PLANT OMICs

Encompassing plant and animal OMICs


MtNOOT gene enhanced high productivity and economical characteristics of tomato (Lycopersicon esculentum)

Ghada Ahmed Abu El-Heba*

Department of Nucleic Acid and Protein Structure, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Centre (ARC), Giza, Egypt

Abstract
Tomato (Lycopersicon esculentum) is the main vegetal crop that has tremendous popularity around the world. Medicago truncatula NOOT gene (Mt-NOOT) encodes a BTB/POZ-ankyrin repeat protein of the NONEXPRESSOR OF PR GENES1 (NPR1 family). It was introduced into Lycopersicon esculentum (Tomato) genome. The tomato plants that ectopically expressed Mt-NOOT obtained several favorable traits and fruit quality. Heteroblasty between the transgenic and the non-transgenic tomato leaves and flower architecture were used to distinguish transgenic and wild lines. Transgenic tomato plants accumulated a significant amount of phenolic compounds and plant pigmentations compared to the wild type. On the other hand, transgenic plants acquired a considerable amount of antioxidant such as CuZnSO superoxide dismutase (SOD), tomato Catalase (CAT), and tomato Cell wall-associated peroxidase (TPX1) than the wild type. Antioxidant high content together with the high content of phenolic compounds enabled the transgenic tomato fruits to gain not only edible benefits, but also a significant higher shelf-time, extended to six months more than the wild type stored at 25°C in dark and dry condition. Surprisingly, transgenic tomato fruits did not show any rotten process during long time storage as they did not acquire any contagious microorganism. Total fruit productivity in transgenic tomato was greater than the control with an estimated ratio of 84%.

Pages 1-10 | Full Text PDFSupplemntary PDF | doi: 1021475/POJ.14.01.21.p3141


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De novo transcriptome sequencing, assembly and characterization of Heliopsis longipes roots vs. leaves to discover putative genes involved in specialized metabolites biosynthesis

Génesis V. Buitimea-Cantúa* and Jorge Molina-Torre

Laboratorio de Fitobioquímica, CINVESTAV Unidad Irapuato, Departamento de Biotecnología y Bioquímica, Irapuato, Guanajuato, México
Tecnologico de Monterrey, Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias. Av. Eugenio Garza Sada 2501, Monterrey, N.L., C.P. 64849, México


Abstract
Heliopsis longipes is a valuable source of specialized metabolites (or secondary metabolites) with medicinal properties mainly in roots. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. In this work, the genes of the biosynthetic pathway of the specialized metabolism from H. longipes roots and leaves through de novo RNA sequencing (RNA-Seq) using the platform of Illumina paired-end sequencing were studied. After de novo transcriptome assembly using the software Newbler, a total of 172,342 non-redundant transcripts with an N50 value of 816 bp was obtained. Further functional classification and annotation with Gene Ontology (GO), BLAST2GO, Kyoto Encyclopedia of Genes and Genome (KEGG), and KEGG automatic annotation server (KAAS), revealed that active genes in tissues are predominately involved in the metabolic process and biosynthesis of specialized metabolite pathways. Differential expression analysis of roots vs. leaves using Cuffdiff software (p-value ≤0.05 and log-fold change ratio (log2) ≥1) revealed that differentially expressed genes (DEGs) were in an organ-specific manner, such as in leaf, DEGs were significantly enriched in photosynthesis, while in roots, were a higher enriched function of plant hormone signal transduction. A total of 63 transcripts DEGs were related to 9 specialized metabolites pathways, in roots the most abundant was the phenylpropanoid biosynthesis, and in leaves was the carotenoids biosynthesis. Several regulatory genes including the basic-helix-loop-helix and basic leucine zipper domain, transcriptions factor families involved in the regulation of phenylpropanoids and carotenoid biosynthesis, respectively, were discovered. This study established a global transcriptome dataset for H. longipes. Data shall be useful to study the functional genomics or genetic engineering of this specie. These results will promote the understanding of the genetic mechanism involved in the biosynthesis of specialized metabolites in H. longipes.

