bims-plasge 2025-08-24 papers

Issue of 2025–08–24
five papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Mol Breed. 2025 Aug;45(8): 68

Mitochondrial candidate gene, orf206, for cytoplasmic male sterility in Pear (Pyrus pyrifolia).

Cytoplasmic male sterility (CMS) caused by mitochondrial genome alterations in flowering plants plays a crucial role in hybrid breeding systems. In pear (Pyrus spp.), pollenless phenotypes have been consistently observed in progeny. However, the genetic basis and inheritance mechanisms of male sterility in pears remain poorly understood. To investigate the inheritance mode, we performed segregation analysis in four F₁ populations derived from crosses using a cultivar carrying CMS-type cytoplasm as the maternal parent. The observed male sterility segregation ratios confirmed a maternal inheritance pattern consistent with the CMS model and suggested differential effects of nuclear fertility restorer genes from various pollen parents. We analyzed whole-genome sequencing data from four pear accessions, identifying an 860 bp mitochondrial DNA sequence associated with male-sterile individuals. This sequence was located near cox3 and apt8, commonly co-located with CMS loci in other plant species. Within this region, we identified orf206, a chimeric open reading frame composed of 113 bp from nad3 in Pyrus betulifolia and 403 bp from atp9-1 of Malus × domestica. The predicted protein encoded by orf206 contained three transmembrane domains, which are typical features of CMS-associated proteins. Our results demonstrate that male sterility in pears is maternally inherited and support orf206 as a strong candidate gene for CMS induction. Furthermore, we developed an InDel marker (CBpMtid03 and CBpMtid07) targeting the CMS-specific mitochondrial sequence enabling the efficient identification of CMS individuals in breeding programs. These findings provide insights into the molecular mechanisms underlying pollen sterility in pears and facilitate marker-assisted selection in pear breeding.
Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-025-01591-z.

Keywords: InDel marker; Next-generation sequencing; Pollen fertility; ‘Niitaka’

DOI: https://doi.org/10.1007/s11032-025-01591-z

Plant Sci. 2025 Aug 14. pii: S0168-9452(25)00339-5. [Epub ahead of print]360 112721

Cytoplasmic male sterility: Sterility induction, fertility restoration and gene-for-gene interaction of CMS/Rf genes.

Ahmad Ali, Muhammad Zeeshan Mola Bakhsh, Shipeng Li, Xiaoyu Zhang, Jinxing Tu, Bin Yi.

Cytoplasmic male sterility (CMS) is a maternally inherited agronomic trait. The CMS lines cannot produce viable pollens (incomplete or nonfunctional), properly dehisce pollen, germinate on the stigma or be accessible to the stigma, thus unable to fertilize the ovule/ egg. Although CMS is not beneficial to the plants itself, it is a valuable resource for hybrid breeding. CMS is caused by the mitochondrial genome carrying chimeric genes (orfs), which frequently originate in the re-arrangements of the mitochondrial genome. The nuclear genome's restorer-of-fertility (Rf) gene suppresses the CMS conditions to restore fertility. The Rf genes interact with CMS-inducing genes at various levels to regulate their activity and restore fertility. In various crop species, different cytotypes carry specific CMS-inducing genes, which require a specific Rf gene for fertility restoration. Although some Rf genes can restore the fertility of more than one cytotype, most cytotypes require specific Rf genes. In this review, we briefly discussed the specificity of Rf genes and cytotypes based on B. napus, Oryza spp, and H. annuus. The findings from these crop species suggest that the relationship of CMS/Rf genes occurs in a gene-for-gene fashion. However, the molecular mechanism behind the Rf-cytotype specificity is not much understood. Studying the in-vitro expression system can help to elucidate the relationship between the CMS and Rf genes. The evolution of PPR in response to the emergence of CMS-inducing mitochondrial orfs and the induction of male sterility via genome editing technologies is also briefly discussed.

Keywords: Cytoplasmic male sterility; Cytotypes; Pollens; Rf genes; gene-for-gene; orfs

DOI: https://doi.org/10.1016/j.plantsci.2025.112721

Nucleic Acids Res. 2025 Aug 11. pii: gkaf781. [Epub ahead of print]53(15):

Plant mitochondrial PORR proteins facilitate group II intron splicing by binding to distinct regions within their target introns.

Chuande Wang, Martine Quadrado, Talla Ngom, Hakim Mireau.

