bims-pisump Biomed News
on Pisum
Issue of 2018–07–29
twelve papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН
  1. Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application.
  2. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples.
  3. Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.
  4. Sex and the flower - developmental aspects of sex chromosome evolution.
  5. The putative peptide gene FEP1 regulates iron deficiency response in Arabidopsis.
  6. Evolutionary ecology of nectar.
  7. Size distribution of small interfering RNAs in various organs at different developmental stages is primarily determined by the dicing activity of Dicer-like proteins in plants.
  8. Phytohormones as targets for improving plant productivity and stress tolerance.
  9. FZP determines grain size and sterile lemma fate in rice.
  10. Staminate flower of Prunus s. l. (Rosaceae) from Eocene Rovno amber (Ukraine).
  11. Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval.
  12. Natural and targeted isovariants of the rice actin depolymerizing factor 2 can alter its functional and regulatory binding properties.
  1. Theor Appl Genet. 2018 Jul 21.
    Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application.
    Sherry Lou Hechanova, Manas R Prusty, Sung-Ryul Kim, LaRue Ballesfin, Joie Ramos, G D Prahalada, Kshirod K Jena.
      Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F1, and the F1 plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC1F1 and 73 BC2F1 plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F1, BC1F1, BC2F2, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.
    DOI:  https://doi.org/10.1007/s00122-018-3147-x
  2. Bioinformatics. 2018 Jul 19.
    Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples.
    Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang.
       Motivation: The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.
    Results: Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.
    Availability: The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp://47.94.193.106/pub.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/bty642
  3. Tree Physiol. 2018 Jul 19.
    Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.
    Longxin Wang, Qingzhang Du, Jianbo Xie, Daling Zhou, Beibei Chen, Haijiao Yang, Deqiang Zhang.
      Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.
    DOI:  https://doi.org/10.1093/treephys/tpy079
  4. Ann Bot. 2018 Jul 18.
    Sex and the flower - developmental aspects of sex chromosome evolution.
    Roman Hobza, Vojtech Hudzieczek, Zdenek Kubat, Radim Cegan, Boris Vyskot, Eduard Kejnovsky, Bohuslav Janousek.
       Background: The evolution of dioecious plants is occasionally accompanied by the establishment of sex chromosomes: both XY and ZW systems have been found in plants. Structural studies of sex chromosomes are now being followed up by functional studies that are gradually shedding light on the specific genetic and epigenetic processes that shape the development of separate sexes in plants.
    Scope: This review describes sex determination diversity in plants and the genetic background of dioecy, summarizes recent progress in the investigation of both classical and emerging model dioecious plants and discusses novel findings. The advantages of interspecies hybrids in studies focused on sex determination and the role of epigenetic processes in sexual development are also overviewed.
    Conclusions: We integrate the genic, genomic and epigenetic levels of sex determination and stress the impact of sex chromosome evolution on structural and functional aspects of plant sexual development. We also discuss the impact of dioecy and sex chromosomes on genome structure and expression.
    DOI:  https://doi.org/10.1093/aob/mcy130
  5. Plant Cell Physiol. 2018 Jul 19.
    The putative peptide gene FEP1 regulates iron deficiency response in Arabidopsis.
    Takashi Hirayama, Gui Jie Lei, Naoki Yamaji, Naoki Nakagawa, Jian Feng Ma.
      Iron is an essential element for all organisms, and plants have developed sophisticated systems to acquire iron and maintain iron homeostasis. We found that an Arabidopsis thaliana abscisic acid-hypersensitive mutant, aba hypersensitive germination2-1 (ahg2-1), that is known to be defective in mitochondrial mRNA regulation had increased expression of iron deficiency response genes. The ahg2-1 mutant had lower heme levels than the wild type. Transcriptome data further revealed that novel genes encoding short polypeptides were highly expressed in this mutant. The expression of one of these genes, which we named FE-UPTAKE-INDUCING PEPTIDE 1 (FEP1), was induced under iron-deficient conditions and was observed in the vascular tissues of the leaves and roots, as well as in leaf mesophyll cells. Notably, deletion or insertion mutations of FEP1 exhibited impaired iron accumulation in shoots but normal iron levels in roots. Artificially induced expression of FEP1 was sufficient to induce iron deficiency response genes, such as basic HELIX-LOOP-HELIX 38 (bHLH38), bHLH39, IRON-REGULATED TRANSPORTER1 (IRT1), and FERRIC REDUCTION OXIDASE2 (FRO2), and led to iron accumulation in planta. Further analysis confirmed that the encoded peptide, but not the FEP1 RNA, was responsible for this activity. Remarkably, the activation of bHLH39 by FEP1 was independent of FER-LIKE IRON DEFICIENCY INDUCED (FIT), a key transcription factor in the iron deficiency response. Taken together, our results indicate that FEP1 functions in iron homeostasis through a previously undescribed regulatory mechanism for iron acquisition in Arabidopsis.
    DOI:  https://doi.org/10.1093/pcp/pcy145
  6. Ann Bot. 2018 Jul 18.
    Evolutionary ecology of nectar.
