bims-plasge 2018-05-13 papers

on Plastid Genes

Issue of 2018‒05‒13
ten papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato.
Genome-wide evidence for divergent selection between populations of a major agricultural pathogen.
Genetic improvement of the shoot architecture and yield in soybean plants via the manipulation of GmmiR156b.
Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection.
Invoking adaptation to decipher the genetic legacy of past climate change.
SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth.
Comparative metabolomic analysis of seed metabolites associated with seed storability in rice (Oryza sativa L.) during natural aging.
Seed coat thickness in the evolution of angiosperms.
The ACC deaminase expressing endophyte Pseudomonas spp. Enhances NaCl stress tolerance by reducing stress-related ethylene production, resulting in improved growth, photosynthetic performance, and ionic balance in tomato plants.
Effects of climate on fatty acid profile in Camelina sativa.

Plant Biotechnol J. 2018 May 05.

Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato.

Mohammad Yazdani, Zhaoxia Sun, Hui Yuan, Shaohua Zeng, Theodore W Thannhauser, Julia Vrebalov, Qiyue Ma, Yimin Xu, Zhangjun Fei, Joyce Van Eck, Shiping Tian, Yaakov Tadmor, James J Giovannoni, Li Li.

  Carotenoids are critically important to plants and humans. The ORANGE (OR) gene is a key regulator for carotenoid accumulation, but its physiological roles in crops remain elusive. In this study, we generated transgenic tomato ectopically overexpressing the Arabidopsis wild type OR (AtORWT ) and a 'golden SNP'-containing OR (AtORHis ). We found that AtORHis initiated chromoplast formation in very young fruit and stimulated carotenoid accumulation at all fruit developmental stages, uncoupled from other ripening activities. The elevated levels of carotenoids in the AtOR lines were distributed in the same sub-plastidial fractions as in wild type tomato, indicating an adaptive response of plastids to sequester the increased carotenoids. Microscopic analysis revealed that the plastid sizes were increased in both AtORWT and AtORHis lines at early fruit developmental stages. Moreover, AtOR overexpression promoted early flowering, fruit set, and seed production. Ethylene production and the expression of ripening-associated genes were also significantly increased in the AtOR transgenic fruit at ripening stages. RNA-Seq transcriptomic profiling highlighted the primary effects of OR overexpression on the genes in the processes related to RNA, protein, and signalling in tomato fruit. Taken together, these results expand our understanding of OR in mediating carotenoid accumulation in plants and suggest additional roles of OR in affecting plastid size as well as flower and fruit development, thus making OR a target gene not only for nutritional biofortification of agricultural products but also for alteration of horticultural traits. This article is protected by copyright. All rights reserved.

Keywords:   OR ; carotenoids; early flowering; fruit set; plastids; tomato

DOI:  https://doi.org/10.1111/pbi.12945
Mol Ecol. 2018 May 05.

Genome-wide evidence for divergent selection between populations of a major agricultural pathogen.

Fanny E Hartmann, Bruce A McDonald, Daniel Croll.

The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and position of selective sweeps across the genome between populations. Using a XtX-based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host-driven selection. Selective sweep regions harbored genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1111/mec.14711
Plant Biotechnol J. 2018 May 05.

Genetic improvement of the shoot architecture and yield in soybean plants via the manipulation of GmmiR156b.

Zhengxi Sun, Chao Su, Jinxia Yun, Qiong Jiang, Lixiang Wang, Youning Wang, Dong Cao, Fang Zhao, Qingsong Zhao, Mengchen Zhang, Bin Zhou, Lei Zhang, Fanjiang Kong, Baohui Liu, Yiping Tong, Xia Li.