Ribozymic introns are widely distributed in eubacteria and organelles such as mitochondria and chloroplasts. In plants, organellar introns often exhibit degenerate RNA structures, lacking essential elements for self-splicing and mobility. Consequently, their splicing relies heavily on host-encoded proteins. The plant organellar RNA recognition (PORR) domain, a recently identified RNA-binding motif, defines a small, plant-specific protein family. In this study, we characterized five novel mitochondria-targeted PORR genes. Functional analyses revealed that all five PORRs play a role in mitochondrial group II intron splicing. While one PORR protein was found necessary for the splicing of a single intron, the other four facilitate the splicing of multiple introns. Splicing defects in each porr mutant resulted in a significant reduction in complex I assembly and activity, along with an increase in the levels of other respiratory complexes. In vivo RNA binding studies revealed that the analyzed PORR proteins bind either to the 3' end of trans-spliced intron 5'-halves or within intron domain I, indicating potential roles in trans-spliced intron rejoining or in the structural organization of domain I. Overall, these findings demonstrate that nuclear-encoded PORR proteins play crucial roles in the splicing of specific mitochondrial group II introns and are essential for mitochondrial biogenesis.

DOI: https://doi.org/10.1093/nar/gkaf781

Genetics. 2025 Aug 19. pii: iyaf167. [Epub ahead of print]

Harnessing cytonuclear diversity to map barley spike traits using the Cytonuclear Multi-Parent Population.

Schewach Bodenheimer, Eyal Bdolach, Avital Be'ery, Lalit Dev Tiwari, Ruth Sarahi Perez-Alfaro, Shengming Yang, Daniel Koenig, Eyal Fridman.

The interplay between nuclear and cytoplasmic genomes, collectively known as cytonuclear interactions (CNIs), is increasingly recognized as a key driver of phenotypic variation and adaptive potential across diverse organisms. Yet, leveraging cytoplasmic diversity and fully understanding the role of CNIs in agriculturally important traits remain major challenges in crop improvement. Here, we present the Cytonuclear Multi-Parent Population (CMPP), a novel interspecific resource comprising 951 doubled haploid lines, generated from two backcrosses between ten genetically diverse wild barley accessions (Hordeum vulgare ssp. spontaneum) used as female founders and the elite cultivar Noga (H. vulgare). Phenotyping across multiple environments revealed that up to 5% of variation in key spike and grain trait values are explained by cytoplasm (η² = 0.05). Notably, wild cytoplasms influenced trait stability, with the B1K-50-04 cytoplasm increasing grain weight stability based on Shukla's measure. Genome-wide association studies employing Nested Association Mapping (NAM), FASTmrMLM, and MatrixEpistasis (ME) identified 76 marker-trait associations (MTAs). The ME approach specifically uncovered 16 cytonuclear QTL (cnQTL) exhibiting cytoplasm-dependent effects. Furthermore, we developed a genomic prediction strategy incorporating interactions between significant MTAs and population structure variables (subfamily and cytoplasm), which achieved cross-validation accuracies comparable to, or even exceeding, models using the full set of 6,679 SNPs, despite utilizing substantially fewer predictors, enabling quicker and more efficient validation runs. The CMPP provides a unique platform for dissecting cytoplasmic effects and CNIs, highlighting the importance of incorporating cytonuclear context in genetic mapping and prediction to effectively harness both nuclear and cytoplasmic diversity for crop improvement.

Keywords: Cytonuclear interactions; barley; crop wild relatives; genomic prediction; multi-parent population

DOI: https://doi.org/10.1093/genetics/iyaf167

J Exp Bot. 2025 Aug 20. pii: eraf378. [Epub ahead of print]

Plant Plastids: From Evolutionary Origins to Functional Specialization and Organelle Interactions.

Luciana Renna, Alessio Papini, Stefano Mancuso, Federica Brandizzi, Giovanni Stefano.

Plastids are highly diverse organelles that play critical roles in supporting life on Earth. Among them, chloroplasts enable photosynthesis, providing phototrophic capabilities to eukaryotes such as plants, algae, and photosynthetic protists. The functions of plastids are indispensable for the survival and development of life. Plastids are widely recognized as endosymbiotic organelles with a single origin. They exhibit morphological diversity, tissue specificity, and the ability to adapt to specific cellular functions. Despite this understanding, significant questions remain unanswered, such as how genetic material from the endosymbiont was transferred and integrated into the host nucleus, the timeline for the full integration of the endosymbiont into the host cell, and the processes by which plastids specialized and adapted to various cell types. While plastids have unique features and specialized roles, they are neither autonomous nor physically isolated. Instead, they interact with other subcellular compartments through yet-to-be-characterized membrane domains or specialized structures. This review explores the origin and evolution of plastids, their protein import machinery, compartmentalization, and interactions with other cellular compartments, while highlighting key unanswered questions in these areas.

Keywords: Endomembrane Compartments; Inter-organellar Communication; Membrane Contact Sites; Organelles; Plastids

DOI: https://doi.org/10.1093/jxb/eraf378