Plant omics

Mechanistic insights into longan (Dimocarpous longan Lour.) transcriptome for physiological characterization for defensive genes and differential gene expression analysis with longan embryogenic callus transcriptome

Longan is one of several subtropical and climateric fruit tree of South East Asia having economic and medicinal importance. To understand the mechanism behind altered expression of genetic variants towards various complex diseases, transcriptome analysis is pivotal in present biological scenario. Availability of transcriptomic data of longan facilitates its further functional genomics analysis, differential gene expression analysis and progressive research on the plant varieties of similar family belonging to Indian subcontinent. In the present study, a total number of 90,762,826 mixed paired end sequence reads from 7 different tissues of longan transcriptome (ID: SRR2864836) and 64,876,528 reads for longan embryogenic callus (EC) transcriptome (ID: SRR412534) were downloaded from SRA database, NCBI using SRA Tool Kit. A total number of 9,304 and 10,679 contigs (including scaffolded regions) were assembled from the longan and longan-EC clean reads. Cloud blast search was performed against multiple protein and nucleotide databases at NCBI to explore the mechanistic insights, of the longan transcriptome. A total 9,304 contigs/ putative transcripts were classified into 10 major biological processes, 30 GO functional groups, 08 various cellular components and 139 KEGG pathways. In blast analysis against Nr database, database of Arabidopsis thaliana, Zea mays and Oryza sativa 33 contigs were reported for possessing disease resistant proteins. Additionally differential gene expression analysis between longan and longan-EC transcripts showed a total of 34 genes to be highly upregulated and 26 downregulated genes. Thus our study paves way for further research to improvise and utilize its economic and medicinal characteristics of longan as reference in context to Indian plants viz. Litchi chinensis, Arytera divericata, Schleichera oleosa (Lour.), etc.

Pages 219-231 |Read More| Supplementary Data| doi: 10.21475/poj.10.05.17.pne721

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A timeline for Eustoma grandiflorum seedling production based on an in vitro germination protocol

Eustoma (Eustoma grandiflorum) is a high-rank ornamental cut flower, and propagation of plant material by seed is an important approach for high-volume production of Eustoma. Successful propagation using different parts of the Eustoma plant has been reported in numerous studies; however, to date there have been no studies comparing the timeline differences between in vitro and conventional germination growth methods. The objective of this study was to develop a convenient and straightforward in vitro protocol that decreases the lag time to germination and the seedling development periods. Seed germination and seedling growth was studied in Eustoma (Voyage type 2 pink) seeds using two different techniques, in vitro germination and conventional sowing in soil. Seeds sown under in vitro conditions exhibited faster (6 days) germination compared with seeds sown directly in soil (11 days). Half-strength Murashige and Skoog medium in vitro-grown seedlings (7 weeks) were more vigorous and produced true leaves earlier compared with conventionally-grown seedlings (15 weeks). In addition, when Eustoma seeds were sown in vitro, germination could be more easily tracked and visually compared with seeds sown in soil media. Therefore, the in vitro seed germination protocol developed in this study is straightforward, reproducible, and will amenable to facilitate efficient seedling production of Eustoma for commercial applications.

Egyptian Deserts Gene Bank, Desert Research Center, Egypt

This study offers the comprehensive analysis of the genetic diversity among six local varieties (Manfalouti; Nab El-Gamal; Hegazy; Wardi; Assuity; Araby) and three international varieties (Wonderful; Marked Bani Rafie; Red Bani Rafie) of pomegranate in Egypt, based on the behavior of ISTR, ISSR and SRAP markers profiles. A set of 24 ISTR, 16 ISSR and 30 SRAP primers combination were compared, concerning exposed the degree of resolution and efficiency of the discriminating capacity technique alongside with the level of genetic polymorphism, to determine which varieties evolved from the others. Considering the results, SRAP assay had superior, more sensitive, higher discrimination capacity and gives much more evidence about the total number of effective alleles (1411), number of polymorphic amplicons (312), PIC (0.94), assay efficiency index (47.04), effective multiples ratio (10.04) and marker index (9.74). Unexpectedly, the ISTR profile demonstrated a significant moderate level of polymorphism among tested genotypes. To further determine the genetic relationships and the distance among varieties, a graphic demonstration of combined UPGMA tree and the PCA analysis did assemble with clear resolution and accurate along with three category. Our findings confirm that combining different marker system were greatly better and more effective considered an important priority step toward diversity study and characterisation. We can point out that, the two-widespread varieties in Egypt Manfalouti, and Nab El-Gamal, formed a high homogeneity in genetic similarity with the Wonderful, as an essential global species for breeding programs, efforts widening the genetic base of pomegranates and the introduction of new genotypes in Egypt.

Pages 237-246 |Read More| doi: 10.21475/poj.10.05.17.pne794

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Application of fungal endophytes can be an alternative to control basal stem rot disease in oil palm, caused by Ganoderma boninense. Chitinase is a type of defensive protein synthesized by plants in response to biotic factors. The purpose of this study was to analyze the chitinase activity of oil palm as a defensive mechanism to fungal endophytes and pathogenic G. boninense. Four species of fungal endophytes, Trichoderma harzianum MTP 10 (Th-MTP10), Trichoderma longibrachiatum KBA 31 (Tl-KBA 31), Lasiodiplodia venezuelensis MJP 28 (Lv-MJP 28), Dothidiomycetes sp. MTD 29 (Dt-MTD 29) and one species of fungal pathogen G. boninense and with their each cell wall suspension were introduced to oil palm plantlets in axenic condition. Chitinase activity was observed from the root of oil palm plantlets inoculated with both living cell and cell wall suspension of endophytic fungi and pathogenic G. boninense. Results showed that chitinase activities varied in each fungal treatment and were significantly differed from control. Fungal cell wall elicitors were able to significantly induce chitinase activity after 1 week post treatment (wpt). Statistically, only the chitinase activity from fungal endophyte Lv-MJP 28 was significantly higher from others for 8 and 12 days. Pre-treatment of oil palm plantlet with fungal cell wall suspension for 1 wpt could induce the chitinase activity higher than control when, oil palm infected with fungal pathogen of Ganoderma boninense.