  The optimization of plant architecture in order to breed high-yielding soybean cultivars is a goal of researchers. Tall plants bearing many long branches are desired, but only modest success in reaching these goals has been achieved. MicroRNA156 (miR156)-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene modules play pivotal roles in controlling shoot architecture and other traits in crops like rice and wheat. However, the effects of miR156-SPL modules on soybean architecture and yield, and the molecular mechanisms underlying these effects, remain largely unknown. In this study, we achieved substantial improvements in soybean architecture and yield by overexpressing GmmiR156b. Transgenic plants produced significantly increased numbers of long branches, nodes, and pods, and they exhibited an increased 100-seed weight, resulting in a 46-63% increase in yield per plant. Intriguingly, GmmiR156b overexpression had no significant impact on plant height in a growth room or under field conditions; however, it increased stem thickness significantly. Our data indicate that GmmiR156b modulates these traits mainly via the direct cleavage of SPL transcripts. Moreover, we found that GmSPL9d is expressed in the shoot apical meristem and axillary meristems of soybean, and that GmSPL9d may regulate axillary bud formation and branching by physically interacting with the homeobox gene WUSCHEL (WUS), a central regulator of axillary meristem formation. Together, our results identify GmmiR156b as a promising target for the improvement of soybean plant architecture and yields, and they reveal a new and conserved regulatory cascade involving miR156-SPL-WUS that will help researchers decipher the genetic basis of plant architecture. This article is protected by copyright. All rights reserved.

Keywords:   GmmiR156 ; SPL ; Soybean; plant architecture; shoot branching; yield

DOI:  https://doi.org/10.1111/pbi.12946
Gene. 2018 May 03. pii: S0378-1119(18)30481-5. [Epub ahead of print]

Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection.

Chunhui Zhu, Xuefeng Li, Jingyuan Zheng.

  Hot pepper (Capsicum annuum L.), which is a member of the Solanaceae family, is becoming an increasingly important vegetable crop worldwide. Cucumber mosaic virus (CMV) is a destructive virus that can cause leaf distortion and fruit lesions, affecting pepper production. However, studies on the responses to CMV infection in pepper at the transcriptional level are limited. In this study, the transcript profiles of pepper leaves after CMV infection were investigated using Illumina and single-molecule real-time (SMRT) RNA-sequencing (RNA-seq). A total of 2143 differentially expressed genes (DEGs) were identified at five different stages. Gene ontology (GO) and KEGG analysis revealed that these DEGs were involved in the response to stress, defense response and plant-pathogen interaction pathways. Among these DEGs, several key genes that consistently appeared in studies of plant-pathogen interactions had increased transcript abundance after inoculation, including chitinase, pathogenesis-related (PR) protein, TMV resistance protein, WRKY transcription factor and jasmonate ZIM-domain protein. Nine of these DEGs were further validated by quantitative real-time-PCR (qRT-PCR). Furthermore, a total of 73, 597 alternate splicing (AS) events were identified in the pepper leaves after CMV infection, distributed in 12, 615 genes. The intron retention of WRKY33 (Capana09g001251) might be involved in the regulation of CMV infection. Taken together, our study provides a transcriptome-wide insight into the molecular basis of resistance to CMV infection in pepper leaves and potential candidate genes for improving resistance cultivars.

Keywords:  Cucumber mosaic virus (CMV); Hot pepper; RNA-seq; Transcriptome

DOI:  https://doi.org/10.1016/j.gene.2018.05.004
Ecology. 2018 May 05.

Invoking adaptation to decipher the genetic legacy of past climate change.

Guillaume de Lafontaine, Joseph D Napier, Rémy J Petit, Feng Sheng Hu.

  Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next-generation sequencing technologies, high-resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern-day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called "temporal conditional neutrality" has taken place: some alleles favored in glacial environments become selectively neutral in modern-day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for addressing the interplay of demographic and adaptive evolutionary responses to Quaternary climate dynamics, the research agenda initially envisioned by Davis and Shaw (2001). This article is protected by copyright. All rights reserved.

Keywords:  Quaternary; adaptation; climate change; gene flow; genetic diversity; genetic drift; migration; natural selection; population genomics; postglacial; range shift

DOI:  https://doi.org/10.1002/ecy.2382
Mol Plant. 2018 May 02. pii: S1674-2052(18)30134-5. [Epub ahead of print]

SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth.

