bims-plasge 2024-07-07 papers

Issue of 2024–07–07
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Mol Plant. 2024 Jul 01. pii: S1674-2052(24)00220-X. [Epub ahead of print]

Structural variations of a new fertility restorer gene, Rf20, underlie the restoration of wild abortive-type cytoplasmic male sterility in rice.

Shufeng Song, Yixing Li, Mudan Qiu, Na Xu, Bin Li, Longhui Zhang, Lei Li, Weijun Chen, Jinglei Li, Tiankang Wang, Yingxin Qiu, Mengmeng Gong, Dong Yu, Hao Dong, Siqi Xia, Yi Pan, Dingyang Yuan, Li Li.

The discovery of a wild abortive-type cytoplasmic male sterile line and the breeding of its restorer line have led to the commercialization of three-line hybrid rice, which has contributed greatly to global food security. However, the molecular mechanisms underlying fertility abortion and the restoration of wild abortive-type cytoplasmic male sterile lines largely remain elusive. In this study, we cloned a restorer gene, Rf20, following a genome-wide association study analysis of the core parent lines of three-line hybrid rice. We found that Rf20 was present in all core parental lines, but different haplotypes and structural variants of its gene resulted in differences in Rf20 expression levels between sterile and restored lines. Rf20 could restore fertility in the wild abortive-type cytoplasmic male sterile line and was found to be responsible for fertility restoration in some cytoplasmic male sterile lines under high temperature. In addition, we found that Rf20 encodes a pentatricopeptide repeat protein that competes with WA352 for binding with COX11. This interaction enhances COX11's function as a scavenger of reactive oxygen species, which in turn restores pollen fertility. In this study, a new model of pentatricopeptide repeat proteins involved in the fertility recovery of cytoplasmic male sterile lines was proposed, which provides an important theoretical basis for the breeding of strong restorer lines and for overcoming high-temperature fertility recovery of some three-line sterile lines.

Keywords: COX11; Cytoplasmic Male Sterility; Rf20; WA352; Wild Abortion

DOI: https://doi.org/10.1016/j.molp.2024.07.001

Heredity (Edinb). 2024 Jul 05.

Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans.

Joseph J Dubie, Vaishali Katju, Ulfar Bergthorsson.

Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.

DOI: https://doi.org/10.1038/s41437-024-00704-2

PLoS Genet. 2024 Jul 01. 20(7): e1011336

A catalogue of recombination coldspots in interspecific tomato hybrids.

Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Hetty C van den Broeck, Elio Schijlen, Henk J Schouten, Yuling Bai, Paul Fransz, Maike Stam, Hans de Jong, Sara Diaz Trivino, Dick de Ridder, Aalt D J van Dijk, Sander A Peters.

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.

DOI: https://doi.org/10.1371/journal.pgen.1011336