bims-plasge 2019-02-10 papers

on Plastid genes

Issue of 2019‒02‒10
six papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield.
RNA editing analysis of ATP synthase genes in the cotton cytoplasmic male sterile line H276A.
The Molecular and Cellular Regulation of Brassicaceae Self-Incompatibility and Self-Pollen Rejection.
Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).
Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome "plasmon" in the Triticum (wheat)-Aegilops complex.
Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops.

Theor Appl Genet. 2019 Feb 07.

Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield.

Adama I Seye, Cyril Bauland, Heloïse Giraud, Valérie Mechin, Matthieu Reymond, Alain Charcosset, Laurence Moreau.

KEY MESSAGE: Silage quality traits of maize hybrids between the Dent and Flint heterotic groups mostly involved QTL specific of each parental group, some of them showing unfavorable pleiotropic effects on yield. Maize (Zea mays L.) is commonly used as silage for cattle feeding in Northern Europe. In addition to biomass production, improving whole-plant digestibility is a major breeding objective. To identify loci involved in the general (GCA, parental values) and specific combining ability (SCA, cross-specific value) components of hybrid value, we analyzed an incomplete factorial design of 951 hybrids obtained by crossing inbred lines issued from two multiparental connected populations, each specific to one of the heterotic groups used for silage in Europe ("Dent" and "Flint"). Inbred lines were genotyped for approximately 20K single nucleotide polymorphisms, and hybrids were phenotyped in eight environments for seven silage quality traits measured by near-infrared spectroscopy, biomass yield and precocity (partly analyzed in a previous study). We estimated variance components for GCA and SCA and their interaction with environment. We performed QTL detection using different models adapted to this hybrid population. Strong family effects and a predominance of GCA components compared to SCA were found for all traits. In total, 230 QTL were detected, with only two showing SCA effects significant at the whole-genome level. More than 80% of GCA QTL were specific of one heterotic group. QTL explained individually less than 5% of the phenotypic variance. QTL co-localizations and correlation between QTL effects of quality and productivity traits suggest at least partial pleiotropic effects. This work opens new prospects for improving maize hybrid performances for both biomass productivity and quality accounting for complementarities between heterotic groups.

DOI: https://doi.org/10.1007/s00122-019-03296-2
Biol Res. 2019 Feb 06. 52(1): 6

RNA editing analysis of ATP synthase genes in the cotton cytoplasmic male sterile line H276A.

Xiangjun Kong, Dongmei Liu, Jie Zheng, Aziz Khan, Bin Li, Yong Diao, Ruiyang Zhou.

  BACKGROUND: Pollen development is an energy-consuming process that particularly occurs during meiosis. Low levels of adenosine triphosphate (ATP) may cause cell death, resulting in CMS (cytoplasmic male sterility). DNA sequence differences in ATP synthase genes have been revealed between the N- and S-cytoplasms in the cotton CMS system. However, very few data are available at the RNA level. In this study, we compared five ATP synthase genes in the H276A, H276B and fertile F1 (H276A/H268) lines using RNA editing, RNA blotting and quantitative real time-PCR (qRT-PCR) to explore their contribution to CMS. A molecular marker for identifying male sterile cytoplasm (MSC) was also developed.RESULTS: RNA blotting revealed the absence of any novel orf for the ATP synthase gene sequence in the three lines. Forty-one RNA editing sites were identified in the coding sequences. RNA editing showed that proteins had 32.43% higher hydrophobicity and that 39.02% of RNA editing sites had proline converted to leucine. Two new stop codons were detected in atp6 and atp9 by RNA editing. Real-time qRT-PCR data showed that the atp1, atp6, atp8, and atp9 genes had substantially lower expression levels in H276A compared with those in H276B. By contrast, the expression levels of all five genes were increased in F1 (H276A/H268). Moreover, a molecular marker based on a 6-bp deletion upstream of atp8 in H276A was developed to identify male sterile cytoplasm (MSC) in cotton.
CONCLUSIONS: Our data substantially contributes to the understanding of the function of ATP synthase genes in cotton CMS. Therefore, we suggest that ATP synthase genes might be an indirect cause of cotton CMS. Further research is needed to investigate the relationship among ATP synthase genes in cotton CMS.

Keywords:  ATP synthase gene; Cotton; Cytoplasmic male sterility; Molecular marker; RNA editing

DOI:  https://doi.org/10.1186/s40659-019-0212-0
Int Rev Cell Mol Biol. 2019 ;pii: S1937-6448(18)30061-3. [Epub ahead of print]343 1-35

The Molecular and Cellular Regulation of Brassicaceae Self-Incompatibility and Self-Pollen Rejection.

