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Frontiers of Agricultural Science and Engineering

  • Cover Illustration

    2016, Vol.3  No.4

    Banana (Musa acuminata) is becoming an excellent model for starch metabolism in fresh starchy fruits due to its relatively high starch content and large starch granules. This picture describes the banana fruits at 20 days after emerging from pseudostem, which represents the beginning of synthesizing starch. A total of 16 BAM genes were identified in the banana genome. Findings obtained from comprehensive transcriptomic analysis indicated [Detail] ...

    Table of Contents

ISSN 2095-7505 (Print)
ISSN 2095-977X (Online)
CN 10-1204/S
Postal Subscription Code 80-906

Frontiers of Agricultural Science and Engineering has been added to Directory of Open Access Journals (DOAJ) on September 12, 2016.

This journal is a member of, and subscribes to the principles of, the Committee on Publication Ethics (COPE)

, Volume 3 Issue 4

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EDITORIAL
REVIEW
Transgenic technologies in cassava for nutritional improvement and viral disease resistance: a key strategy for food security in Africa
Maliwan NACONSIE,Peng ZHANG
Front. Agr. Sci. Eng. . 2016, 3 (4): 285-294.  https://doi.org/10.15302/J-FASE-2016119
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As a major staple food source in Africa and other tropical developing countries, cassava (Manihot esculenta) provides basic sustenance for many subsistence farmers. However, cassava roots mainly accumulate starch with limited contribution of other nutrients such as proteins and vitamins. Also, two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), cause great losses in cassava production in sub-Saharan Africa and the Indian sub-continent. Genetic engineering provides promising approaches to improve nutritional value and increase resistance to viral diseases in cassava. This report presents several successful case studies on engineering protein content by overexpression of nutritious storage proteins and improving cassava resistance to viral diseases by RNA interference. Perspectives on the sustainable acquisition of new knowledge and development of biotechnology to solve these bottlenecks are discussed.

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RESEARCH ARTICLE
Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication of cassava (Manihot esculenta)
Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG
Front. Agr. Sci. Eng. . 2016, 3 (4): 295-307.  https://doi.org/10.15302/J-FASE-2016126
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Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

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Annotation and validation of genes involved in photosynthesis and starch synthesis from a Manihot full-length cDNA library
Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG
Front. Agr. Sci. Eng. . 2016, 3 (4): 308-320.  https://doi.org/10.15302/J-FASE-2016113
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A full-length cDNA library from leaf and root tissues of cassava (Manihot esculenta) Arg7 and one accession of its wild ancestor W14 (M. esculenta ssp. flabellifolia) has been constructed. The library is comprised of four sub-libraries, containing 32640 recombinant clones, 6028 cDNA clones from their 5′ ends, and 128 clones from the 3′ ends were sequenced. In total, 5013 high-quality expressed sequence tags (ESTs) and 1259 unigenes were obtained. Of these, 746 unigenes were identified by their sequence homologies to ESTs from model plants, and 323 unigenes were mapped onto 114 different KEGG pathways. From these, 24 differentially expressed genes involved in starch metabolism and photosynthesis were identified and five of them were selected to compare their expression level between Arg7 and W14. Notably, Arg7 has a higher net photosynthesis rate in leaves, higher ribulose-1,5-bisphosphate carboxy-lase oxygenase activities in leaves, and higher AGPase activity in roots. This resource is the first EST collection from wild cassava and should be of value for gene discovery, genome annotation and studies of Manihot evolution.

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A bacterial artificial chromosome-based physical map of Manihot esculenta ssp. flabellifolia
Yuhua FU,Zhiqiang XIA,Shujuan WANG,Xin CHEN,Cheng LU,Mingcheng LUO,Hongbin ZHANG,Wenquan WANG
Front. Agr. Sci. Eng. . 2016, 3 (4): 321-329.  https://doi.org/10.15302/J-FASE-2016124
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Cassava (Manihot esculenta) is known as the third most important food crop in the tropics and also used for industrial feedstock for biofuels. Two new bacterial artificial chromosome (BAC) libraries were constructed for W14 (M. Esculenta ssp. flabellifolia), a wild ancestor of domesticated cassava. The libraries were constructed with EcoRI and HindIII insertion vectors, respectively. The EcoRI library has 29952 clones with an average insert size of 115 kb, while the HindIII library consists of 29952 clones with an average insert of 129 kb. The combined libraries contain a total of 59904 clones with an average insert size of 125 kb, representing approximately 10 × haploid genome equivalents. A total of 29952 clones were fingerprinted and resulted in a cassava physical map composed of 2485 contigs with an average physical length of 336 kb and 2909 singletons, representing approximately 762 Mb of the cassava genome. 5000 clones located at the ends of BAC contigs were selected and sequenced. A total of 6077 SNPs and 231 indels were identified, that covered 459 gene sequences, of which 6 genes were associated with starch and sucrose metabolism. This BAC-based physical map provides valuable tools to understand the genetics and evolution of cassava.

