PLANT OMICS

Metabolomics differentiation of oil palm (Elaeis guineensis Jacq.) spear leaf with contrasting susceptibility to Ganoderma boninense

 Nurul Liyana Rozali, Mohd Ambar Yarmo, Abu Seman Idris, Ahmad Kushairi, Umi Salamah Ramli*

Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia

School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia

Abstract

Basal stem rot (BSR) disease caused by Ganoderma boninense is the most serious and destructive disease in oil palm, especially in Southeast Asia and required urgent control measures to combat the disease outbreak. Information of understanding metabolite response of oil palm to BSR is limited. Therefore, parental palms with contrasting susceptibility to G. boninense based on previous oil palm progenies testing using root inoculation technique to identify oil palm progenies partially tolerant and susceptible to G. boninense were examined by metabolomics approach using gas chromatography x gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF-MS). Analysis of metabolomics data from GC×GC-TOF-MS was conducted by supervised multivariate analysis of partial least squares-discriminant analysis (PLS) and orthogonal partial least squares-discriminant analysis (OPLS-DA) that allowed cross-validation and response permutation test functions. As a result, seven potential metabolites that contribute to the contrasting susceptibility of oil palms to G. boninense were identified as mannose, xylose, glucopyranose, myo-inositol and hexadecanoic acid which were found high in partially tolerant oil palm whereas cadaverine and turanose were found high in susceptible oil palm as observed in fold changes of detected GC×GC-TOF-MS peaks. The results suggest that the employed strategy is a potential approach to profile and characterize leaf metabolome with contrasting susceptibility to G. boninense. This result provide baseline in future studies utilizing metabolomics in identifying potential biomarkers by screening larger population of truly resistant palms to G. boninense.

Pages 45-52 |Read Moredoi: 10.21475/poj.10.02.17.pne364

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In silico mining and characterization of simple sequence repeats (SSRs) from Euphorbia esula expressed sequence tags (ESTs): A potential crop for biofuel

Surojit Sen*, Budheswar Dehury, Jagajjit Sahu, Sunayana Rathi, Raj Narain Singh Yadav

Centre for Biotechnology and Bioinformatics, Dibrugarh University, Assam, India

Biomedical Informatics Centre, Regional Medical Research centre (ICMR), Chandrasekharpur, Bhubaneswar-751023, Odisha, India

Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, Assam, India

Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat-785013, Assam, India

Department of Life Sciences, Dibrugarh University, Dibrugarh-786004, Assam, India

Abstract

Euphorbia esula (leafy spurge) is a perennial noxious weed native to Eurasia, which can also be potentially useful as a biofuel, medicine, or a pest control agent. In this study, we analysed publicly available ESTs of ‘NCBI dbEST’ (http://www.ncbi.nlm.nih.gov/dbEST) using in silico tools to have an insight into the genetic makeup of the plant. Mining of simple sequence repeats (SSRs) was performed by MISA, primer designing by Primer3 while functional annotation, gene ontology and enrichment analysis were performed by Blast2GO. SSR mining from 47543 ESTs revealed a total 3248 SSRs, of which di-, tri- and hexa-nucleotide repeats were 352 (10.83%), 822 (25.30%), 17 (0.52%) respectively. A total of 527 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 210 unique SSR-FDM (Functional Domain Markers) were assigned for significant functional domains by InterProScan. The gene ontology (GO) analysis provided 1213 number of unique GO terms which were subjected to enrichment analysis to obtain 95 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were GO:0005886 for cellular component, GO:0003677 for molecular function and GO:0044255 in case of biological process, indicating the potential of the species as a fuel crop. Many SSR markers were functionally annotated to various biotic and abiotic stress responsive genes. Further studies may help us to understand these traits of extreme adaptive features. This will provide opportunity to genetically manage and modify crops for resistance to these stresses.

