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Li W.,CAS Wuhan Botanical Garden | Li W.,Chinese Academy of Sciences | Li W.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Li W.,University of Chinese Academy of Sciences | And 9 more authors.
PLoS ONE | Year: 2015

Red-fleshed kiwifruit (Actinidia chinensis Planch. 'Hongyang') is a promising commercial cultivar due to its nutritious value and unique flesh color, derived from vitamin C and anthocyanins. In this study, we obtained transcriptome data of 'Hongyang' from seven developmental stages using Illumina sequencing. We mapped 39-54 million reads to the recently sequenced kiwifruit genome and other databases to define gene structure, to analyze alternative splicing, and to quantify gene transcript abundance at different developmental stages. The transcript profiles throughout red kiwifruit development were constructed and analyzed, with a focus on the biosynthesis and metabolism of compounds such as phytohormones, sugars, starch and L-ascorbic acid, which are indispensable for the development and formation of quality fruit. Candidate genes for these pathways were identified through MapMan and phylogenetic analysis. The transcript levels of genes involved in sucrose and starch metabolism were consistent with the change in soluble sugar and starch content throughout kiwifruit development. The metabolism of L-ascorbic acid was very active, primarily through the L-galactose pathway. The genes responsible for the accumulation of anthocyanin in red kiwifruit were identified, and their expression levels were investigated during kiwifruit development. This survey of gene expression during kiwifruit development paves the way for further investigation of the development of this uniquely colored and nutritious fruit and reveals which factors are needed for high quality fruit formation. This transcriptome data and its analysis will be useful for improving kiwifruit genome annotation, for basic fruit molecular biology research, and for kiwifruit breeding and improvement. Copyright: © 2015 Li et al.


Hu M.,Hainan University | Hu M.,Chinese Academy of Sciences | Hu M.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Hu W.,Chinese Academy of Sciences | And 5 more authors.
Frontiers in Plant Science | Year: 2016

Reverse transcription quantitative real-time polymerase chain reaction (real-time PCR, also referred to as quantitative RT-PCR or RT-qPCR) is a highly sensitive and high-throughput method used to study gene expression. Despite the numerous advantages of RT-qPCR, its accuracy is strongly influenced by the stability of internal reference genes used for normalizations. To date, few studies on the identification of reference genes have been performed on cassava (Manihot esculenta Crantz). Therefore, we selected 26 candidate reference genes mainly via the three following channels: reference genes used in previous studies on cassava, the orthologs of the most stable Arabidopsis genes, and the sequences obtained from 32 cassava transcriptome sequence data. Then, we employed ABI 7900 HT and SYBR Green PCR mix to assess the expression of these genes in 21 materials obtained from various cassava samples under different developmental and environmental conditions. The stability of gene expression was analyzed using two statistical algorithms, namely geNorm and NormFinder. geNorm software suggests the combination of cassava4.1_017977 and cassava4.1_006391 as sufficient reference genes for major cassava samples, the union of cassava4.1_014335 and cassava4.1_006884 as best choice for drought stressed samples, and the association of cassava4.1_012496 and cassava4.1_006391 as optimal choice for normally grown samples. NormFinder software recommends cassava4.1_006884 or cassava4.1_006776 as superior reference for qPCR analysis of different materials and organs of drought stressed or normally grown cassava, respectively. Results provide an important resource for cassava reference genes under specific conditions. The limitations of these findings were also discussed. Furthermore, we suggested some strategies that may be used to select candidate reference genes. © 2016 Hu, Hu, Xia, Zhou and Wang.


Zhao P.,Chinese Academy of Sciences | Zhao P.,Hainan University | Liu P.,Hong Kong Baptist University | Shao J.,Hong Kong Baptist University | And 9 more authors.
Journal of Experimental Botany | Year: 2015

