bims-pisump 2018-06-03 papers

on Pisum

Issue of 2018‒06‒03
seven papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Genetic analysis of yield and agronomic traits under reproductive stage drought stress in rice using a high-resolution linkage map.
Diversity of Organellar Genomes in Non-photosynthetic Diatoms.
Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).
Understanding the genetic regulation of anthocyanin biosynthesis in plants - Tools for breeding purple varieties of fruits and vegetables.
In pea stipules a functional photosynthetic electron flow occurs despite a reduced dynamicity of LHCII association with photosystems.
Targeted cloning of a large gene cluster from Lecanicillium genome by Cre/loxP based method.
Definition of two new symbiovars, sv. lupini and sv. mediterranense, within the genera Bradyrhizobium and Phyllobacterium efficiently nodulating Lupinus micranthus in Tunisia.

Gene. 2018 May 23. pii: S0378-1119(18)30583-3. [Epub ahead of print]

Genetic analysis of yield and agronomic traits under reproductive stage drought stress in rice using a high-resolution linkage map.

Uttam Bhattarai, Prasanta K Subudhi.

  Drought stress at the reproductive stage of rice crop leads to huge loss in grain yield. Identification and introgression of large effect drought tolerant QTLs are necessary to develop drought tolerant rice varieties. Compared to the high-density linkage maps, widely spaced markers lead to identification of QTLs with large confidence intervals which are difficult to incorporate in a breeding program. A previously generated genotyping-by-sequencing (GBS) based linkage map consisting of 4748 SNP markers was used to map QTLs in Cocodrie × N-22 recombinant inbred line (RIL) population. Twenty-one QTLs were discovered for days to flowering (DTF), plant height (PH), leaf rolling score (LRS), plant dry matter content (DM), spikelet fertility (SF), grain yield (GY), yield index (YI), and harvest index (HI) under drought stress. A major QTL qPH1.38 was identified in a narrow confidence interval on chromosome 1. The QTLs, qDTF3.01 and qPH1.38, overlapped with the previously identified QTL qDTY1.1 and Hd9, respectively. Another large-effect QTL qLRS1.37 was identified close to the sd1 locus on chromosome 1. A grain yield QTL qGY1.42 located on chromosome 1 contained only 4 candidate genes. There was no overlapping of QTLs for the root traits and the yield attributes. The important candidate genes present within the large effect QTL regions are MYB transcription factors, no apical meristem protein (NAC), potassium channel protein, nuclear matrix protein1, and chlorophyll A-B binding protein. The large effect QTLs (qDTF3.01, qPH1.38, and qLRS1.37) and a novel grain yield QTL qGYS1.42 can be used to incorporate in elite breeding lines to develop drought-tolerant rice varieties.

Keywords:  Candidate genes; Genotyping by sequencing (GBS); QTL mapping; Recombinant inbred lines; Reproductive stage; Single nucleotide polymorphism

DOI:  https://doi.org/10.1016/j.gene.2018.05.086
Protist. 2018 Apr 27. pii: S1434-4610(18)30033-6. [Epub ahead of print]169(3): 351-361

Diversity of Organellar Genomes in Non-photosynthetic Diatoms.

Ryoma Kamikawa, Tomonori Azuma, Ken-Ichiro Ishii, Yusei Matsuno, Hideaki Miyashita.

  We determined the complete sequences of the plastid and mitochondrial genomes of three non-photosynthetic Nitzschia spp., as well as those of a photosynthetic close relative, Nitzschia palea. All the plastid genomes and the three mitochondrial genomes determined were found to be circularly mapping, and the other mitochondrial genomes were predicted to be of a linear form with telomere-like structures at both ends. We found that all the non-photosynthetic plastid genomes are streamlined and lack a common gene set: two RNA genes, and 60 protein-coding genes, most of which are related to photosynthetic functions. Nevertheless, the non-photosynthetic plastid genomes commonly retain ATP synthase complex genes, although atpE is missing in Nitzschia sp. NIES-3581 and three other non-photosynthetic species lack atpF instead of atpE. This observation suggests an evolutionary constraint against the loss of ATP synthase complex genes. All the non-photosynthetic diatom plastid genomes lacked two genes, thiS and thiG, involved in thiamin biosynthesis. Consistent with this gene loss, non-photosynthetic Nitzschia spp. were incapable of thriving in vitamin B1-lacking media. This study clearly demonstrated not only the evolutionary trends of plastid genome reduction but also the linkage between plastid genome reduction and a biological change of nutrient requirements in Nitzschia.