Pages 11-22 | Full Text PDF| doi: 10.21475/POJ.14.01.21.p3067


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Quality of soybean seeds submitted to different treatments and storage conditions

Francielen Lima da Silva, Letícia Barão Medeiros, Fabiano Carlos Ferreira, Géri Eduardo Meneghello, Francisco Amaral Villela, Tiago Zanatta Aumonde, Tiago Pedó

Universidade Federal do Rio Grande do Sul, Brazil
Universidade Federal de Pelotas, Brazil
Sementes Petrovina, Brazil


Abstract
Chemical seed treatment is a recommended technique to protect seeds from pathogens that can affect their quality. The objective of this work was to analyse the quality of soybean seeds with different treatments under different storage temperatures. Seeds of cultivar ‘M 8378 IPRO’ produced in Mato Grosso, Brazil were used. A completely randomised design was used in a 4 × 3 two-factorial scheme. The seeds were treated with three different combinations of chemicals (fungicides, insecticides, polymer and drying powder) in addition to the control (untreated seeds) combined with three different storage temperatures (13 °C, 19 °C and uncontrolled temperature), with three repetitions. Quality was assessed by the germination test (TG), accelerated aging (AA), field emergence (FE), tetrazolium test (TZ) and isoenzyme analysis. The uncontrolled storage temperature negatively influenced the variables germination, accelerated aging and field emergence. The vigour and viability of the tetrazolium test showed that untreated seeds had better physiological quality than seeds with chemical treatment. The expression of isoenzymes showed a difference between treatments. Even with the stress caused by the seed treatment, this tool is very important for the initial protection of the seedlings.

Pages 23-29 | Full Text PDF| doi: 1021475/POJ.14.01.21.p3247
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Pre-emergence herbicidal activity and persistence of 2,4-di-tertbutylphenol in relation to soil types

Norhafizah Md Zain, Mazira Che Mat, Chuah Tse Seng*

Faculty of Agro-based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600 Jeli Kelantan, Malaysia
Institute of Food Security and Sustainable Agriculture (IFSSA), Universiti Malaysia Kelantan, 17600 Jeli, Kelantan, Malaysia
Department of Biological Science, Faculty of Science and Technology, University of Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
Faculty of Plantation and Agro-technology, Universiti Teknologi MARA, Perlis Branch, Arau Campus, 02600 Arau Perlis, Malaysia


Abstract
Although 2,4-di-tert-butylphenol (2,4-DTBP) has demonstrated strong phytotoxic effect on various weedy plants in previous findings, research on its pre-emergence herbicidal activity in the soil is still scanty. The aim of this study was to investigate the effects of two soil types on pre-emergence herbicidal activity and persistence of 2,4-DTBP. The bioassay was carried out in a growth chamber where goosegrass [Eleusine indica (L.) Gaertn.] seeds were sown in different rates of 2,4-DTBP in two soil series under sterilized and non-sterilized soil conditions. Bioassays of each treatment were conducted in four replicates and arranged in completely randomized design. 2,4-DTBP exhibited potent pre-emergence activity as a root inhibitor where it completely inhibited (100% inhibition) of the root growth of E. indica in sandy loam soil at an application rate of 6.14 kg ai/ha. 2,4-DTBP was rapidly detoxified in silt loam soil as a result of high microbial activity where it completely lost its phytotoxicity by giving 100% emergence within 10 weeks even it was applied at an application as high as 20.4 kg ai/ha. However, 2,4-DTBP remained highly phytotoxic in sandy loam soil where it reduced the root and shoot growth by 47 and 36%, respectively, throughout 10 weeks duration of the investigation. The presence of microbes in non-sterilized soil further suggest that soil microbes may modify the chemical structure of the 2,4-DTBP, which in turn decreased its toxicity. The high level of pre-emergence herbicidal activity in conjunction with its biodegradation in silt loam soil imply that 2,4-DTBP may have potential for development as a natural-soil applied herbicide.

