bims-plasge 2023-02-05 papers

Issue of 2023–02–05
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Front Plant Sci. 2022 ;13 1108276

Heat stress tolerance in peas (Pisum sativum L.): Current status and way forward.

Jyoti Devi, Vidya Sagar, Gyan P Mishra, Prakash Kumar Jha, Nakul Gupta, Rakesh K Dubey, Prabhakar M Singh, Tusar K Behera, P V Vara Prasad.

In the era of climate change, the overall productivity of pea (Pisum sativum L.) is being threatened by several abiotic stresses including heat stress (HS). HS causes severe yield losses by adversely affecting several traits in peas. A reduction in pod yield has been reported from 11.1% to 17.5% when mean daily temperature increase from 1.4 to 2.2°C. High-temperature stress (30.5-33°C) especially during reproductive phase is known to drastically reduce both seed yield and germination. HS during germination and early vegetative stage resulted in poor emergence and stunted plant growth along with detrimental effects on physiological functions of the pea plant. To combat HS and continue its life cycle, plants use various defense strategies including heat escape, avoidance or tolerance mechanisms. Ironically, the threshold temperatures for pea plant and its responses are inconsistent and not yet clearly identified. Trait discovery through traditional breeding such as semi leaflessness (afila), upright growing habit, lodging tolerance, lower canopy temperature and small seeded nature has highlighted their utility for greater adaptation under HS in pea. Screening of crop gene pool and landraces for HS tolerance in a targeted environment is a simple approach to identify HS tolerant genotypes. Thus, precise phenotyping using modern phenomics tools could lead to increased breeding efficiency. The NGS (next generation sequencing) data can be associated to find the candidate genes responsible for the HS tolerance in pea. In addition, genomic selection, genome wide association studies (GWAS) and marker assisted selection (MAS) can be used for the development of HS tolerant pea genotypes. Additionally, development of transgenics could be an alternative strategy for the development of HS tolerant pea genotypes. This review comprehensively covers the various aspects of HS tolerance mechanisms in the pea plant, screening protocols, omic advances, and future challenges for the development of HS tolerant genotypes.

Keywords: Pisum; QTLs; breeding; heat shock proteins (HSPs); heat stress; threshold temperature

DOI: https://doi.org/10.3389/fpls.2022.1108276

PLoS Genet. 2023 Feb 03. 19(2): e1010633

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes.

Jiří Macas, Laura Ávila Robledillo, Jonathan Kreplak, Petr Novák, Andrea Koblížková, Iva Vrbová, Judith Burstin, Pavel Neumann.

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.

DOI: https://doi.org/10.1371/journal.pgen.1010633

J Exp Bot. 2023 Feb 04. pii: erad044. [Epub ahead of print]

Plastids: diving into their diversity, functions, and their role in plant development.

Julio Sierra, Lina Escobar-Tovar, Patricia Leon.

Plastids are a group of essential, heterogenous semiautonomous organelles characteristic of plants that perform photosynthesis and a diversity of metabolic pathways that impact growth and development. Plastids are remarkably dynamic and can interconvert in response to specific developmental and environmental cues functioning as central metabolic hub in plant cells. By far the best studied plastid is the chloroplast, but in recent years the combination of modern techniques and genetic analyses has expanded our current understanding of plastid morphological and functional diversity in both model and non-model plants. These studies have provided evidence of an unexpected diversity of plastid subtypes with specific characteristics. In this review we describe recent findings that provide insights into the characteristics of these specialized plastids and their functions. We concentrate on the emerging evidence that supports the model that signals derived from particular plastid types play pivotal roles in plant development, environmental, and defense responses. Furthermore, we provide examples of how new technologies are illuminating the functions of these specialized plastids and the overall complexity of their differentiation processes. Finally, we discuss future research directions such as the use of ectopic plastid differentiation as a valuable tool to characterize factors involved in plastid differentiation. Collectively, we highlight important advances in the field that can also impact future agricultural and biotechnological improvement in plants.

Keywords: Plastids; development; differentiation; pathogen defense; retrograde signaling; stress

DOI: https://doi.org/10.1093/jxb/erad044

medRxiv. 2023 Jan 19. pii: 2023.01.19.23284696. [Epub ahead of print]

Nuclear genetic control of mtDNA copy number and heteroplasmy in humans.

Rahul Gupta, Masahiro Kanai, Timothy J Durham, Kristin Tsuo, Jason G McCoy, Patrick F Chinnery, Konrad J Karczewski, Sarah E Calvo, Benjamin M Neale, Vamsi K Mootha.

Human mitochondria contain a high copy number, maternally transmitted genome (mtDNA) that encodes 13 proteins required for oxidative phosphorylation. Heteroplasmy arises when multiple mtDNA variants co-exist in an individual and can exhibit complex dynamics in disease and in aging. As all proteins involved in mtDNA replication and maintenance are nuclear-encoded, heteroplasmy levels can, in principle, be under nuclear genetic control, however this has never been shown in humans. Here, we develop algorithms to quantify mtDNA copy number (mtCN) and heteroplasmy levels using blood-derived whole genome sequences from 274,832 individuals of diverse ancestry and perform GWAS to identify nuclear loci controlling these traits. After careful correction for blood cell composition, we observe that mtCN declines linearly with age and is associated with 92 independent nuclear genetic loci. We find that nearly every individual carries heteroplasmic variants that obey two key patterns: (1) heteroplasmic single nucleotide variants are somatic mutations that accumulate sharply after age 70, while (2) heteroplasmic indels are maternally transmitted as mtDNA mixtures with resulting levels influenced by 42 independent nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These nuclear loci do not appear to act by mtDNA mutagenesis, but rather, likely act by conferring a replicative advantage to specific mtDNA molecules. As an illustrative example, the most common heteroplasmy we identify is a length variant carried by >50% of humans at position m.302 within a G-quadruplex known to serve as a replication switch. We find that this heteroplasmic variant exerts cis -acting genetic control over mtDNA abundance and is itself under trans -acting genetic control of nuclear loci encoding protein components of this regulatory switch. Our study showcases how nuclear haplotype can privilege the replication of specific mtDNA molecules to shape mtCN and heteroplasmy dynamics in the human population.

DOI: https://doi.org/10.1101/2023.01.19.23284696