Findings establish BrBGLU10 as an important regulator of pollen development and a potential target for fertility-related applications via gene editing in B. rapa and related Brassica crops.
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) play diverse roles in plant development and stress responses. However, a comprehensive pan-genomic characterization of this gene family across diverse Brassica rapa accessions is still lacking. Here, we conducted a pan-genome-wide analysis of BGLU genes across 21 B. rapa accessions. A total of 1840 BGLU genes were identified and clustered into 57 orthologous gene groups (OGGs), comprising 22 core, 19 dispensable, and 16 private groups. Phylogenetic reconstruction assigned these OGGs to five subgroups, and duplication analysis revealed whole-genome duplication as the predominant driver of family expansion, accounting for 47.51% of duplicated genes. Expression profiling identified two core genes, BrBGLU10 and BrBGLU56, as specifically expressed in fertile floral buds and differentially regulated between fertile and sterile lines. CRISPR/Cas9-mediated knockout of BrBGLU10 resulted in approximately 36% pollen abortion and drastically reduced seed set upon self-pollination, supporting its important role in pollen development. Collectively, these findings establish BrBGLU10 as an important regulator of pollen development and a potential target for fertility-related applications via gene editing in B. rapa and related Brassica crops.
An evolutionary and transcriptional atlas of the wheat TaBSK family is delivered and candidate genes for functional validation and molecular breeding toward salt-tolerant wheat varieties are provided.
Yongtao Zhao, Jun-Sen Wang, Zhong-Zhou Zhang et al.· Current Issues in Molecular...· 0 citations
The PR10 gene family plays a critical role in plant stress responses. Phylogenetic analysis across species indicated that the PR10 gene first appeared during plant terrestrialization and underwent significant expansion. And, PR10 is conserved in leguminous plants, yet its genomic architecture and functional mechanisms in alfalfa (Medicago sativa L.) remains unclear. In this study, a pan-genomic analysis of 28 alfalfa accessions identified a total of 1657 MsPR10 genes, with tandem duplication accounting for the majority of gene expansion (61.19%). These MsPR10 genes were clustered into 81 Orthologous Gene Groups (OGGs) based on conservative levels, ranging from core to cloud genes. Significant expansion of PR10 genes in Zhongmu No.1 alfalfa (ZMNO) was associated with elevated transposon activity and selective pressure. Transcriptomic analysis indicated MsPR10.SC10 may be a key gene in alfalfa salt-tolerance. Transgenic alfalfa plants overexpressing MsPR10.SC10 were generated by Agrobacterium-mediated transformation. Detailed physiological tests suggested overexpression of MsPR10.SC10 enhanced salt tolerance of alfalfa by maintaining ion homeostasis (reducing Na+/K+ ratio), boosting antioxidant capacity by increasing SOD/ POD activity and reducing H2O2/ MDA accumulation, and regulates the expression of salt stress responsive genes. This study reveals the pan-genomic architecture of the PR10 gene family members in alfalfa, and provides valuable candidate gene for breeding of salt tolerant alfalfa cultivar and may also other crops.
G. barbadense represents an indispensable germplasm resource for high-quality textile fiber and disease resistance; nevertheless, systematic information regarding its ZRT/IRT-like protein (ZIP) gene family remains limited. Here, a total of 46 GbZIP genes were identified across the G. barbadense genome. Comprehensive bioinformatic investigations revealed uneven chromosomal distribution and confirmed that segmental/whole-genome duplications, supplemented by localized tandem duplications, drove family expansion. Members clustered within the same phylogenetic clades shared conserved motif organization and gene architecture, while promoter regions harbored abundant cis-acting elements associated with phytohormone and stress signaling. Transcriptome profiling indicated distinct expression patterns across vegetative/reproductive tissues, fiber and ovule developmental stages, and diverse abiotic stress conditions (cold, hot, drought, and salt). Quantitative Real-Time PCR (qRT-PCR) further validated that several GbZIP candidates exhibited temporal expression variations upon exposure to cadmium toxicity, V. dahliae infection, and combined Cd-V. dahliae stress. Specifically, GbZIP13, GbZIP18, GbZIP27, and GbZIP36 displayed prominent broad-spectrum responses to all three stress conditions, whereas GbZIP16, GbZIP29, and GbZIP30 showed stress-specific regulatory divergence. Overall, this study aims to systematically analyze the evolutionary characteristics and expression patterns of the GbZIP family, and to specifically evaluate the response differences under Cd stress, V. dahliae stress, and combined stress, in order to identify potential key candidate genes.