Pages 30-37 | Full Text PDF| doi: 1021475/POJ.14.01.21.p3265
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Root proteome alterations in sugarcane promoted by the regrowth cycle in commercial production

Rone Charles Maranho, Mariana Mancini Benez, Gustavo Barizon Maranho, Eduardo Jorge Pilau, Claudete Aparecida Mangolin, Maria de Fátima P. S. Machado*

Postdoctoral in Agronomy, Graduate student in the Agronomy, Department of Chemistry, Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil

Abstract
The decrease in agricultural productivity in successive cutting of sugarcane plants is associated with several extrinsic and intrinsic factors. However, no studies have focused on the physiological potential of sett roots in successive cuts in sugarcane culture. There have been no proteomic studies on sugarcane sett roots at different stages of cutting. In this study, the UPLC-ESI-TOF-MS system and bioinformatics tools were used to identify proteins of sett roots in the first and fifth cuts of sugarcane cultivar RB966928 in the sprouting stage. Differences in the proteome of sett roots of RB966928 in the first and fifth cuts detected in this study supports the hypothesis that the proteome of sett roots may change after successive cuts in sugarcane culture. A reduction in the number of proteins was observed in the roots of the fifth cut, whereas 34% of proteins, identified exclusively in the first cut, were absent in the fifth cut. Proteome analysis of sett roots in the first and fifth cuts showed that the changes after successive cuts were quantitative (number of proteins) and mainly qualitative. In this study, the detailed list of proteins identified in the first cut but absent in the fifth cut is relevant. The findings of this study may aid further research that employ biotic or abiotic elicitors to induce gene expression of essential proteins absent in sett roots of the fifth cut, and thus increasing the agricultural productivity and longevity of cane fields.

Pages 38-49 | Full Text PDF| Supplementary PDF| doi: 1021475/POJ.14.01.21.p3286
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Karyotype and genome size determination of Jarilla chocola, an additional sister clade of Carica papaya

Dessireé Patricia Zerpa-Catanho, Tahira Jatt, Ray Ming*

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Botany, Shah Abdul Latif University, Khaipur, Sindh, 66020, Pakistan


Abstract
Jarilla chocola is an herbaceous plant species that belongs to the Jarilla genus and the Caricaceae family. No information on chromosome number or genome size has been reported for J. chocola that confirms the occurrence of dysploidy events and explore the existence of heteromorphic sex chromosomes. Therefore, the total number of chromosomes of this species was determined by karyotyping and counting the number of chromosomes observed, and the genome size of female and male plants was estimated separately by flow cytometry. Results showed that J. chocola has eight pairs of chromosomes (2n = 2x = 16), and its chromosomes are classified as metacentric for five pairs, submetacentric for two pairs and telocentric for one pair. The nuclear DNA content (1C-value) in picograms and diploid genome size was estimated separately from female and male plants using two species as the standards, Phaseolus vulgaris (1C = 0.60 pg) and Carica papaya (1C = 0.325 pg), to look for the possible existence of heteromorphic sex chromosomes. C. papaya proved to be a better standard for the determination of J. chocola DNA content and diploid genome size. No significant difference on the DNA content was observed between female (1C = 1.02 ± 0.003 pg) and male (1C = 1.02 ± 0.008 pg) plants. The estimated genome size of J. chocola per haploid genome in base pairs was calculated from the obtained C-values. Results showed an estimated genome size per haploid genome of 1018.44 ± 3.07 Mb and 1022.08 ± 7.76 Mb for female and male plants, respectively. Due to the observed chromosome number and genome size, only the occurrence of one of two previously reported dysploidy events in Jarilla could be confirmed for J. chocola and no evidence of heteromorphic sex chromosomes was found. These results provide fundamental information of the J. chocola genome and will expedite investigation of sex chromosomes and genome evolution in this species, the Jarilla genus and the Caricaceae family.

Pages 50-56 | Full Text PDF| doi: 10.21475/POJ.14.01.21.p2944