bims-plasge 2019-01-20 papers

on Plastid genes

Issue of 2019‒01‒20
six papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Undesired fertility restoration in msm1 barley associates with two mTERF genes.
Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids.
Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode.
The conserved theme of ribosome hibernation: from bacteria to chloroplasts of plants.
The genetic basis of inbreeding depression in potato.
Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton.

Theor Appl Genet. 2019 Jan 18.

Undesired fertility restoration in msm1 barley associates with two mTERF genes.

Timm Bernhard, Michael Koch, Rod J Snowdon, Wolfgang Friedt, Benjamin Wittkop.

KEY MESSAGE: The novel Rfm3 locus causing undesired fertility restoration in the msm1 cytoplasm of winter barley is located on the short arm of chromosome 6H. Undesired fertility restoration of cytoplasmic male sterile (CMS) mother lines in absence of the functional Rfm1 restorer gene is a significant problem for hybrid breeding in winter barley. Here, we describe that a novel restorer locus on the short arm of chromosome 6H, designated Rfm3, is closely linked to two mitochondrial transcription termination factor family (mTERF) protein coding genes. Genome-wide association studies in a multiparental mapping population revealed that two of the most significantly associated markers are located very close to these genes, with one marker lying directly within one mTERF gene sequence. Sequences of the candidate genes in the parental lines, segregating individuals and an independent set of breeding lines clearly revealed haplotypes discriminating completely sterile, partially fertile and Rfm1-restorer lines. The haplotypes segregate for several single nucleotide polymorphisms, a 6 bp insertion-deletion (InDel) polymorphism and another 2 bp InDel. CMS-unstable genotypes carrying haplotypes associated with undesired fertility restoration showed significantly higher grain setting on bagged spikes when plants were subjected to elevated temperatures during anthesis, indicating a temperature influence on pollen fertility. SNPs associated with desirable Rfm3 haplotypes can be implemented in marker-assisted selection of stable CMS mother lines.

DOI: https://doi.org/10.1007/s00122-019-03281-9
Mol Biol Evol. 2019 Jan 17.

Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids.

Paulina Martinez Palacios, Marie-Pierre Jacquemot, Marion Tapie, Agnès Rousselet, Mamoudou Diop, Carine Remoue, Matthieu Falque, Andrew Lloyd, Eric Jenczewski, Gilles Lassalle, Anne-Marie Chevre, Christine Lelandais, Martin Crespi, Philippe Brabant, Johann Joets, Karine Alix.

Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neo-allopolyploids to form and adapt. Nevertheless, how neo-allopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small non-coding RNAs (sRNAs) in mediating the transcriptional response of neo-allopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate post-transcriptional gene silencing (PTGS) by mRNA cleavage whereas 24-nt sRNAs repress transcription (transcriptional gene silencing, TGS) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized B. napus allotetraploids originating from crosses between diploid B. oleracea and B. rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target non-coding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various non-coding elements and stress-related genes, thus ensuring genome stability during the first steps of neo-allopolyploid formation.

DOI: https://doi.org/10.1093/molbev/msz007
Theor Appl Genet. 2019 Jan 18.

Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode.

Bart Van Gansbeke, Kelvin H P Khoo, John G Lewis, Kenneth J Chalmers, Diane E Mather.

KEY MESSAGE: The cereal cyst nematode resistance locus Rha2 was mapped to a 978 kbp region on the long arm of barley chromosome 2H. Three candidate genes are discussed. The cereal cyst nematode (CCN) Heterodera avenae is a soil-borne obligate parasite that can cause severe damage to cereals. This research involved fine mapping of Rha2, a CCN resistance locus on chromosome 2H of barley. Rha2 was previously mapped relative to restriction fragment length polymorphisms (RFLPs) in two mapping populations. Anchoring of flanking RFLP clone sequences to the barley genome assembly defined an interval of 5077 kbp. Genotyping-by-sequencing of resistant and susceptible materials led to the discovery of potentially useful single nucleotide polymorphisms (SNPs). Assays were designed for these SNPs and applied to mapping populations. This narrowed the region of interest to 3966 kbp. Further fine mapping was pursued by crossing and backcrossing the resistant cultivar Sloop SA to its susceptible ancestor Sloop. Evaluation of F2 progeny confirmed that the resistance segregates as a single dominant gene. Genotyping of 9003 BC2F2 progeny identified recombinants. Evaluation of recombinant BC2F3 progeny narrowed the region of interest to 978 kbp. Two of the SNPs within this region proved to be diagnostic of CCN resistance across a wide range of barley germplasm. Fluorescence-based and gel-based assays were developed for these SNPs for use in marker-assisted selection. Within the candidate region of the reference genome, there are nine high-confidence predicted genes. Three of these, one that encodes RAR1 (a cysteine- and histidine-rich domain-containing protein), one that is predicted to encode an acetylglutamate kinase and one that is predicted to encode a tonoplast intrinsic protein, are discussed as candidate genes for CCN resistance.