Junling Huai, Xinyu Zhang, Jialong Li, Tingting Ma, Ping Zha, Yanjun Jing, Rongcheng Lin.

Plants continuously monitor environmental conditions (such as light and temperature) and adjust their growth and development accordingly. The transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4) regulates both light and temperature signaling pathways. Here, we identified ENHANCED PHOTOMORPHOGENIC2 (EPP2) as a new repressor of photomorphogenesis in red, far-red, and blue light. Map-based cloning revealed that EPP2 encodes the SEUSS (SEU) transcription regulator. The C-terminus of SEU has transcriptional activation activity and SEU physically interacts with PIF4. Moreover, SEU promotes the expression of many genes, including auxin biosynthetic and responsive genes, and regulates IAA levels in plants. SEU associates with regulatory regions in INDOLE-3-ACETIC ACID INDUCIBLE6 (IAA6) and IAA19 in a PIF4-independent manner, whereas the binding of PIF4 to these genes requires SEU. Furthermore, mutations in SEU affect H3K4me3 methylation at IAA6 and IAA19, and SEU positively regulates warm temperature-mediated hypocotyl growth together with PIF4. Therefore, our results reveal that SEU acts as a central regulator to integrate light and temperature signals to control plant growth by coordinating with PIF4.

DOI: https://doi.org/10.1016/j.molp.2018.04.005
Plant Physiol Biochem. 2018 May 01. pii: S0981-9428(18)30178-5. [Epub ahead of print]127 590-598

Comparative metabolomic analysis of seed metabolites associated with seed storability in rice (Oryza sativa L.) during natural aging.

Shijuan Yan, Wenjie Huang, Jiadong Gao, Hua Fu, Jun Liu.

  Seed storability is an important trait for crop breeding, however, the mechanism underlying seed storability remains largely unknown. Here, a mass spectrometry-based comparative metabolomic study was performed for rice seeds before and after 24-month natural storage between two hybrid rice cultivars, IIYou 998 (IIY) with low storability and BoYou 998 (BY) with relative high storability. A total of 48 metabolites among 90 metabolite peaks detected were conclusively identified, and most of them are involved in the primary metabolism. During the 24-month storage, 19 metabolites with significant changes in abundance were found in the storage-sensitive IIY seeds, but only 8 in the BY seeds, most of which are free amino acids and soluble sugars. The observed changes of the metabolites in IIY seeds that are consistent with our protoemics results are likely to be involved in its sensitivity to storage. Levels of all identified 18 amino acid-related metabolites and most sugar-related metabolites were significantly higher in IIY seeds both before and after storage. However the level of raffinose was lower in IIY seeds before and after storage, and did not change significantly throughout the storage period in both two cultivars, suggesting its potential role in seed storability. Taken together, these results may help to improve our understanding of seed storability.

Keywords:  Chemical compounds; Fuctose; GC-MS; Glucose; Leucine; Lysine; Metabolomics; Methionine; Oryza sativa L; PubChem CID: 10542; PubChem CID: 5793; PubChem CID: 5962; PubChem CID: 5984; PubChem CID: 5988; PubChem CID: 6106; PubChem CID: 6137; PubChem CID: 6287; PubChem CID: 6288; PubChem CID: 6305; Raffinose; Storability; Sucrose; Threonine; Tryptophan; Valine

DOI:  https://doi.org/10.1016/j.plaphy.2018.04.020
Cell Mol Life Sci. 2018 May 05.

Seed coat thickness in the evolution of angiosperms.

Olivier Coen, Enrico Magnani.

  The seed habit represents a remarkable evolutionary advance in plant sexual reproduction. Since the Paleozoic, seeds carry a seed coat that protects, nourishes and facilitates the dispersal of the fertilization product(s). The seed coat architecture evolved to adapt to different environments and reproductive strategies in part by modifying its thickness. Here, we review the great natural diversity observed in seed coat thickness among angiosperms and its molecular regulation in Arabidopsis.