    Amy L Parachnowitsch, Jessamyn S Manson, Nina Sletvold.
       Background: Floral nectar is an important determinant of plant-pollinator interactions and an integral component of pollination syndromes, suggesting it is under pollinator-mediated selection. However, compared to floral display traits, we know little about the evolutionary ecology of nectar. Combining a literature review with a meta-analysis approach, we summarize the evidence for heritable variation in nectar traits and link this variation to pollinator response and plant fitness. We further review associations between nectar traits and floral signals and discuss them in the context of honest signalling and targets of selection.
    Scope: Although nectar is strongly influenced by environmental factors, heritable variation in nectar production rate has been documented in several populations (mean h2 = 0.31). Almost nothing is known about heritability of other nectar traits, such as sugar and amino acid concentrations. Only a handful of studies have quantified selection on nectar traits, and few find statistically significant selection. Pollinator responses to nectar traits indicate they may drive selection, but studies tying pollinator preferences to plant fitness are lacking. So far, only one study conclusively identified pollinators as selective agents on a nectar trait, and the role of microbes, herbivores, nectar robbers and abiotic factors in nectar evolution is largely hypothetical. Finally, there is a trend for positive correlations among floral cues and nectar traits, indicating honest signalling of rewards.
    Conclusions: Important progress can be made by studies that quantify current selection on nectar in natural populations, as well as experimental approaches that identify the target traits and selective agents involved. Signal-reward associations suggest that correlational selection may shape evolution of nectar traits, and studies exploring these more complex forms of natural selection are needed. Many questions about nectar evolution remain unanswered, making this a field ripe for future research.
    DOI:  https://doi.org/10.1093/aob/mcy132
  7. Plant Cell Physiol. 2018 Jul 19.
    Size distribution of small interfering RNAs in various organs at different developmental stages is primarily determined by the dicing activity of Dicer-like proteins in plants.
    Midori Tabara, Misato Ohtani, Motoki Kanekatsu, Hiromitsu Moriyama, Toshiyuki Fukuhara.
      RNA silencing is a fundamental mechanism to maintain plant growth and development, and regulation of the size distribution of small interfering RNAs (siRNAs) is critical in the control of normal gene expression throughout a plant's lifecycle. However, the cause of organ- and developmental stage-specific accumulation of siRNAs has never been reported. Whereas 24-nt siRNAs accumulated about 5.3-fold more than 21-nt siRNAs in Arabidopsis rosette leaves, 21-nt and 24-nt siRNAs accumulated to similar levels in Arabidopsis pollen grains, rice spikelets and maize anthers. We successfully detected two distinct dsRNA-cleaving activities that produced 21-nt and 24-nt RNAs in cell-free extracts prepared from various organs at different developmental stages of A. thaliana, Brassica rapa, rice and maize. Although DCL4 transcript was expressed more than DCL3 transcript in most organs, the 21-nt RNA-producing activity of DCL4 or its orthologues was very low and was 5- to 10-fold lower than the 24-nt RNA-producing activity of DCL3 or its orthologues particularly in leaves, indicating that DCL4 activity is negatively regulated translationally or post-translationally in leaves. High dicing activity of DCL3 and DCL4 was detected in immature inflorescences, developing seeds, germinating embryos and callus, all of which contain actively dividing cells. In various organs at different developmental stages, the size distribution of siRNAs was positively correlated with the dicing activity of two Dicers, DCL3 and DCL4, or their orthologues. Taken together, the size distribution of siRNAs in most organs is primarily determined by the dicing activity of DCL3 and DCL4.
    DOI:  https://doi.org/10.1093/pcp/pcy144
  8. J Plant Physiol. 2018 Jul 18. pii: S0176-1617(18)30395-X. [Epub ahead of print]229 32-40
    Phytohormones as targets for improving plant productivity and stress tolerance.
    Joanna Ciura, Jerzy Kruk.
      In this review, we summarize the results of experiments that lead to altered levels of phytohormones in transgenic plants to improve plant productivity. The available data indicate that manipulating the level of phytohormones might also be a promising way to enhance the environmental stress tolerance of crop plants. In the regulation of the level of phytohormones, both biosynthesis and their catabolism pathways can be targeted for engineering purposes. Moreover, the signaling pathways of phytohormones should explored in this respect. In genetic modifications, conditional promoters must be developed to avoid undesired effects on growth. In order to find a practical application, the effects of genetic modifications should be further verified under field conditions and over a longer time scale.
    Keywords:  Phytohormones; Plant growth regulators; Stress tolerance; Transgenic plants
    DOI:  https://doi.org/10.1016/j.jplph.2018.06.013
  9. J Exp Bot. 2018 Jul 19.
    FZP determines grain size and sterile lemma fate in rice.
    Deyong Ren, Jiang Hu, Qiankun Xu, Yuanjiang Cui, Yu Zhang, Tingting Zhou, Yuchun Rao, Dawei Xue, Dali Zeng, Guangheng Zhang, Zhenyu Gao, Li Zhu, Lan Shen, Guang Chen, Longbiao Guo, Qian Qian.