Cassava is one of the most drought-tolerant crops, however, the underlying mechanism for its ability to survive and produce under drought remains obscure. In this study, two cassava cultivars, SC124 and Arg7, were treated by gradually reducing the soil water content. Their responses to the drought stress were examined through their morphological and physiological traits and isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. SC124 plants adapted a 'survival' mode under mild drought stress as evidenced by early stomatal closure and a reduction in the levels of various photosynthetic proteins and photosynthetic capacity, resulting in early growth quiescence. In contrast, Arg7 plants underwent senescence of older leaves but continued to grow, although at a reduced rate, under mild drought. SC124 plants were more capable of surviving prolonged severe drought than Arg7. The iTRAQ analysis identified over 5000 cassava proteins. Among the drought-responsive proteins identified in the study were an aquaporin, myo-inositol 1-phosphate synthases, and a number of proteins involved in the antioxidant systems and secondary metabolism. Many proteins that might play a role in signalling or gene regulation were also identified as drought-responsive proteins, which included several protein kinases, two 14-3-3 proteins, several RNA-binding proteins and transcription factors, and two histone deacetylases. Our study also supports the notion that linamarin might play a role in nitrogen reallocation in cassava under drought. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.


Huang M.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Fu L.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Sun X.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Di R.,Rutgers University | Zhang J.,Key Laboratory of Biology and Genetic Resources of Tropical Crops
Acta Physiologiae Plantarum | Year: 2016

The starch-rich duckweed Landoltia punctata is a valuable aquatic plant in wastewater purification, bioenergy production, and many other applications. A highly efficient callus induction and plant regeneration protocol is desirable so that biotechnology can be used to develop new varieties with added value and adaptation. We studied both known and unknown factors that influence callus induction in L. punctata and obtained almost 100 % induction rate in 30 days. The optimum medium for callus induction was MS basal medium supplemented with 1 % sorbitol, 15 mg/L 2,4-D, and 2 mg/L 6-BA. Green fragile callus was induced from the meristematic region in the budding pouches. The optimum photoperiod for callus induction was 16-h day, and the optimum explant orientation was dorsal side down on the medium. The optimum medium for callus subculture was WPM basal medium supplemented with 2 % sorbitol, 4 mg/L 2,4-D, and 0.5 mg/L TDZ. Green callus could be maintained by subculture once every 4 weeks. However, when the subculture cycle was prolonged to 6 weeks or longer, yellow fragile embryogenic callus was obtained. The optimum plant regeneration medium was MS medium supplemented with 0.5 % sucrose, 1 % sorbitol, and 1.0 mg/L 6-BA with frond regeneration rates of approximately 90 %. The regenerated fronds rooted in Hoagland’s liquid medium in 1 week. The callus induction and frond regeneration protocol was tested for its efficiency in geographically distinct strains 5502, 8721, and 9264. Thus, we obtained a rapid and efficient protocol for callus induction and frond regeneration of L. punctata, which takes only 9 weeks. © 2016, Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.


Chang W.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Chang W.,Chinese Academy of Sciences | Liu X.,Key Laboratory of Biology and Genetic Resources of Tropical Crops | Liu X.,Chinese Academy of Sciences | And 5 more authors.
Plant Cell Reports | Year: 2016

Key message: SpAQP1was strongly induced by salt in an ABA-independent way, promoted seed germination and root growth in transgenic tobaccos and increased salt tolerance by increasing the activities of antioxidative enzymes. Abstract: Aquaporin (AQP) plays crucial roles in the responses of plant to abiotic stresses such as drought, salt and cold. Compared to glycophytes, halophytes often have excellent salt and drought tolerances. To uncover the molecular mechanism of halophyte Sesuvium portulacastrum tolerance to salt, in this study, an AQP gene, SpAQP1, from S. portulacastrum was isolated and characterized. The amino acid sequence of SpAQP1 shared high homology with that of plant plasma membrane intrinsic proteins (PIPs) and contained the distinct molecular features of PIPs. In the phylogenic tree, SpAQP1 was evidently classified as the PIP2 subfamily. SpAQP1 is expressed in roots, stems and leaves, and was significantly induced by NaCl treatment and inhibited by abscisic acid (ABA) treatment. When heterologously expressed in yeast and tobacco, SpAQP1 enhanced the salt tolerance of yeast strains and tobacco plants and promoted seed germination and root growth under salt stress in transgenic plants. The activity of antioxidative enzymes including superoxide dismutase, peroxidase and catalase was increased in transgenic plants overexpressing SpAQP1. Taken together, our studies suggested that SpAQP1 functioned in the responses of S. portulacastrum to salt stress and could increase salt tolerance by enhancing the antioxidative activity of plants. © 2015, Springer-Verlag Berlin Heidelberg.

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