Pages 53-63 |Read More|Supplementary Datadoi: 10.21475/poj.10.02.17.pne370

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Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Alsamman M. Alsamman*, S. S. Adawy, S. D. Ibrahim, B. A. Hussein, E. H. A. Hussein

Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt

Department of Genetics, faculty of agriculture Cairo University, Giza, Egypt

Abstract

The Selective Amplification of Start Codon Polymorphic Loci (SASPL) has been developed as a new PCR-based molecular marker. SASPL was validated for the analysis of varietal diversity on ten olive varieties. Validation included in vitro comparison against RAPD, SCoT and SAMPL markers. Assessment of these techniques included primer selectivity, genome coverage and the ability to target genic regions through in silico PCR analysis. Candidate PCR fragments were further sequenced to annotate non-identified genes in olive. Eight SASPL primers were compared to 24 RAPD, 39 SCoT and 12 SAMPL primers. The TA produced by the RAPD, SCoT, SAMPL and the eight SASPL primers were 359, 642, 571 and 269 amplicons, respectively. The highest average number of TA was revealed by SAMPL (47.6), average of PA (18.1) and genetic similarity (GS) (96%) among the olive varieties. On the other hand, SASPL analysis provided higher average number of TA (33.6), average of PA (16.2) and GS (93%) than SCoT and RAPD. The highest average of (PIC) (0.2909) was exhibited by SASPL analysis and the lowest average (0.2038) was revealed by SCoT. The highest number of UB (111) was revealed by SCoT and the lowest UB (43) was obtained by SASPL. Across the four marker types, variety Maraki was characterized by the highest number of unique markers (74). Meanwhile, the variety Manzanillo was characterized by the lowest number of unique markers (8). In addition, in the in silico analysis SASPL exhibited the highest chromosomal coverage (0.59%) and targeted genes (1090) using the lowest number of primers. Additionally, the average area covered by the SASPL primers (354kb) was larger than SCoT and SAMPL. RAPD analysis provided the lowest potential, chromosomal coverage (0.04%) and number of targeted genes (17) compared to SASPL, SCoT and SAMPL analysis. The total coverage of the genome, revealed by combined data was higher (1.21%) than that of each technique separately. Meanwhile, the difference between the actual and the total genomic regions covered by the combined data was about 652kb. Our results suggested that the newly developed SASPL marker is the most adequately and each of the studied marker target different genomic areas, while some areas are shared. Two SCoT and one RAPD fragment were sequenced and showed a high similarity to genes of high physiological functions; such as cyclic plant-specific DNA-binding transcription factor, SANT domain and Copia-type retrotransposon.

Pages 64-77 |Read More|Supplementary Datadoi: 10.21475/poj.10.02.17.pne385

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Mineral deficiencies influence on tomato leaves: pigments, hydrogen peroxide and total phenolic compounds contents

Khalid Y. Alsharafa

Department of Biological Science, Faculty of Science, Mutah University, Mutah- Karak 61710, P.O. Box(7),  Jordan