      In grass, the spikelet is a unique inflorescence structure that directly determines grain yield. Despite a great deal of research, the molecular mechanisms behind spikelet development are not fully understood. In the study, FZP encodes an ERF domain protein, and functions in grain size and sterile lemma identity. Mutation of FZP causes smaller grains and degenerated sterile lemmas. The small fzp-12 grains were caused by a reduction in cell number and size in the hulls. Interestingly, the sterile lemma underwent a homeotic transformation into a rudimentary glume in the fzp-12 and fzp-13 mutants, whereas the sterile lemma underwent a homeotic transformation into a lemma in FZP over-expressing plants, suggesting that FZP specifically determines the sterile lemma identity. We confirmed the function of FZP by complementation, CRISPR-Cas9 gene editing, and cytological and molecular tests. Additionally, FZP interacts specifically with the GCC-box and DRE motifs, and may be involved in regulation of the downstream genes. Our results revealed that FZP plays a vital role in the regulation of grain size, and first provides clear evidence in support of the hypothesis that the lemma, rudimentary glume, and sterile lemma are homologous organs.
    DOI:  https://doi.org/10.1093/jxb/ery264
  10. J Plant Res. 2018 Jul 21.
    Staminate flower of Prunus s. l. (Rosaceae) from Eocene Rovno amber (Ukraine).
    Dmitry D Sokoloff, Michael S Ignatov, Margarita V Remizowa, Maxim S Nuraliev, Vladimir Blagoderov, Amin Garbout, Evgeny E Perkovsky.
      The late Eocene ambers provide plethora of animal and plant fossils including well-preserved angiosperm flowers from the Baltic amber. The Rovno amber from NW Ukraine resembles in many aspects the Baltic amber; however, only fossilized animals and some bryophytes have yet been studied from the Rovno amber. We provide the first detailed description of an angiosperm flower from Rovno amber. The flower is staminate with conspicuous hypanthium, double pentamerous perianth and whorled androecium of 24 stamens much longer than the petals. Sepals are sparsely pubescent and petals are densely hirsute outside. The fossil shares important features with extant members of Prunus subgen. Padus s. l. (incl. Laurocerasus, Pygeum and Maddenia), especially with its evergreen paleotropical species. It is described here as a new species Prunus hirsutipetala D.D.Sokoloff, Remizowa et Nuraliev. Our study provides the first convincing record of fossil flowers of Rosaceae from Eocene of Europe and the earliest fossil flower of Prunus outside North America. Our record of a plant resembling extant tropical species supports palaeoentomological evidences for warm winters in northwestern Ukraine during the late Eocene, as well as suggesting a more significant role of tropical insects in Rovno amber than inferred from Baltic amber.
    Keywords:  Amber; Eocene; Europe; Flower; Fossil; Prunus hirsutipetala; Rosaceae
    DOI:  https://doi.org/10.1007/s10265-018-1057-2
  11. New Phytol. 2018 Jul 21.
    Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval.
    Liming Cai, Zhenxiang Xi, André M Amorim, M Sugumaran, Joshua S Rest, Liang Liu, Charles C Davis.
      Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.
    Keywords:  climatic upheaval; flowering plants; genome evolution; global change; phylogenomics; speciation
    DOI:  https://doi.org/10.1111/nph.15357
  12. Biochem Biophys Res Commun. 2018 Jul 18. pii: S0006-291X(18)31569-9. [Epub ahead of print]
    Natural and targeted isovariants of the rice actin depolymerizing factor 2 can alter its functional and regulatory binding properties.
    Sonali Sengupta, Kanniah Rajasekaran, Niranjan Baisakh.
      Actin depolymerizing factors (ADFs) are ubiquitous actin-binding proteins that play essential roles in maintaining cellular actin dynamics by depolymerizing/severing F-actin. Plant ADF isoforms show functional divergence via differential biochemical and cellular properties. We have shown previously that ADF2 of rice (OsADF2) and smooth cordgrass (SaADF2) displayed contrasting biochemical properties and stress response in planta. As a proof-of-concept that amino acid variances contribute to such functional difference, single amino acid mutants of OsADF2 were generated based on its sequence differences with SaADF2. Biochemical studies showed that the single-site amino acid mutations altered actin binding, depolymerizing, and severing properties of OsADF2. Phosphosensitive mutations, such as serine-6>threonine, changed the regulatory phosphorylation efficiency of ADF2 variants. The N-terminal mutations had greater effect on the phosphorylation pattern of OsADF2, whereas C-terminal mutations affected actin binding and severing. The presence of introduced mutations in isovariants of monocot ADF suggests that these residues are significant control points regulating their functional divergence, including abiotic stress response.
    Keywords:  Actin depolymerizing factor 2; Isovariant; Mutation; Phosphorylation; Rice
    DOI:  https://doi.org/10.1016/j.bbrc.2018.07.073
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