Genome-Wide Analysis of Proline-Rich Extensin-Like Receptor Kinases (PERKs) Gene Family Reveals Their Roles in Plant Development and Stress Conditions in Oryza sativa L

Genome-Wide Analysis of the PERK Gene Family in Brassica napus L. and Their Potential Roles in Clubroot Disease

The proline-rich extensin-like receptor kinase (PERK) gene family is crucial to various molecular and cellular processes in plants. We identified 50 PERK genes in Brassica napus to explore their evolutionary dynamics, structural diversity, and functional roles. These genes were grouped into four classes and unevenly distributed across 18 chromosomes. Phylogenetic studies and Ka/Ks ratios revealed purifying selection during the evolution process. They exhibited significant diversification in gene length, molecular weight, and isoelectric points, suggesting specialized function. Gene structure and motif analyses revealed variations among the BnPERK family members, with conserved tyrosine kinase domains suggesting functional importance. Cis-element analysis predicted the involvement in hormone signaling and stress responses. Expression profiling showed diverse patterns across tissues and hormone treatments, highlighting potential roles in growth regulation and hormone signaling. Protein-protein interaction networks suggested BnPERK proteins interact with a wide array of proteins, implicating them in multiple biological processes. The transcriptional downregulation of four BnPERK genes upon Plasmodiophora brassicae infection implied a role in clubroot disease response. Furthermore, the Arabidopsis perk9 mutant displayed relieved disease severity and enhanced basal immune response, suggesting the negative role of PERK9 in plant immunity. The study highlighted the potential role of BnPERKs in crop improvement strategies against clubroot disease.

Genome-Wide Identification and Analysis of Glycosyltransferases in Colletotrichum graminicola

Corn leaf blight and stem rot caused by Colletotrichum graminicola are significant diseases that severely affect corn crops. Glycosyltransferases (GTs) catalyze the transfer of sugar residues to diverse receptor molecules, participating in numerous biological processes and facilitating functions ranging from structural support to signal transduction. This study identified 101 GT genes through functional annotation of the C. graminicola TZ-3 genome. Subsequent analyses revealed differences among the C. graminicola GT (CgGT) genes. Investigation into subcellular localization indicated diverse locations of CgGTs within subcellular structures, while the presence of multiple domains in CgGTs suggests their involvement in diverse fungal biological processes through versatile functions. The promoter regions of CgGT genes are enriched with diverse cis-acting regulatory elements linked to responses to biotic and abiotic stresses, suggesting a key involvement of CgGT genes in the organism's multi-faceted stress responses. Expression pattern analysis reveals that most CgGT genes were differentially expressed during the interaction between C. graminicola and corn. Integrating gene ontology functional analysis revealed that CgGTs play important roles in the interaction between C. graminicola and corn. Our research contributes to understanding the functions of CgGT genes and investigating their involvement in fungal pathogenesis. At the same time, our research has laid a solid foundation for the development of sustainable agriculture and the utilization of GT genes to develop stress-resistant and high-yield crop varieties.

A Comprehensive Genome-Wide Investigation of the Cytochrome 71 (OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice (Oryza sativa L.)

The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.