Keywords:  Fertilization; Integument; Ovule; Seed coat; Seed coat thickness; Seed evolution; Seed maternal tissues

DOI:  https://doi.org/10.1007/s00018-018-2816-x
Plant Physiol Biochem. 2018 Apr 30. pii: S0981-9428(18)30196-7. [Epub ahead of print]127 599-607

The ACC deaminase expressing endophyte Pseudomonas spp. Enhances NaCl stress tolerance by reducing stress-related ethylene production, resulting in improved growth, photosynthetic performance, and ionic balance in tomato plants.

Khin Thuzar Win, Tanaka Fukuyo, Okazaki Keiki, Yoshinari Ohwaki.

  Plant growth promoting bacteria (PGPB) endophytes that express 1-aminocyclopropane-1-carboxylate (ACC) deaminase reportedly confer plant tolerance to abiotic stresses such as salinity by lowering stress-related ethylene levels. Two preselected ACC deaminase expressing endophytic Pseudomonas spp. strains, OFT2 and OFT5, were compared in terms of their potential to promote plant growth, leaf water contents, photosynthetic performance, and ionic balance of tomato plants under conditions of moderate NaCl stress (75 mM). Salinity stress strongly affected growth, leaf water contents, and photosynthetic performance of tomato seedlings, and inoculation with either OFT2 or OFT5 ameliorated these adverse effects. Decreases in plant biomass due to salinity stress were significant in both uninoculated control plants and in plants inoculated with OFT2 compared with plants without NaCl stress. However, no reductions in total biomass were observed in plants that were inoculated with the OFT5 strain. Strain OFT5 influenced growth, physiological status, and ionic balance of tomato plants more efficiently than strain OFT2 under NaCl stress. In particular, inoculated OFT5 reduced salt-induced ethylene production by tomato seedlings, and although it did not reduce shoot uptake of Na, it promoted shoot uptake of other macronutrients (P, K, and Mg) and micronutrients (Mn, Fe, Cu, and Zn). These nutrients may activate processes that alleviate the effects of salt, suggesting that OFT5 can be used to improve nutrient uptake and plant growth under moderate salt-affected conditions by reducing stress-related ethylene levels.

Keywords:  ACC deaminase; Ethylene; Mineral ions; Photosynthesis; Plant growth; Salt stress

DOI:  https://doi.org/10.1016/j.plaphy.2018.04.038
Cell Mol Biol (Noisy-le-grand). 2018 Apr 30. 64(5): 91-96

Effects of climate on fatty acid profile in Camelina sativa.

Zahra Raziei, Danial Kahrizi, Hosein Rostami-Ahmadvandi.

Due to the importance of Camelina for low expectation (water and other inputs) and as an oil crop, Soheil cultivar was cultivated in Ardebil, Hamedan, Rasht, Ilam, Kermanshah, Karaj, Mashhad, Ahvaz and Bushehr Provinces. Fatty acids were measured with MG-Mass. Results showed that morphological traits were not very dependent on the climate, but the profile of the fatty acids was dependent. ANOVA of the effects of climate on the saturated fatty acid showed that there were significant differences between climates for all studied SFAs (P<0.01) with the exception of Lauric acid. Mean squares of the effects of climate on the Unsaturated Fatty Acids (MUFA) in showing that there were significant differences between climates for all studied MUFAs (P<0.01). Mean squares of the effects of climate on the amount of polyunsaturated fatty acids (PUFA), oil percentage and protein content of seeds indicated that there were significant differences between climates for all these studied traits. Mean squares of the effects of climate on the amount of polyunsaturated fatty acids (PUFA), oil percentage and protein content of seeds indicated that there were significant differences between climates for all these studied traits. The statistical analysis for the effects of Climate on the ratio of the Saturated Fatty Acid (SFA) in Camelina sativa showed that there were significant differences (P<0.01) for SFA, MUSFA, PUFA, MP, P:S and MP:S. Briefly, in the cold climates, the percentage of unsaturated fatty acids was higher. So it is possible to the cultivation of this plant in cold provinces for nutritional purposes and in tropical provinces for industrial and sanitary purposes.

Keywords: Camelina sativa.; Climate; Fatty acid profile; MUSFA; PUFA; SFA