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BMC Plant Biology

Edouard Severing, Luigi Faino, Suraj Jamge, Marco Busscher, Yang Kuijer-Zhang, Francesca Bellinazzo, Jacqueline Busscher-Lange, Virginia Fernández, Gerco C Angenent, Richard G H Immink, Alice Pajoro
BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. RESULTS: Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves...
July 13, 2018: BMC Plant Biology
Meiyu Ke, Zhen Gao, Jianqing Chen, Yuting Qiu, Liangsheng Zhang, Xu Chen
BACKGROUND: Flowers open at sunrise and close at sunset, establishing a circadian floral movement rhythm to facilitate pollination as part of reproduction. By the coordination of endogenous factors and environmental stimuli, such as circadian clock, photoperiod, light and temperature, an appropriate floral movement rhythm has been established; however, the underlying mechanisms remain unclear. RESULTS: In our study, we use waterlily as a model which represents an early-diverging grade of flowering plants, and we aim to reveal the general mechanism of flower actions...
July 11, 2018: BMC Plant Biology
Geeta Kumari, Ka Ho Wong, Aida Serra, Joon Shin, Ho Sup Yoon, Siu Kwan Sze, James P Tam
BACKGROUND: Jasmintides jS1 and jS2 from Jasminum sambac were previously identified as a novel family of cysteine-rich peptides (CRPs) with an unusual disulfide connectivity. However, very little else is known about jasmintides, particularly their molecular diversity and functions. Here, we report the discovery and characterization of a novel suite of jasmintides from J. sambac using transcriptomic, peptidomic, structural and functional tools. RESULTS: Transcriptomic analysis of leaves, flowers and roots revealed 14 unique jasmintide precursors, all of which possess a three-domain architecture comprising a signal peptide, a pro-domain and a mature jasmintide domain...
July 11, 2018: BMC Plant Biology
Jason D Fiedler, Christina Lanzatella, Serge J Edmé, Nathan A Palmer, Gautam Sarath, Rob Mitchell, Christian M Tobias
BACKGROUND: Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible. RESULTS: Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated...
July 9, 2018: BMC Plant Biology
Jianzi Huang, Xuehong Hao, Ye Jin, Xiaohuan Guo, Qing Shao, Kavitha S Kumar, Yogesh K Ahlawat, David E Harry, Chandrashekhar P Joshi, Yizhi Zheng
BACKGROUND: Pongamia (Millettia pinnata syn. Pongamia pinnata), an oilseed legume species, is emerging as potential feedstock for sustainable biodiesel production. Breeding Pongamia for favorable traits in commercial application will rely on a comprehensive understanding of molecular mechanism regulating oil accumulation during its seed development. To date, only limited genomic or transcript sequences are available for Pongamia, while a temporal transcriptome profiling of developing seeds is still lacking in this species...
July 9, 2018: BMC Plant Biology
G Ramakrishna, Parampreet Kaur, Deepti Nigam, Pavan K Chaduvula, Sangita Yadav, Akshay Talukdar, Nagendra Kumar Singh, Kishor Gaikwad
BACKGROUND: Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation...
July 9, 2018: BMC Plant Biology
Jian Ruan, Feng Guo, Yingying Wang, Xinguo Li, Shubo Wan, Lei Shan, Zhenying Peng
BACKGROUND: Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented. RESULTS: The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experienced AS throughout the plant, while in the case of others, the effect was organ-specific...
July 4, 2018: BMC Plant Biology
Summaira Riaz, Gabriella De Lorenzis, Dianne Velasco, Anne Koehmstedt, David Maghradze, Zviad Bobokashvili, Mirza Musayev, Goran Zdunic, Valerie Laucou, M Andrew Walker, Osvaldo Failla, John E Preece, Mallikarjuna Aradhya, Rosa Arroyo-Garcia
BACKGROUND: The mountainous region between the Caucasus and China is considered to be the center of domestication for grapevine. Despite the importance of Central Asia in the history of grape growing, information about the extent and distribution of grape genetic variation in this region is limited in comparison to wild and cultivated grapevines from around the Mediterranean basin. The principal goal of this work was to survey the genetic diversity and relationships among wild and cultivated grape germplasm from the Caucasus, Central Asia, and the Mediterranean basin collectively to understand gene flow, possible domestication events and adaptive introgression...
June 27, 2018: BMC Plant Biology
Mengjing Sun, Roeland E Voorrips, Greet Steenhuis-Broers, Wendy Van't Westende, Ben Vosman
BACKGROUND: The green peach aphid (GPA), Myzus persicae, is economically one of the most threatening pests in pepper cultivation, which not only causes direct damage but also transmits many viruses. Breeding aphid resistant pepper varieties is a promising and environmentally friendly method to control aphid populations in the field and in the greenhouse. Until now, no strong sources of resistance against the GPA have been identified. Therefore the main aims of this study were to identify pepper materials with a good level of resistance to GPA and to elucidate possible resistance mechanisms...
June 27, 2018: BMC Plant Biology
Ainur Ismagul, Nannan Yang, Elina Maltseva, Gulnur Iskakova, Inna Mazonka, Yuri Skiba, Huihui Bi, Serik Eliby, Satyvaldy Jatayev, Yuri Shavrukov, Nikolai Borisjuk, Peter Langridge
BACKGROUND: The relatively low efficiency of biolistic transformation and subsequent integration of multiple copies of the introduced gene/s significantly complicate the genetic modification of wheat (Triticum aestivum) and other plant species. One of the key factors contributing to the reproducibility of this method is the uniformity of the DNA/gold suspension, which is dependent on the coating procedure employed. It was also shown recently that the relative frequency of single copy transgene inserts could be increased through the use of nanogram quantities of the DNA during coating...