Abstract

The detection of hydrogen peroxide, chlorophyll pigments, anthocynin, carotenoids, total phenolic compounds and lipid peroxidation levels as potential stress signaling molecules in tomato (Lycopersicon esculentum Mill.) leaves in response to specific mineral deficiency were studied. The stress signaling molecules were measured in the plant leaves at different growth time points cultured in specific mineral deficient nutrient solutions. The results showed that hydrogen peroxide was significantly increased after 48 and 72h of growth in NO3¯ and S deficient nutrient solutions. While the significant accumulation of H2O2 in the plant leaves was observed after 72h and 96h of growth in K+ deficient nutrient solution. In the case of Mg2+ and Fe2+ deficiency the significant accumulation was observed after 72h cultivation. The only significant reduction in chlorophyll a content was detected after 96h cultivation under Mg2+ specific deficiency with no significant changes due to NO3¯, SO4, Fe2+, K+, Ca2+ and PO4 deficiencies. Meanwhile, chlorophyll b contents were significantly reduced in the plant leaves grown for 48h under Mg2+ and Ca2+ specific mineral deficiency. Longer cultivation in Mg2+ dificient hydroponic culture for 96h resulted in 215% increment in chlorophyll b content. No significant changes in chlorophy b contents were detected in hydroponic cultures  dificient in NO3¯, SO4, Fe2+, and PO4. Impose of minerals deficiencies on anthocyanins and carotenoids contents were showed parallel changes. Both increased significantly in response to PO4 and NO3¯ specific deficiencies after 48h and in the case of Mg2+ deficiency after 72h. Meanwhile, SO4deficiency caused the significant increase of both after 72h and 96h. Regarding TPC the results clarified that Mg2+, Ca2+ and K+ specific deficiencies caused significant reductions that appeared after 48h. In contrast, S deficiency caused significant increase in TPC values after 72h. On the other hand, the estimated levels of MDA showed significant increment under Ca2+ and K+ and PO4 specific deficiencies at all time points while in the case of Mg2+ and Fe deficiencies the increment was first reported after 48h and with the later one (Fe) the increment continues up to 96h. These results indicate that some of presented metabolites could be used as stress markers. These results support the possible role of anthocyanins, carotenoids, hydrogen peroxide, total phenolic compounds contents and MDA as early signaling metabolites in tomato plants under specific mineral deficiency.

Pages 78-87 |Read More| doi: 10.21475/poj.10.02.17.pne386

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Genomic sequence characterization of Begomovirus infecting soybean and molecular evolutionary genomics of Legume yellow mosaic viruses (LYMVs)

Shunmugiah V. Ramesh*, Bhagat S. Chouhan, Girish K. Gupta, Syed M. Husain, Suresh Chand

ICAR-Indian Institute of Soybean Research (ICAR-IISR), Indore 452 001, Madhya Pradesh, India

School of Life Sciences, Devi Ahilya Vishwavidhyalaya (DAVV), Indore 452 001, Madhya Pradesh, India

Abstract

Begomoviruses infecting legumes (family Geminiviridae) pose a serious threat to the cultivation of grain legumes. Eventhough legume yellow mosaic viruses (LYMVs) cause significant loss in yield of legumes, studies regarding evolutionary lineage analysis of LYMVs are very rare. Previously, we have shown that Mungbean yellow mosaic virus (MYMV) and Mungbean yellow mosaic India virus (MYMIV) are major begomoviruses causing yellow mosaic disease (YMD) of soybean in India.  In this study, complete genome sequence of begomovirus causing yellow mosaic disease of soybean in Central Indian region was characterized. Furthermore, whole genome sequences of legume begomoviruses [DNA A (108 isolates) and DNA B (89 isolates)] were analyzed to infer genetic diversity, gene flow and evolutionary lineage using nucleotide sequence-based computational approaches. Analysis of nucleotide diversity disclosed that LYMV population as a whole is diverse compared to MYMV and MYMIV. Test of neutral evolution also reiterates the operation of purifying selection and population expansion of MYMV and MYMIV. However, LYMVs as a whole, show decrease in population size and act of balancing or neutral selection. Genetic differentiation studies reveal greater diversity between MYMV and MYMIV. Frequent gene flow was detected between Dolichos yellow mosaic virus (DoYMV), Rhynchosia yellow mosaic India virus (RhYMIV) and other LYMVs. Recombinant events have been detected among LYMV species suggesting frequent genetic exchanges. Molecular phylogeny also revealed distinctness of Old World begomoviruses as New World begomoviruses formed a separate basal cluster. Hence, it is concluded that genetic exchanges are recorded among the LYMVs, and implications of breaching this seclusion is also discussed.