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Efficient regeneration system applicable to five Musa cultivars
Juhua LIU,Peiguang SUN,Jing ZHANG,Jiashui WANG,Jianbin ZHANG,Jingyi WANG,Caihong JIA,Pengzhao GAO,Biyu XU,Zhiqiang JIN
Front. Agr. Sci. Eng. . 2016, 3 (4): 330-334.  https://doi.org/10.15302/J-FASE-2016118
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Banana (Musa spp.) is an important staple food, economic crop, and nutritional fruit worldwide. Hybridization is seriously hampered by the long generation time, polyploidy, and sterility of most cultivars. Establishment of an efficient regeneration and transformation system for banana is critical for their genetic improvement. An efficient and reproducible transformation system for banana using direct organogenesis was developed. Media containing benzylaminopurine (BA) combined with one of four other growth regulators was evaluated for the regeneration efficiency of five Musa cultivars and the ability to induce/support development of new banana shoots. The result indicated that the greatest number of shoots per explant for all five Musa cultivars was obtained using MS medium supplemented with 8.9 mmol·L1 BA and 9.1 mmol·L1 thidiazuron (TDZ). In 240–270 d, one immature male flower could regenerate between 380 and 456, 310–372, 200–240, 130–156, and 100–130 well-developed shoots for Gongjiao, Red banana, Rose banana, Baxi, and Xinglongnaijiao, respectively. Such a system will facilitate molecular breeding and functional genomics of banana.

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Cold stress responsive microRNAs and their targets in Musa balbisiana
Jingyi WANG,Juhua LIU,Caihong JIA,Hongxia MIAO,Jianbin ZHANG,Zhuo WANG,Biyu XU,Zhiqiang JIN
Front. Agr. Sci. Eng. . 2016, 3 (4): 335-345.  https://doi.org/10.15302/J-FASE-2016121
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Cold stress is an environmental factor affecting plant development and production. Recently, microRNAs (miRNAs) have been found to be involved in several plant processes such as growth regulation and stress responses. Although miRNAs and their targets have been identified in several banana species, their participation during cold accumulation in banana remains unknown. In this study, two small RNA libraries were generated from micropropagated plantlets of Musa balbisiana grown at normal and low temperature (5°C). A total of 69 known miRNAs and 32 putative novel miRNAs were detected in the libraries by Solexa sequencing. Sixty-four cold-inducible miRNAs were identified through differentially expressed miRNAs analysis. Among 43 miRNAs belonging to 26 conserved miRNA families with altered expression, 18 were upregulated and 25 downregulated under cold stress. Of 21 putative novel miRNAs with altered expression, four were downregulated and 17 upregulated. Furthermore, eight miRNAs were validated by stem-loop qRT-PCR and their dynamic differential expression was analyzed. In addition, 393 target genes of 58 identified cold-responsive miRNAs were predicted and categorized by function. These results provide important information for further characterization and functional analysis of cold-responsive miRNAs in banana.

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Genome-wide identification and expression analysis of the β-amylase genes strongly associated with fruit development, ripening, and abiotic stress response in two banana cultivars
Hongxia MIAO,Peiguang SUN,Yulu MIAO,Juhua LIU,Jianbin ZHANG,Caihong JIA,Jingyi WANG,Zhuo WANG,Zhiqiang JIN,Biyu XU
Front. Agr. Sci. Eng. . 2016, 3 (4): 346-356.  https://doi.org/10.15302/J-FASE-2016127
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β-amylase (BAM) is an important enzyme involved in conversion of starch to maltose in multiple biological processes in plants. However, there is currently insufficient information on the BAM gene family in the important fruit crop banana. This study identified 16 BAM genes in the banana genome. Phylogenetic analysis showed that MaBAMs were classified into four subfamilies. Most MaBAMs in each subfamily shared similar gene structures. Conserved motif analysis showed that all identified MaBAM proteins had the typical glyco hydro 14 domains. Comprehensive transcriptomic analysis of two banana genotypes revealed the expression patterns of MaBAMs in different tissues, at various stages of fruit development and ripening, and in responses to abiotic stresses. Most MaBAMs showed strong transcript accumulation changes during fruit development and late-stage ripening. Some MaBAMs showed significant changes under cold, salt, and osmotic stresses. This finding indicated that MaBAMs might be involved in regulating fruit development, ripening, and responses to abiotic stress. Analysis of five hormone-related and seven stress-relevant elements in the promoters of MaBAMs further revealed that BAMs participated in various biological processes. This systemic analysis provides new insights into the transcriptional characteristics of the BAM genes in banana and may serve as a basis for further functional studies of such genes.