June 26, 2018: BMC Plant Biology
Haibo Wang, Shuang Zhao, Ke Mao, Qinglong Dong, Bowen Liang, Chao Li, Zhiwei Wei, Mingjun Li, Fengwang Ma
BACKGROUND: Improvement of water-use efficiency (WUE) can effectively reduce production losses caused by drought stress. A better understanding of the genetic determination of WUE in crops under drought stress has great potential value for developing cultivars adapted to arid regions. To identify the genetic loci associated with WUE and reveal genes responsible for the trait in apple, we aim to map the quantitative trait loci (QTLs) for carbon isotope composition, the proxy for WUE, applying two contrasting irrigating regimes over the two-year experiment and search for the candidate genes encompassed in the mapped QTLs...
June 26, 2018: BMC Plant Biology
Raj Deepika Chauhan, Getu Beyene, Nigel J Taylor
BACKGROUND: Morphogenic culture systems are central to crop improvement programs that utilize transgenic and genome editing technologies. We previously reported that CMD2-type cassava (Manihot esculenta) cultivars lose resistance to cassava mosaic disease (CMD) when passed through somatic embryogenesis. As a result, these plants cannot be developed as products for deployment where CMD is endemic such as sub-Saharan Africa or the Indian sub-continent. RESULT: In order to increase understanding of this phenomenon, 21 African cassava cultivars were screened for resistance to CMD after regeneration through somatic embryogenesis...
June 25, 2018: BMC Plant Biology
Luz G Muñoz-Sanhueza, YeonKyeong Lee, Molly Tillmann, Jerry D Cohen, Anne Kathrine Hvoslef-Eide
BACKGROUND: Quantitative measurement of actual auxin levels in plant tissue is complimentary to molecular methods measuring the expression of auxin related genes. Current analytical methods to quantify auxin have pushed the limit of detection to where auxin can be routinely quantified at the pictogram (pg) level, reducing the amount of tissue needed to perform these kinds of studies to amounts never imagined a few years ago. In parallel, the development of technologies like laser microdissection microscopy (LMD) has allowed specific cells to be harvested from discrete tissues without including adjacent cells...
June 25, 2018: BMC Plant Biology
Shu Wei, Xiang Li, Margaret Y Gruber, Biruk A Feyissa, Lisa Amyot, Abdelali Hannoufa
BACKGROUND: Trichomes and phenylpropanoid-derived phenolics are structural and chemical protection against many adverse conditions. Their production is regulated by a network that includes a TTG1/bHLH/MYB tri-protein complex in Arabidopsis. CSN5a, encoding COP9 signalosome subunit 5a, has also been implicated in trichome and anthocyanin production; however, the regulatory roles of CSN5a in the processes through interaction with the tri-protein complex has yet to be investigated. RESULTS: In this study, a new csn5a mutant, sk372, was recovered based on its altered morphological and chemical phenotypes compared to wild-type control...
June 25, 2018: BMC Plant Biology
Niels Aerts, Suzanne de Bruijn, Hilda van Mourik, Gerco C Angenent, Aalt D J van Dijk
BACKGROUND: Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6 GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed...
June 25, 2018: BMC Plant Biology
Xiaoyan Tang, Yiheng Wang, Yun Zhang, Shengnan Huang, Zhiyong Liu, Danli Fei, Hui Feng
BACKGROUND: Plastome mutants are ideal resources for elucidating the functions of plastid genes. Numerous studies have been conducted for the function of plastid genes in barley and tobacco; however, related information is limited in Chinese cabbage. RESULTS: A chlorophyll-deficient mutant of Chinese cabbage that was derived by ethyl methanesulfonate treatment on isolated microspores showed uniformly pale green inner leaves and slow growth compared with that shown by the wild type "Fukuda 50' ('FT')...
June 25, 2018: BMC Plant Biology
Heleen Coenen, Tom Viaene, Michiel Vandenbussche, Koen Geuten
BACKGROUND: MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants. RESULTS: We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events...
June 22, 2018: BMC Plant Biology
Jianxia Jiang, Jinjuan Bai, Shuxia Li, Xiaorong Li, Liyong Yang, Yuke He
BACKGROUND: Numerous regulatory genes participate in plant thermotolerance. In Arabidopsis, HEAT-INDUCED TAS1 TARGET2 (HTT2) is an important thermotolerance gene that is silenced by ta-siR255, a trans-acting siRNA. ta-siR255 is absent from heading Chinese cabbage (Brassica rapa ssp. pekinensis). Our previous attempt to overexpress the endogenous BrpHTT2 gene of heading Chinese cabbage (B. rapa ssp. pekinensis) failed because of cosuppression. In theory, heading Chinese cabbage can overexpress Arabidopsis HTT2 to improve thermotolerance in the absence of ta-siR255-mediated gene silencing and the weak potential of coexpression...
June 20, 2018: BMC Plant Biology
Bhakti Prinsi, Alfredo Simone Negri, Osvaldo Failla, Attilio Scienza, Luca Espen
BACKGROUND: Roots play a central role in plant response to water stress (WS). They are involved in its perception and signalling to the leaf as well as in allowing the plant to adapt to maintaining an adequate water balance. Only a few studies have investigated the molecular/biochemical responses to WS in roots of perennial plants, such as grapevine. This study compares two grapevine rootstock genotypes (i.e. 101.14 and M4) with different tolerance to WS, evaluating the responses at proteomic and metabolite levels...
June 20, 2018: BMC Plant Biology
Zhen Peng, Shoupu He, Wenfang Gong, Feifei Xu, Zhaoe Pan, Yinhua Jia, Xiaoli Geng, Xiongming Du
BACKGROUND: Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. RESULTS: In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels...
June 20, 2018: BMC Plant Biology
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