Keywords:  ATP synthase complex; Nitzschia; mitochondria; plastids; vitamin B1.

DOI:  https://doi.org/10.1016/j.protis.2018.04.009
Mol Phylogenet Evol. 2018 May 24. pii: S1055-7903(17)30744-3. [Epub ahead of print]

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).

Charles S P Foster, Murray J Henwood, Simon Y W Ho.

  Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics.

Keywords:  Molecular systematics; Pimelea; chloroplast genome; monophyly; phylogenetic clustering; riceflowers

DOI:  https://doi.org/10.1016/j.ympev.2018.05.018
Phytochemistry. 2018 May 24. pii: S0031-9422(18)30147-X. [Epub ahead of print]153 11-27

Understanding the genetic regulation of anthocyanin biosynthesis in plants - Tools for breeding purple varieties of fruits and vegetables.

Samuel Chaves-Silva, Adolfo Luís Dos Santos, Antonio Chalfun-Júnior, Jian Zhao, Lázaro E P Peres, Vagner Augusto Benedito.

  Anthocyanins are naturally occurring flavonoids derived from the phenylpropanoid pathway. There is increasing evidence of the preventative and protective roles of anthocyanins against a broad range of pathologies, including different cancer types and metabolic diseases. However, most of the fresh produce available to consumers typically contains only small amounts of anthocyanins, mostly limited to the epidermis of plant organs. Therefore, transgenic and non-transgenic approaches have been proposed to enhance the levels of this phytonutrient in vegetables, fruits, and cereals. Here, were review the current literature on the anthocyanin biosynthesis pathway in model and crop species, including the structural and regulatory genes involved in the differential pigmentation patterns of plant structures. Furthermore, we explore the genetic regulation of anthocyanin biosynthesis and the reasons why it is strongly repressed in specific cell types, in order to create more efficient breeding strategies to boost the biosynthesis and accumulation of anthocyanins in fresh fruits and vegetables.

Keywords:  Anthocyanin; Biofortification; Biosynthesis; Functional food; Genetic regulation; Nutraceutical; Plant breeding

DOI:  https://doi.org/10.1016/j.phytochem.2018.05.013
Biochim Biophys Acta. 2018 May 24. pii: S0005-2728(18)30129-4. [Epub ahead of print]

In pea stipules a functional photosynthetic electron flow occurs despite a reduced dynamicity of LHCII association with photosystems.

Martina Giovanardi, Laura Pantaleoni, Lorenzo Ferroni, Cristina Pagliano, Pascal Albanese, Costanza Baldisserotto, Simonetta Pancaldi.

  The flexible association of the light harvesting complex II (LHCII) to photosystem (PS) I and PSII to balance their excitation is a major short-term acclimation process of the thylakoid membrane, together with the thermal dissipation of excess absorbed energy, reflected in non-photochemical quenching of chlorophyll fluorescence (NPQ). In Pisum sativum, the leaf includes two main photosynthetic parts, the basal stipules and the leaflets. Since the stipules are less efficient in carbon fixation than leaflets, the adjustments of the thylakoid system, which safeguard the photosynthetic membrane against photodamage, were analysed. As compared to leaflets, the stipules experienced a decay in PSII photochemical activity. The supramolecular organization of photosystems in stipules showed a more conspicuous accumulation of large PSII-LHCII supercomplexes in the grana, but also a tendency to retain the PSI-LHCI-LHCII state transition complex and the PSI-LHCI-PSII-LHCII megacomplexes probably located at the interface between appressed and stroma-exposed membranes. As a consequence, stipules had a lower capacity to perform state transitions and the overall thylakoid architecture was less structurally flexible and ordered than in leaflets. Yet, stipules proved to be quite efficient in regulating the redox state of the electron transport chain and more capable of inducing NPQ than leaflets. It is proposed that, in spite of a relatively static thylakoid arrangement, LHCII interaction with both photosystems in megacomplexes can contribute to a regulated electron flow.