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The secondary laticifer differentiation in rubber tree is induced by trichostatin A, an inhibitor of histone acetylation
Shixin ZHANG,Shaohua WU,Weimin TIAN
Front. Agr. Sci. Eng. . 2016, 3 (4): 357-362.  https://doi.org/10.15302/J-FASE-2016125
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The secondary laticifer, a specific tissue in the secondary phloem of rubber tree, is differentiated from the vascular cambia. The number of the secondary laticifer in the trunk bark of rubber tree is positively correlated with rubber yield. Although jasmonates have been demonstrated to be crucial in the regulation of secondary laticifer differentiation, the mechanism for the jasmonate-induced secondary laticifer differentiation remains to be elucidated. By using an experimental morphological technique, the present study revealed that trichostatin A (TSA), an inhibitor of histone deacetylation, could induce the secondary laticifer differentiation in a concentration-dependent manner. The results suggest that histone acetylation is essential for the secondary laticifer differentiation in rubber tree.

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Relationship between the number of tapping-induced secondary laticifer lines and rubber yield among Hevea germplasm
Yueyi CHEN,Xinsheng GAO,Xiaofei ZHANG,Weimin TIAN
Front. Agr. Sci. Eng. . 2016, 3 (4): 363-367.  https://doi.org/10.15302/J-FASE-2016122
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The lack of suitable early selection parameters means that traditional rubber breeding for yield is time-consuming and inefficient. Laticifer is a tissue specific for natural rubber biosynthesis and storage in rubber tree. The number of the secondary laticifers in the trunk bark tissues is positively correlated with rubber yield in the matured rubber trees that are regularly tapped. In the present study, the rubber yield from 280 of 4–5 year-old virgin trees from 7 cross combinations was compared with the number of newly differentiated secondary laticifers caused by tapping. Results showed that the number of tapping-induced lines of secondary laticifers varied in different germplasm and was positively related to the rubber yield, indicating this could be used as a suitable parameter for early evaluation of yield potential of rubber trees.

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Optimum nitrogen fertilization of Calophyllum inophyllum seedlings under greenhouse conditions
Wentao ZOU,Ruifeng JIA,Jinchang YANG,Rongsheng LI,Guangtian YIN
Front. Agr. Sci. Eng. . 2016, 3 (4): 368-374.  https://doi.org/10.15302/J-FASE-2016120
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A greenhouse pot experiment was conducted to study the effects of nitrogen fertilization on Calophy- llum inophyllum seedlings grown with 0, 50, 100, 150, 200, 300, 400 and 600 mg N per seedling according to exponential functions. Seedling height, root collar diameter, leaf area and total biomass increased with increasing fertilization from 0 to 200 mg N per seedling and decreased with further increase in fertilization from 300 to 600 mg N per seedling. The net photosynthetic rate, stomatal conductance, intercellular CO2 concentration and transpiration rate of C. inophyllum seedlings showed a unimodal parabolic trend, with peak values of 7.29 mmol·m2·s1, 0.071 mol·m2·s1, 220 mmol·mol1 and 1.34 mmol·m2·s1, respectively, when the rate of fertilization was 200 mg N per seedling. Photosynthetic gas exchange parameters were significantly different among nitrogen treatments. Based on the critical values of leaf N and P concentration and N/P ratio, the optimum amount of nitrogen of C. inophyllum seedlings was 200–400 mg per seedling for leaf N and P concentration, and 100–400 mg per seedling for N/P ratio. It was concluded that 200–400 mg N per seedling was the most suitable nitrogen range for C. inophyllum seedlings.

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COMMENTS
Comments on the special issue on tropical crops of FASE
Luiz J C B CARVALHO
Front. Agr. Sci. Eng. . 2016, 3 (4): 375-376.  https://doi.org/10.15302/J-FASE-2016129
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