Pages 88-96 |Read More |Supplementary Datadoi: 10.21475/poj.10.02.17.pne391

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Preliminary genome-wide association mapping of rice bacterial leaf blight resistance loci using major Korean races of Xoo (Xanthomonas oryzae)

Asjad Ali, Do Yoon-Hyun, Tae-Hwan Noh, Yu-Mi Choi, Sukyeung Lee, Sejong Oh, Myung-Chul Lee*

National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea

National Institute of Crop Science (NICS), RDA, 181, Iseo-myeon, Wanju, Jeollabuk-do, 55365, Korea

Abstract

Bacterial leaf blight (BLB), caused by X. oryzae pv. oryzae (Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a collection of 96 accessions was used in the genome-wide association study (GWAS) for BLB resistance loci against four Korean races of Xoo that were represented by the prevailing BLB isolates under Xoo differential system. The results of the bioassay using a selected set of 96 accessions showed that a large number of accessions (93.75%) were resistant to K1 race, while the least number of accessions (34.37%) resisted K3a race. For races K2 and K3, the resistant germplasm proportion remained between 66.67 to 70.83%. The genotypic data produced SNP matrix for a total of 293,379 SNPs. After imputation the missing data was removed, which exhibited 34,724 SNPs for association analysis. GWAS results showed strong signals of association at a threshold of [-log10(P-value)] more than 5 (K1 and K2) and more than 4 (K3 and K3a) for nine of the 39 SNPs, which are plausible candidate loci of resistance genes. These SNP loci were positioned on rice chromosome 2, 9, and 11 for K1 and K2 races, whereas on chromosome 4, 6, 11, and 12 for K3 and K3a races. The significant loci detected have also been illustrated, NBS-LRR type disease resistance protein, SNARE domain containing protein, Histone deacetylase 19, NADP-dependent oxidoreductase, and other expressed and unknown proteins. Our results provide a better understanding of the distribution of genetic variation of BLB resistance to Korean pathogen races and breeding of resistant rice cultivars.

Pages 97-106 |Read More| doi: 10.21475/poj.10.02.17.pne400

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Relative tolerance of different species of Brassica to cadmium toxicity: Coordinated role of antioxidant defense and glyoxalase systems

Jubayer Al Mahmud, Mirza Hasanuzzaman*, Kamrun Nahar, Anisur Rahman, Masayuki Fujita*

Laboratory of Plant Stress Responses, Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795, Japan

Department of Agroforestry and Environmental Science, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh

Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh

Department of Agricultural Botany, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh

Abstract

The present study was carried out to examine the metal accumulation and tolerance abilities of three Brassica species (B. napus, B. campestris, and B. juncea) seedlings exposed to two levels of cadmium (Cd) stress (0.25 and 0.5 mM CdCl2 for three days). Of the Brassica species studied, B. juncea accumulated the highest amount of Cd in a dose-dependent manner, and in every case, the Cd content was higher in the roots than the shoots. Cadmium stress reduced seedlings biomass, leaf relative water content (RWC), and chlorophyll (chl) content, whereas proline (Pro), MDA, and H2O2 content and lipoxygenase (LOX) activity increased in all species. Under Cd stress, ascorbate (AsA) content reduction was lower and glutathione (GSH) content increase was higher in B. juncea compared with other species. Monodehydroascorbate reductase (MDHAR), glutathione reductase (GR), and superoxide dismutase (SOD) activities increased significantly in B. juncea under Cd stress compared with the other species. Catalase (CAT) activity did not decrease in B. juncea due to Cd stress, compared with the other species. Dehydroascorbate reductase (DHAR) activity decreased with both levels of Cd stress in all species except for B. juncea under 0.25 mM CdCl2 stress. Glyoxalase system components performed better in B. juncea than the other species under Cd stress. Methylglyoxal (MG) increased substantially under both levels of Cd stress, but MG content was lower in B. juncea compared with the others. Considering the antioxidant defense and glyoxalase systems performance B. juncea is relatively tolerant species to Cd toxicity though it accumulated highest Cd.

 

Pages 107-117 |Read More| doi: 10.21475/poj.10.02.17.pne409



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