cycle (cycle 18), a time considered more resistant to flooding. Maize plants were flooded for 12 and 24h, and roots were collected for anatomic (aerenchyma density in the root cortex) and gene expression analyses by qRT-PCR. Our results showed that there was a proportional graded increase in aerenchyma formed in the root cortex with increased flooding time that was most pronounced during selection cycle 18. Antioxidant enzyme gene expression levels at both time points were similar: high expression just after germination, decreased expression after 12h, and increased expression after 24h of flooding. Aerenchyma formation was detectable after 24h of flooding, which coincided with the highest antioxidant enzyme gene expression levels. These results indicate that the correlation between antioxidant enzyme activities and flooding can act as a molecular flag to improve flood tolerance in 'Saracura'. Our results are important to understand the induction of aerenchyma formation and flooding tolerance in 'Saracura'.

    Published
  • presentation
    van Wesemael, Jelle;Kissel, Ewaut;Campos, Nádia;Carpentier, Sebastien; 2016. Quantification and identification of allele specific proteins for polyploid non-model crops: proof of principle for 3 banana genotypes/phenotypes.
    LIRIAS1718657
    description
    Oral abstract

    Published
  • journal-article
    Campos, Nádia;Paiva, Luciano V;Panis, Bart;Carpentier, Sebastien; 2016. The proteome profile of embryogenic cell suspensions of Coffea arabica L. Proteomics ; 2016; Vol. 16; iss. 6; pp. 1001 - 1005
    LIRIAS93863
    description
    Somatic embryogenesis, is a process by which new viable embryos are produced from somatic tissues. Somatic embryogenesis is not only a useful biotechnological tool for the massive clonal propagation and genetic engineering but it also allows to obtain fundamental knowledge about the molecular changes that take place during embryogenesis. We present the proteome profile of two embryogenic cell suspensions. We identified 1052 non-redundant proteins. We present their known GO annotations and show two protein networks sharing the GO annotations related to stress and embryogenic capacity via the free program Cytoscape. To our knowledge these results give the first high-throughput proteome description of embryogenic cell suspensions and provide new information about somatic embryos for the whole plant community. The published proteome is a first step toward understanding somatic embryogenesis in coffee and toward a better annotation of proteins in an important non-model crop. All data are available via ProteomeXchange with identifier PXD002963.
    Publisher: WILEY-VCH Verlag
    Published
  • journal-article
    Campos, NA;da Silva, GJ;de Paula, MFB;Rodrigues, TB;Rodrigues, LAZ;Paiva, LV; 2016. A direct organogenesis protocol from shoot segments of Solanum tuberosum cv. Monalisa. Australian Journal of Crop Science; 2016; Vol. 10; iss. 7; pp. 964 - 968
    LIRIAS1611942
    description
    Transgenic technology is an excellent alternative for improvement of crop production and disease free crops such as potato, which is one of the most important crops worldwide. One of the first steps to apply the transgenic technique is the establishment of an efficient plant regeneration protocol. This is a limiting step in this kind of study, since most protocols are species-specific and some of them do not adequately respond to in vitro culture or present low regeneration rates. The objective of this study was to stablish an efficient regeneration protocol of Solanum tuberosum cv. Monalisa from internodes explants. This work is important since most in vitro protocols are based on shoots. Twenty five treatments were performed, with each treatment being composed of six internodes in flasks containing MS medium supplemented with a fixed concentration of zeatin riboside (3 mg.L -1 ) (ZEA), varying concentrations of naphthaleneacetic acid (0 to 1 mg. L -1 ) (NAA), and gibberellic acid (0 to 3 mg.L -1) (GA 3 ). The treatment composed of ZEA, 0.05 mg.L -1 of NAA, and 0.10 mg.L -1 of GA 3 was considered the best for shoot regeneration from potato internodes. The study was able to establish a specific regeneration protocol for Monalisa cultivar. This result can be very useful since it is possible to obtain plants from internode, without the requirement of meristematic regions, enabling the obtainment of a higher number of plants.

    Published
  • presentation
    van Wesemael, Jelle;Campos, Nádia;Carpentier, Sebastien; 2016. Allele mining for drought tolerance via proteomics: a proof of principle of allele discovery for the banana biodiversity.
    LIRIAS1718639
    description
    Oral abstract

    Published
  • presentation
    Carpentier, Sebastien;Kissel, Ewaut;van Wesemael, Jelle;Campos, Nádia; 2016. The quest for tolerant varieties: the use of proteomics to understand stress and identify variety specific alleles.
    LIRIAS1718672
    description
    Abstract

    Published
  • journal-article
    Porto, BN;Alves, JD;Magalhaes, PC;Castro, EM;Campos, NA;Souza, KRD;Magalhaes, MM;Andrade, CA;Santos, MO; 2013. Calcium-Dependent Tolerant Response of Cell Wall in Maize Mesocotyl Under Flooding Stress. Journal Of Agronomy And Crop Science; 2013; Vol. 199; iss. 2; pp. 134 - 143
    LIRIAS945629
    description
    The aim of the present study was to find out the effect of calcium on flooded maize seedlings by anatomical and ultra-structural analyses and by measuring the enzyme activity and gene expression of polygalacturonase (PG) and superoxide dismutase (SOD). For this, maize seeds were placed to germinate in germination paper saturated with CaCl 2 0.75& %. Then, 4-day-old seedlings were subjected to flooding in the presence or absence of CaCl 2 . Mesocotyl sections were sampled daily for the anatomical and ultra-structural analyses, RT-qPCR and activity of SOD and PG. The results showed that the presence of calcium in the flooding buffer increases the tolerance of maize seedlings by 1& day when compared to seedlings flooded in the absence of this element. The reason for this longer survival is that calcium maintains the integrity of the cell wall and attenuates the effects of oxidative stress. Owing to this fact, the seedlings remained alive and firm for up to 7& days. © 2012 Blackwell Verlag GmbH.
    Publisher: Wiley
    Published