DOI: https://doi.org/10.1007/s00122-019-03279-3
Biol Chem. 2018 Dec 01. pii: /j/bchm.just-accepted/hsz-2018-0436/hsz-2018-0436.xml. [Epub ahead of print]

The conserved theme of ribosome hibernation: from bacteria to chloroplasts of plants.

Raphael Trösch, Felix Willmund.

  Cells are highly adaptive systems that respond and adapt to changing environmental conditions such as temperature fluctuations or altered nutrient availability. Such acclimation processes involve reprogramming of the cellular gene-expression profile, tuning of protein synthesis, remodelling of metabolic pathways and morphological changes of the cell shape. Nutrient starvation can lead to limited energy supply and consequently, remodelling of protein synthesis is one of the key steps of regulation since the translation of the genetic code into functional polypeptides may consume up to 40% of a cell's energy during proliferation. In eukaryotic cells, downregulation of protein synthesis during stress is mainly mediated by modification of the translation initiation factors. Prokaryotic cells suppress protein synthesis by the active formation of dimeric so-called "hibernating" 100S ribosome complexes. Such a transition involves a number of proteins which are found in various forms in prokaryotes but also in chloroplasts of plants. We review here the current understanding of these hibernation factors and elaborate conserved principles which are shared between prokaryotic and plant species.

Keywords:  100S ribosomes; energy availability; hibernation factors; protein synthesis; starvation; stringent response

DOI:  https://doi.org/10.1515/hsz-2018-0436
Nat Genet. 2019 Jan 14.

The genetic basis of inbreeding depression in potato.

Chunzhi Zhang, Pei Wang, Die Tang, Zhongmin Yang, Fei Lu, Jianjian Qi, Nilesh R Tawari, Yi Shang, Canhui Li, Sanwen Huang.

Inbreeding depression confers reduced fitness among the offspring of genetic relatives. As a clonally propagated crop, potato (Solanum tuberosum L.) suffers from severe inbreeding depression; however, the genetic basis of inbreeding depression in potato is largely unknown. To gain insight into inbreeding depression in potato, we evaluated the mutation burden in 151 diploid potatoes and obtained 344,831 predicted deleterious substitutions. The deleterious mutations in potato are enriched in the pericentromeric regions and are line specific. Using three F2 populations, we identified 15 genomic regions with severe segregation distortions due to selection at the gametic and zygotic stages. Most of the deleterious recessive alleles affecting survival and growth vigor were located in regions with high recombination rates. One of these deleterious alleles is derived from a rare mutation that disrupts a gene required for embryo development. This study provides the basis for genome design of potato inbred lines.

DOI: https://doi.org/10.1038/s41588-018-0319-1
Mol Biol Rep. 2019 Jan 18.

Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton.

Man Wu, Longyun Li, Guoyuan Liu, Xihua Li, Wenfeng Pei, Xingli Li, Jinfa Zhang, Shuxun Yu, Jiwen Yu.

  Fiber length is one of the most important fiber quality traits in Upland cotton (Gossypium hirsutum L.), the most important fiber crop, and its improvement has been impeded in part by a lack of knowledge regarding its genetic basis. Introgressed backcross inbred lines (BILs) or near isogenic lines (NILs) differing in fiber length in the same genetic background, developed through advanced backcrossing between Upland cotton and extra-long staple cotton (G. barbadense L.), provide an important genomic resource for studying the molecular genetic basis of fiber length. In the present study, a long-fiber group and a short-fiber group, each with five BILs of Upland cotton, were selected from a BIL population between G. hirsutum and G. barbadense. Through a microarray-based comparative transcriptome analysis of developing fibers at 10 days postanthesis from the two groups, 1478 differentially expressed genes (DEGs) were identified. A total of 166 DEGs were then mapped to regions of fiber length quantitative trait loci (QTL), including 12 QTL hotspots and 2 QTL identified previously in the BIL population from which the two sets of BILs were selected. Several candidate genes possibly underlying the genetic control of fiber length differences between G. barbadense and G. hirsutum, including GhACX and GhKIF, were identified in this study. These results provide a list of positional candidate genes for the fine-scale mapping and map-based cloning of fiber length QTL, which will facilitate targeted gene transfer from G. barbadense to Upland cotton to further improve fiber quality.

Keywords:  Affymetrix microarray; Fiber quality traits; Gossypium barbadense; Gossypium hirsutum; Quantitative RT-PCR

DOI:  https://doi.org/10.1007/s11033-019-04589-x