bims-plasge 2025-04-06 papers

Issue of 2025–04–06
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Mol Plant. 2025 Mar 31. pii: S1674-2052(25)00108-X. [Epub ahead of print]

The dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants.

Coordinated gene transcription in plastid and nucleus is essential for the photosynthetic apparatus assembly during chloroplast biogenesis. Despite identification of several transcription factors regulating the transcription of nuclear-encoded photosynthetic genes,no transcription factor regulating plastid gene transcription has been discovered. Here we report that BAI1 ("albino" in Chinese), a nucleus-plastid dual-targeted C2H2-type zinc finger transcription factor in Arabidopsis, positively regulates and orchestrates the transcription of nuclear and plastid genes. The knockout of BAI1 leads to the blockage of chloroplast formation, albino seedling, and lethality. In plastid, BAI1 is a newly identified functional component of the pTAC (transcriptionally active chromosome complex), which physically interacts with another pTAC component, pTAC12/PAP5/HMR to enable the effective assembly of PEP (plastid-encoded RNA polymerase) complex. The transcript levels of investigated PEP-dependent genes were reduced in the bai1 mutant, while the accumulation of NEP (nuclear-encoded RNA polymerase)-dependent transcripts was increased, indicating that BAI1 plays a vital role in maintaining PEP activity. BAI1 directly binds to the promoter regions of RbcSs, a nuclear gene, and RbcL, a plastid gene, to activate their expression for efficient RubisCO assembly. AtBAI1 homologs TaBAI1, GmBAI1a and GmBAI1b from both monocot and dicot can fully complement the defects of Arabidopsis bai1 mutant. In contrast, PpBAI1, from Physcomitrium patens, only partially complements the bai1 mutant. The phylogenetic analysis of BAI1 and HMR elucidated that both components originated from late-diverging streptophyte algae, following the conservative evolutionary path during plant terrestrialization. In summary, this work unveils a BAI1-mediated transcription regulatory mechanism synchronizing transcription of nuclear and plastid genes, which is required for hybrid photosynthetic complex assembly and could be an intrinsic feature facilitating plant terrestrialization.

Keywords: C2H2-type zinc finger transcription factor BAI1; chloroplast biogenesis; coordination of nuclear and plastid gene transcription; photosynthetic apparatus assembly; plant terrestrialization

DOI: https://doi.org/10.1016/j.molp.2025.03.018

Plant Genome. 2025 Jun;18(2): e70021

Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication.

Azalea Guerra-García, Jana Balarynová, Petr Smykal, Eric J von Wettberg, Scott D Noble, Kirstin E Bett.

Seed dormancy is an adaptation that delays germination to prevent the start of this process during unsuitable conditions. It is crucial in wild species but its loss was selected during crop domestication to ensure a fast and uniform germination. Water uptake, or imbibition, is the first step of germination. In the Fabaceae family, seeds have physical dormancy, in which seed coats are impermeable to water. We used an interspecific cross between an elite lentil line (Lens culinaris) and a wild lentil (L. orientalis) to investigate the genetic basis of imbibition capacity through quantitative trait locus (QTL) mapping and by using RNA from embryos and seed coats at different development stages, and phenotypic data of seed coat thickness (SCT) and proportion of imbibed seeds (PIS). Both characteristics were consistent throughout different years and locations, suggesting a hereditary component. QTL results suggest that they are each controlled by relatively few loci. Differentially expressed genes (DEGs) within the QTL were considered candidate genes. Two glycosyl-hydrolase genes (a β-glucosidase and a β-galactosidase), which degrade complex polysaccharides in the cell wall, were found among the candidate genes, and one of them had a positive correlation (β-glucosidase) between gene expression and imbibition capacity, and the other gene (β-galactosidase) presented a negative correlation between gene expression and SCT.

DOI: https://doi.org/10.1002/tpg2.70021

Plant Mol Biol. 2025 Apr 03. 115(2): 55

Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses.

Abhinandan S Patil, Manoj D Oak, Shreyash Gijare, Aditya Gobade, Santosh Jaybhay, Vilas D Surve, Suresha P G, Dattatraya Salunkhe, Balasaheb N Waghmare, Bhanudas Idhol, Ravindra M Patil, Deepak Pawar.

Soybean domestication has been essential for crop evolution, adaptation, and modern breeding. Despite advancements in understanding soybean genetics, the genetic basis of DRTs has yet to be fully explored, particularly in the context of genome-wide association studies (GWASs) and gene interaction analyses (epistasis). This study evaluated 198 diverse soybean accessions using 23,574 high-quality SNPs obtained via ddRAD-seq. Nine key DRTs-including those related to seed size (length, width, and thickness), seed coat color, cotyledon color, hypocotyl color, stem growth habit, flower color, pod color, pubescence, and pod-shattering-were phenotyped in two environments. A GWASs conducted via the FarmCPU and BLINK models identified 78 significant SNPs, 14 consistently detected across both environments and models, demonstrating stability. Notably, the SNP rs.Gm16.29778273 linked to pod-shattering resistance. The functional annotation linked three known quantitative trait loci /genes and revealed 11 novel candidate genes associated with DRTs, providing insights into their roles via Gene Ontology (GO) terms. The main effect SNP × SNP interaction analysis revealed that the significant SNP rs.Gm13.16695800 exhibits a pleiotropic effect, controlling both hypocotyl and flower color. Furthermore, 324 epistatic interactions were identified, influencing the expression of DRTs, thereby highlighting the complex genetic architecture underlying these traits. These findings offer valuable insights into domestication and the traits linked to higher yield. They provide a solid foundation for developing marker-assisted selection (MAS) strategies and functional studies to improve soybean breeding for resilient, high-yielding varieties.

Keywords: Candidate genes; Domestication-related traits; Epistasis; Genome-wide association study; Marker-assisted selection; Marker‒trait associations; Pleiotropy; Pod-shattering resistance; SNP markers; Seed size; Soybean domestication; ddRAD-seq

DOI: https://doi.org/10.1007/s11103-025-01583-9