Pages 247-251 |Read More| doi: 10.21475/poj.10.05.17.pne853

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Major crop production does not yet match the population growth rate because multiple abiotic stresses hamper the growth and yield of these crops. Most of the plants can tolerate adverse climatic conditions by performing some adaptive machineries but to certain extent. Till date various biotechnological and molecular breeding research approaches have been directed towards developing resistance to single stress factor. However, development of crop plants resistant to a single stress is not an ideal solution in the current agriculture scenario. Occurrence of multiple stresses at a single point of time makes it difficult to formulate research strategies. Considering the huge loss of crop productivity due to these environmental factors, there is an urgent need to direct our research focus towards developing sustainable multi-stress resistance in plants to counter the adverse effect of climate change on the productivity of crops. RNA helicases are ubiquitous proteins that are found in both prokaryotes and eukaryotes. The largest RNA helicase family comprises the DEAD-box RNA helicases which are involved in many aspects of RNA metabolism and in diverse biological processes in plants including regulation of multiple abiotic stress responses. The DEAD-box RNA helicases can be considered as means to identify pathways involved in multiple abiotic stress tolerance. In this review, we summarize the recent advances in elucidating the functions of the DEAD-box RNA helicases in multiple abiotic stress responses and future challenges. We also briefly discussed about our recent research efforts (published and on-going) in this direction. This review would help to formulate new research endeavours utilizing the DEAD-box helicase genes in development of multiple abiotic stress tolerant plants through genetic engineering and biotechnology. Target specific multiplex and multigene CRISPR/Ca9 genome editing would be ideal approach to edit different abiotic stress responsive DEAD-box RNA helicase genes to develop sustainable multiple abiotic stress tolerance in crop plants.

Pages 252-262 |Read More| doi: 10.21475/poj.10.05.17.pne855

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Abstract

The major problem with in vitro propagation of lilies is small bulblet size, and the initial size of bulblets not only strongly affects growth and morphogenesis rates but also the transition between various vegetative and reproductive phases during development after planting. Therefore, bulblet growth is the most important factor in understanding how lily bulblets grow in vitro and the role of starch converted from sucrose in the medium on the growth mechanism in lilies, with the aim of revealing the effective in vitro culture condition to enhance in vivo performance of lily bulblets. The results of this study show bulblet growth correlates with the use of starch granule reserves inside explant tissue and in the medium. The main factor determining the growth of bulblets in vitro is explant size due to internal storage of starch, which plays a vital role in bulblet growth irrespective of cultivar. Furthermore, internal storage of sucrose plays a vital role and influences regeneration and bulblet growth in both in vitro and in vivo cultures. Therefore, the size of the bulblets produced in vitro strongly affects performance after planting. There is a high correlation (R2= 0.9672) between bulb weight after the growth season and initial bulb weight and therefore, the ontogenetic age of bulblets at planting. Hence, culturing lily scale explants in a high sucrose concentration during regeneration of bulblets in vitro to increase bulblet size is the main point of interest for future production.

In this study, thirty Linum usitatissimum varieties were classified based on pigments, malondialdehyde, betaine and proline contents as well as antioxidant enzymes activity under cold stress. Based on the UPGMA clustering, varieties were divided into three clusters. Cluster I comprised of 13 varieties with low cold tolerance. Cluster II contained 5 varieties with moderate cold tolerance and cluster III manifested of 12 varieties with high cold tolerance. Our analyses based on multiple physiological indexes, revealed cold hardiness difference among Linum usitatissimum varieties which could provide good reference for commercial flax production. The TN-97-55, TN-97-92, TN-97-290 and TN-97-291 were identified as tolerant varieties and recommended for cultivation in clod areas.

Weed has become one of the most serious problems in aerobic rice systems. Weed management in aerobic rice system needs a manipulation of optimum N fertilizer application to control the weed and simultaneously enhance aerobic rice growth performance. In this study, three types of N sources (urea, ammonium sulphate and ammonium nitrate) with concentration starting from (0, 60, 120, 180 and 240 kg ha-1) were evaluated for effective control of the bioassay species, Eleusine indica, while observing the rice injury level. The data on weed (emergence and shoot fresh weight), while rice growth (root length, shoot fresh weight, shoot height and leaf greenness) was collected in this study. It was found that urea at a higher application rate of 240 kg ha-1 strongly inhibit the emergence and shoot growth of E. indica by >78%. Conversely, ammonium sulphate and ammonium nitrate gave moderate inhibition (58-65% inhibition) on weed emergence and shoot growth at higher application rates of 240 kg ha-1, respectively. Significant stimulation effect on rice root growth, shoot height, shoot fresh weight and leaf greenness was noticed at a low application rate of 60 kg ha-1 urea, while ammonium sulphate and ammonium nitrate only exerts its stimulation effect starting at 120 kg ha-1. Stimulation effect on the rice growth was likely negligible at 0 and 4 DAS across urea, ammonium sulphate and ammonium nitrate application rates. However, the rice plants growth increases with increasing growth stage. The finding suggest that application of urea at 240 kg ha-1 starting from 8 DAS of rice growth stage was the most efficient application rate in inhibiting E. indica with the stimulation effect on the growth of rice seedlings.