Keywords:  Chlorophyll fluorescence; Native gel electrophoresis; Phosphorylation; Photosystem; Pisum sativum; Thylakoid membrane

DOI:  https://doi.org/10.1016/j.bbabio.2018.05.013
J Microbiol Methods. 2018 May 23. pii: S0167-7012(18)30318-X. [Epub ahead of print]150 47-54

Targeted cloning of a large gene cluster from Lecanicillium genome by Cre/loxP based method.

Havy N Nguyen, Kei-Ichi Ishidoh, Hiroshi Kinoshita, Takuya Nihira.

  Functionally related genes often form a large gene cluster on fungal genomes. To analyze, by heterologous expression system, overall pathway in which a series of related genes are involved, the whole gene cluster should be introduced intact into the host strain. However, the construction of a genomic library based on cosmid or bacterial artificial chromosome, and screening of a clone harboring the target region are time consuming and usually require additional cloning of missing regions. The available PCR-based methods are convenient, but are likely to cause unexpected errors during long-range PCR. Therefore, in this study we developed a method for targeted cloning of a large gene cluster based on Cre/loxP-mediated recombination. loxP sequences were integrated at both edges of the targeted region, and the region was excised and cloned as a circular fosmid by in vitro Cre recombination. To facilitate the Cre/loxP-based method, a competent host-vector system was developed, including a double auxotrophic Lecanicillium PTk3 (ΔpyrG trp1-ku80-) strain and two vectors for introducing the loxP sequences, pUTlox and pCCPlox. A targeted region longer than 45 kb in length was successfully cloned by the Cre/loxP-based method.

Keywords:  Cre/loxP; Gene cluster cloning; Lecanicillium; Targeted cloning method

DOI:  https://doi.org/10.1016/j.mimet.2018.05.017
Syst Appl Microbiol. 2018 May 04. pii: S0723-2020(18)30187-5. [Epub ahead of print]

Definition of two new symbiovars, sv. lupini and sv. mediterranense, within the genera Bradyrhizobium and Phyllobacterium efficiently nodulating Lupinus micranthus in Tunisia.

Abdelhakim Msaddak, Mokhtar Rejili, David Durán, Luis Rey, José Manuel Palacios, Juan Imperial, Tomás Ruiz-Argüeso, Mohamed Mars.

  In this study, a polyphasic approach was used to analyze three representative strains (LmiH4, LmiM2 and LmiT21) from a collection of six previously described strains isolated in Tunisia from root nodules of Lupinus micranthus. The phylogenetic analysis of the concatenated rrs, recA and glnII genes showed that strain LmiH4 had 100% concatenated gene sequence identity with the type strain Bradyrhizobium retamae Ro19T. Similarly, strain LmiM2 shared 100% concatenated gene sequence identity with the species Bradyrhizobium valentinum LmjM3T. However, strain LmiT21 showed an identical concatenated gene sequence with reference strain Phyllobacterium sophorae CCBAU03422T. The recA-glnII concatenated protein-coding genes used produced incongruent phylogenies compared with 16S rDNA phylogeny. The nodC gene analysis showed that the strains were phylogenetically divergent to the Bradyrhizobium symbiovars defined to date, and represented two new symbiovars. Plant infection analysis revealed that the three strains showed moderate host range and symbiotic specificities. Based on their symbiotic characteristics, we propose that the three strains isolated from Lupinus micranthus nodules belong to two new symbiovars, with the first denominated lupini within the two species Bradyrhizobium valentinum (type strain LmiM2) and B. retamae (type strain LmiH4), and the second denominated mediterranense within the species P. sophorae (type strain LmiT21).

Keywords:  Bradyrhizobium; Lupinus micranthus; Phyllobacterium; Phylogeny; Symbiovars

DOI:  https://doi.org/10.1016/j.syapm.2018.04.004