bims-pisump Biomed News
on Pisum
Issue of 2018–06–17
six papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН
  1. Genome of wild mandarin and domestication history of mandarin.
  2. Gene network of oil accumulation reveals expression profiles in developing embryos and fatty acid composition in Upland cotton.
  3. Global transcriptome analysis of grapevine (Vitis vinifera L.) leaves under salt stress reveals differential response at early and late stages of stress in table grape cv. Thompson Seedless.
  4. Effects of water stress on water use efficiency of irrigated and rainfed wheat in the Loess Plateau, China.
  5. Identification of nicotianamine synthase genes in Triticum monococcum and their expression under different Fe and Zn concentrations.
  6. Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models.
  1. Mol Plant. 2018 Jun 06. pii: S1674-2052(18)30187-4. [Epub ahead of print]
    Genome of wild mandarin and domestication history of mandarin.
    Lun Wang, Fa He, Yue Huang, Jiaxian He, Shuizhi Yang, Jiwu Zeng, Chongling Deng, Xiaolin Jiang, Yiwen Fang, Shaohua Wen, Rangwei Xu, Huiwen Yu, Xiaoming Yang, Guangyan Zhong, Chuanwu Chen, Xiang Yan, Changfu Zhou, Hongyan Zhang, Zongzhou Xie, Robert M Larkin, Xiuxin Deng, Qiang Xu.
      Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to occur in South China, which has been one of the cultivation centers for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. The citric acid level was dramatically reduced in cultivated mandarins. To understand the genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. The results showed that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South of the Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group, there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a genomic region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.
    DOI:  https://doi.org/10.1016/j.molp.2018.06.001
  2. J Plant Physiol. 2018 Jun 04. pii: S0176-1617(18)30256-6. [Epub ahead of print]228 101-112
    Gene network of oil accumulation reveals expression profiles in developing embryos and fatty acid composition in Upland cotton.
    Yanpeng Zhao, Yumei Wang, Yi Huang, Yupeng Cui, Jinping Hua.
      Cottonseed oil accumulated dramatically from 20 days post-anthesis (DPA) to 30 DPA in Upland cotton (Gossypium hirsutum L.). To reveal the gene network of oil accumulation and fatty acid composition in developing embryos, embryos at 10, 20 and 30 DPA in cottonseed were sampled and used for transcriptome sequencing (RNA-Seq). In total, 8629, 7891, and 12,555 differentially expressed genes (DEGs) were identified in the comparison sets of '20 DPA vs 10 DPA', '30 DPA vs 20 DPA', and '30 DPA vs 10 DPA', respectively. The gene network highlighted the dynamic expression profiles of oil accumulation in fatty acid (FA) synthesis, FA desaturation, and triacylglycerol (TAG) biosynthesis. WRI1 and NF-YB6 were suggested elite transcription factors in regulating lipid metabolism. Compared with the gene expression levels in developing seeds, GhPDAT was highly expressed and might play a more important role than GhDGAT in transforming diacylglycerol to TAG in cotton. Expression patterns of 12 FA-biosynthesis-related genes were validated by quantitative real-time PCR (qRT-PCR) method. To reveal the reason for the high content of linoleic acid (C18:2) in cottonseed oil, we carried out a comparative analysis of gene expression levels in Upland cotton, rapeseed (Brassica napus), and oleaster (Olea europaea). Compared with in rapeseed and oleaster, GhFAD2 genes were up-regulated and GhFAD3 genes down-regulated in cottonseed, taking into account the relative high amount of C18:2 but low content of linolenic acid (C18:3) in Upland cotton. The present study offers new information to interpret the mechanism of the FA biosynthesis network and to alter FA composition in cotton breeding projects.
    Keywords:  Developing embryos; Fatty acid composition; Gene network; Gossypium hirsutum; Oil accumulation; RNA-Seq
    DOI:  https://doi.org/10.1016/j.jplph.2018.06.002
  3. Plant Physiol Biochem. 2018 May 31. pii: S0981-9428(18)30249-3. [Epub ahead of print]129 168-179
    Global transcriptome analysis of grapevine (Vitis vinifera L.) leaves under salt stress reveals differential response at early and late stages of stress in table grape cv. Thompson Seedless.
    Anuradha Upadhyay, Tulsi Gaonkar, Ajay Kumar Upadhyay, Satisha Jogaiah, Manisha P Shinde, Narendra Y Kadoo, Vidya S Gupta.
      Among the different abiotic stresses, salt stress has a significant effect on the growth and yield of grapevine (Vitis vinifera L.). In this study, we employed RNA sequence based transcriptome analysis to study salinity stress response in grape variety Thompson Seedless. Salt stress adversely affected the growth related and physiological parameters and the effect on physiological parameters was significant within 10 days of stress imposition. A total of 343 genes were differentially expressed in response to salt stress. Among the differentially expressed genes (DEGs) only 42 genes were common at early and late stages of stress. The gene enrichment analysis revealed that GO terms related to transcription factors were over-represented. Among the DEGs, 52 were transcription factors belonging to WRKY, EREB, MYB, NAC and bHLH families. Salt stress significantly affected several pathways like metabolic pathways, biosynthesis of secondary metabolites, membrane transport development related pathways etc. 343 DEGs were distributed on all the 19 chromosomes, however clustered regions of DEGs were present on chromosomes 2, 5, 6 and 12 suggesting probable QTLs for imparting tolerance to salt and other abiotic stresses. Real-time PCR of selected genes in control and treated samples of grafted and own root vines demonstrated that rootstock influenced expression of salt stress responsive genes. Microsatellite regions were identified in ten selected salt responsive genes and highly polymorphic markers were identified using fifteen grape genotypes. This information will be useful for the identification of key genes involved in salt stress tolerance in grape. The identified DEGs could also be useful for genome wide analysis for the identification of polymorphic markers for their subsequent use in molecular breeding for developing salt tolerant grape genotypes.