Eli Jany, Hayley Nelles, Daphne R Goring.

  In flowering plants, sexual reproduction is actively regulated by cell-cell communication between the male pollen and female pistil, and many species possess self-incompatibility systems for the selective rejection of self-pollen to maintain genetic diversity. The Brassicaceae self-incompatibility pathway acts early on when pollen grains have landed on the stigmatic papillae at the top of the pistil. Extensive studies have revealed that self-pollen rejection in the Brassicaceae is initiated by an S-haplotype-specific interaction between two polymorphic proteins: the pollen S-locus protein 11/S cysteine-rich (SP11/SCR) ligand and the stigma S receptor kinase (SRK). While the different S-haplotypes are typically codominant, there are several examples of dominant-recessive interactions, and a small RNA-based regulation of SP11/SCR expression has been uncovered as a mechanism behind these genetic interactions. Recent research has also added to our understanding of various cellular components in the pathway leading from the SP11/SCR-SRK interaction, including two signaling proteins, the M-locus protein kinase (MLPK) and the ARM-repeat containing 1 (ARC1) E3 ligase, as well as calcium fluxes and induction of autophagy in the stigmatic papillae. Finally, a better understanding of the compatible pollen responses that are targeted by the self-incompatibility pathway is starting to emerge, and this will allow us to more fully understand how the Brassicaceae self-incompatibility pathway causes self-pollen rejection. Here, we provide an overview of the field, highlighting recent contributions to our understanding of Brassicaceae self-incompatibility, and draw comparisons to a recently discovered unilateral incompatibility system.

Keywords:  Autophagy; Brassicaceae; Calcium; E3 ligase; Kinase; Pistil; Pollen; Self-incompatibility; Small RNAs; Unilateral incompatibility

DOI:  https://doi.org/10.1016/bs.ircmb.2018.05.011
Front Plant Sci. 2018 ;9 1993

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).

Alexandra M Przewieslik-Allen, Amanda J Burridge, Paul A Wilkinson, Mark O Winfield, Daniel S Shaw, Lorna McAusland, Julie King, Ian P King, Keith J Edwards, Gary L A Barker.

  The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.

Keywords:  Aegilops; genotyping array; introgression; single nucleotide polymorphism (SNP); wheat; wheat relative

DOI:  https://doi.org/10.3389/fpls.2018.01993
Proc Natl Acad Sci U S A. 2019 Feb 06. pii: 201817037. [Epub ahead of print]

Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome "plasmon" in the Triticum (wheat)-Aegilops complex.

Koichiro Tsunewaki, Naoki Mori, Shigeo Takumi.

  The term "plasmon" is used to indicate the whole cytoplasmic genetic system, whereas "genome" refers to the whole nuclear genetic system. Although maternal inheritance of the plasmon is well documented in angiosperms, its genetic autonomy from the coexisting nuclear genome still awaits critical examination. We tested this autonomy in two related studies: One was to determine the persistence of the genetic effect of the plasmon of Aegilops caudata (genome CC) on the phenotype of common wheat, Triticum aestivum strain "Tve" (genome AABBDD), during 63 y (one generation per year) of repeated backcrosses of Ae. caudata and its offspring with pollen of the same Tve wheat, and the second was to reconstruct an Ae. caudata strain from the genome of this strain and its plasmon that had been resident in Tve wheat for 50 generations, and to compare the phenotypic and organellar DNA characteristics between the native and reconstructed strains. Results indicated no change in the effect of Ae. caudata plasmon on Tve wheat during its stay in wheat for more than half a century, and no difference between the native and reconstructed caudata strains in their phenotype and simple sequence repeats in their organellar DNAs, thus demonstrating the prolonged genetic autonomy of the plasmon from the coexisting genomes of wheat and several other species that were used in the reconstruction of Ae. caudata The relationship between the proven genetic autonomy of the plasmon under changing nuclear conditions and its diversification during evolution of the Triticum-Aegilops complex is discussed.

Keywords:  Triticum–Aegilops complex; alloplasmic wheat; maternal lineage; plasmon autonomy; species reconstruction

DOI:  https://doi.org/10.1073/pnas.1817037116
DNA Res. 2019 Jan 30.

Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops.

Yuka Miki, Kentaro Yoshida, Nobuyuki Mizuno, Shuhei Nasuda, Kazuhiro Sato, Shigeo Takumi.

Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.

DOI: https://doi.org/10.1093/dnares/dsy047