Yahui Deng, Nan Zhao, Ji-Di Sun et al.· Biology· 0 citations
Auxin is a central phytohormone involved in regulating plant growth, development, and stress responses, with the
Aux/IAA
gene family functioning as an essential component of the auxin signaling pathway. To elucidate the genomic features and potential functions of the
Aux/IAA
gene family in pumpkin (
Cucurbita moschata
), we performed a genome-wide identification and systematic characterization.
A total of 72
CmIAA
genes were identified, encoding proteins ranging from 158 to 1275 amino acids with predicted isoelectric points of 4.57–9.81. These genes were unevenly distributed across 20 chromosomes, with Chr17 harboring the highest number, while no
CmIAA
genes were detected on Chr3. Phylogenetic analysis classified the genes into nine subgroups (Groups Ⅰ–Ⅸ), with Groups Ⅰ, Ⅵ, and Ⅸ exhibiting relative expansion. Gene structure and conserved motif analyses revealed subgroup-specific motif compositions, with motif 1 representing the core conserved domain. Intraspecific collinearity analysis identified 54 segmentally duplicated gene pairs but no tandem duplication events, whereas interspecific synteny revealed extensive orthologous relationships between pumpkin and
Cucurbita pepo
and
Cucurbita maxima
. Promoter analysis showed that
CmIAA
genes contain multiple cis-elements associated with hormone responses and abiotic stress responses, including ABRE, MBS, and DRE. Tissue expression analysis demonstrated that many
CmIAA
genes exhibited tissue-preferential expression patterns. Under abiotic stress conditions,
CmIAA
69 showed a salt-specific expression pattern, whereas
CmIAA
39 and
CmIAA
58 responded to both salt and drought treatments, indicating that these
CmIAA
genes play distinct roles in pumpkin responses to different abiotic stresses.
This study systematically characterized the
Aux/IAA
gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features. These findings provide valuable genetic resources for further functional studies and inform the potential roles of
CmIAA
genes in abiotic stress responses.
Background: Siraitia grosvenorii (monk fruit) is a dioecious medicinal crop native to southern China, yet its terpene synthase (TPS) gene family and the molecular basis of floral sexual dimorphism remain unexplored. Methods: Genome-wide identification of the TPS gene family was performed using HMMER and BLAST-based approaches. Phylogenetic classification, gene structure and conserved motif characterization, and comparative synteny analyses were conducted. Transcriptome data from leaves and fruits at different developmental stages were analyzed for tissue-specific expression profiling. Promoter cis-element analysis, protein–protein interaction network prediction, and molecular docking were performed to characterize the fruit-specific candidate SgTPS49. Results: A total of 58 SgTPS genes were identified and classified into six subfamilies, with TPS-a and TPS-b comprising 72.4% of the family. Approximately 88% of SgTPS genes arose from lineage-specific tandem duplication. Female flowers exhibited monoterpene-dominant scents and smaller corollas, whereas male flowers displayed a mid-morning sesquiterpene burst and greater morphological variation. SgTPS49 was specifically upregulated at 20 days post-pollination and possessed a unique promoter architecture devoid of classical hormone-responsive elements. Molecular docking supported its annotation as a putative monoterpene synthase with favorable GPP binding. Conclusions: This study provides the first comprehensive genomic resource for the SgTPS family in S. grosvenorii, reveals significant sexual dimorphism in floral traits, and identifies SgTPS49 as a key candidate for future functional validation.
Xiaozhen Zhu, Qifeng Lu, Changqi Liu et al.· Genes· 0 citations
This work sets a starting point for furthur investigation into cotton GolS genes and provides novel resources for breeding programmes aimed at enhancing abiotic stress tolerance in cotton.
Umm e Abaida Noor, Muhammad Shaban, M. Azmat et al.· Biologia· 0 citations