    Keywords:  Abiotic stress; Grapes; Polymorphic markers; RNA-Seq; Rootstock effect; Salinity
    DOI:  https://doi.org/10.1016/j.plaphy.2018.05.032
  4. Sci Total Environ. 2018 Jun 07. pii: S0048-9697(18)32090-4. [Epub ahead of print]642 1-11
    Effects of water stress on water use efficiency of irrigated and rainfed wheat in the Loess Plateau, China.
    Ning Jin, Wei Ren, Bo Tao, Liang He, Qingfu Ren, Shiqing Li, Qiang Yu.
      The Loess Plateau, the largest arid and semi-arid zone in China, has been confronted with more severe water resource pressure and a growing demand for food production under global changes. For developing sustainable agriculture in this region, it is critical to learn spatiotemporal variations in water use efficiency (WUE) of main crops (e.g. winter wheat in this region) under various water management practices. In this study, we classified irrigated and rainfed wheat areas based on MODIS data, and calculated the winter wheat yield by using an improved light use efficiency model. The actual evapotranspiration (ETa) of winter wheat and the evapotranspiration drought index (EDI) were also investigated. Then we mainly examined the synergistic relationship between crop yield, ETa, and WUE, and analyzed the variations in WUE of irrigated and rainfed wheat under water stress during the 2010-2011 growing season. The results suggested that winter wheat in the Loess Plateau was primarily dominated by rainfed wheat. The average yield of irrigated wheat was 3928.4 kg/ha, 22.2% more than that of rainfed wheat. High spatial heterogeneities of harvest index (HI) and maximum light use efficiency (εmax) were found in the Loess Plateau. The ETa of irrigated wheat was 10.2% more than that of rainfed wheat. The ratio of irrigated and rainfed wheat under no water stress was 31.55% and 17.16%, respectively. With increasing water stress, the WUE of rainfed wheat decreased more quickly than that of irrigated wheat. The WUE variations in winter wheat under water stress depended strongly on the synergistic effects of two WUE components (crop yield and ETa) and their response to environmental conditions as well as water management practices (irrigated or rainfed). Our findings enhance our current understanding of the variations in WUE as affected by water stress under various water use conditions in arid and semi-arid areas.
    Keywords:  Irrigated and rainfed wheat; Light use efficiency model; MODIS NDVI time series; Water stress; Water use efficiency (WUE)
    DOI:  https://doi.org/10.1016/j.scitotenv.2018.06.028
  5. Gene. 2018 Jun 06. pii: S0378-1119(18)30667-X. [Epub ahead of print]
    Identification of nicotianamine synthase genes in Triticum monococcum and their expression under different Fe and Zn concentrations.
    Xuye Du, Huinan Wang, Jiefang He, Bin Zhu, Juan Guo, Wenqian Hou, Qingbei Weng, Xiaocun Zhang.
      In graminaceous plants, nicotianamine (NA) is an important component of metal acquisition. NA is synthesized from S-adenosyl-l-methionine (SAM) catalyzed by nicotianamine synthase (NAS). Here, eight Triticum monococcum NAS (TmNAS) genes were cloned and characterized. Amino acid sequence analysis showed that TmNAS genes had high sequence identity with those from Triticum aestivum, Zea mays, Oryza sativa and Hordeum vulgare. Phylogenetic analysis showed that NAS genes were classified into two distinct groups, e.g. group I and group II. Expression analysis demonstrated that two of the TmNAS genes in group II were highly expressed in shoot tissues, and the other six TmNAS genes in group I were expressed in root tissues. Further analysis indicated that root-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-deficiency growth, while shoot-specific TmNAS genes were up-regulated under conditions of Fe- or Zn-sufficiency. These results help us understand the NAS genes in T. monococcum and provide novel genetic resources for improving Fe and Zn concentrations in common wheat.
    Keywords:  Expression; Fe; Nicotianamine synthase; Triticum monococcum; Zn
    DOI:  https://doi.org/10.1016/j.gene.2018.06.015
  6. Mol Phylogenet Evol. 2018 Jun 07. pii: S1055-7903(18)30187-8. [Epub ahead of print]
    Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models.
    Ling Fang, Frederik Leliaert, Phil M Novis, Zhenhua Zhang, Huan Zhu, Guoxiang Liu, David Penny, Bojian Zhong.
      Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to recover the optimal phylogenetic relationships by minimizing conflicting signals.
    Keywords:  GC-heterogeneous sites; Green algae; heterogeneous models; phylogenetic signals; phylogenomics
    DOI:  https://doi.org/10.1016/j.ympev.2018.06.006
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