Genome-wide analysis and expression profiling of CPK gene families in Sorghum bicolor (L.) Moench reveal their hormone-mediated responses during seed germination
This study identifies key candidate SbCPK genes associated with seed germination and hormonal signal transduction, providing a fundamental theoretical basis for further elucidating the calcium signaling-mediated molecular regulatory mechanisms of PHS in sorghum.
Abstract
Introduction Sorghum (Sorghum bicolor (L.) Moench) is an economically vital crop worldwide for food, forage, and bioenergy production, and also serves as the core raw material for Guizhou-flavored Chinese Baijiu. Pre-harvest sprouting (PHS) severely impairs sorghum grain yield, quality, and industrial economic value. Calcium-dependent protein kinases (CPKs/CDPKs) are plant-specific calcium sensors that exert essential regulatory functions in seed development, dormancy, and germination. Nevertheless, the genome-wide characteristics of the sorghum SbCPK family and their molecular mechanisms underlying seed germination regulation remain largely elusive. Methods In this study, we systematically identified the SbCPK gene family based on the BTx623 v2.1 reference genome, and comprehensively analyzed their physicochemical properties, phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, collinearity, and promoter cis-acting elements. Using the sorghum cultivar `Hongyingzi' as experimental material, we integrated transcriptome profiling and qRT-PCR assays to characterize the tissue-specific expression patterns of SbCPKs and their transcriptional responses to exogenous ABA and ACC (ethylene precursor) treatments Results A total of 30 SbCPK genes were identified across the sorghum genome, which were unevenly distributed on 10 chromosomes and formed 8 tandem duplication clusters. Phylogenetic analysis classified these SbCPKs into four distinct subfamilies, which exhibited high evolutionary conservation with CPK homologs in maize and rice. Gene structures and motif compositions were conserved among the four subfamilies, and abundant cis-elements associated with ABA, ethylene, stress responses and seed development were detected in the promoters of SbCPK genes. Tissue expression profiling revealed that SbCPK5, SbCPK9, SbCPK11, and SbCPK19 were specifically and highly expressed in sorghum embryos. Exogenous ABA significantly inhibited seed germination and upregulated the transcript levels of SbCPK6, SbCPK8, SbCPK9, SbCPK11, and SbCPK21. In contrast, ACC markedly promoted seed germination, specifically induced the expression of SbCPK19, and repressed the expression of multiple other SbCPK members. These results indicate that SbCPK family genes exhibit obvious differential expression in response to ABA and ethylene signals during sorghum seed germination. Discussion Collectively, this study identifies key candidate SbCPK genes associated with seed germination and hormonal signal transduction, providing a fundamental theoretical basis for further elucidating the calcium signaling-mediated molecular regulatory mechanisms of PHS in sorghum.
The cultivated peanut (Arachis hypogaea L.) is an important oilseed and economic crop worldwide, with seed protein content being a key target for quality improvement. The Sugars Will Eventually be Exported Transporter (SWEET) gene family encodes sugar transporters that play crucial roles in plant growth and development, stress tolerance, pathogen interactions, and seed filling. In this study, 43 AhSWEET genes were identified in the cultivated peanut genome and classified into four phylogenetic clades. Members within the same clade generally show similar exon-intron structures and conserved motif compositions, suggesting evolutionary conservation within subgroups. Promoter cis-regulatory elements analysis indicated that AhSWEET genes contain multiple elements associated with light response, hormone signaling, stress response, and growth and development, implying their potential involvement in diverse biological processes. Subcellular localization predictions indicated that most AhSWEET proteins are likely localized to the plasma membrane, consistent with their putative roles in transmembrane sugar transport. This was further supported by transient expression analysis of selected AhSWEET-eGFP fusion proteins in Nicotiana benthamiana leaves. Comparative phylogenetic and synteny analyses reveal that AhSWEET5, AhSWEET21, AhSWEET27, and AhSWEET43 are closely related to soybean GmSWEET10a and GmSWEET10b, which are known to regulate seed size and storage-compound accumulation. Transcriptome data and quantitative reverse transcriptase PCR analysis showed that these candidate genes are preferentially expressed in seed-related tissues, particularly the testa and embryo, suggesting possible sugar allocation during peanut seed development. Overall, this study provides a systematic characterization of the AhSWEET gene family and identifies several candidate genes for future functional studies aimed at improving peanut seed quality, including protein accumulation.
Lina He, Pengyu Qu, Xiaona Li et al.· International Journal of Mol...· 0 citations
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 three-amino-acid-loop-extension (TALE) gene family encodes a group of plant-specific homeodomain transcription factors that play indispensable roles in plant growth, development, and adaptation to environmental stresses. Although TALE genes have been extensively investigated in several plant species, their genome-wide characteristics and potential functions in maize, particularly in response to phosphorus deficiency, remain poorly understood. In the present study, a comprehensive genome-wide identification and characterization of the maize TALE gene family were conducted using bioinformatics approaches, followed by an investigation of their transcriptional responses to low-phosphorus (LP) stress. A total of 40 ZmTALE genes (ZmTALE1–ZmTALE40) were identified and phylogenetically classified into four subfamilies: BEL1-like, KNOX I, KNOX II, and KNOX III. Members within the same subfamily exhibited highly conserved gene structures and motif compositions, reflecting their evolutionary conservation. Chromosomal localization and synteny analyses demonstrated that segmental duplication has been the predominant force driving the expansion of the ZmTALE gene family during maize evolution. Promoter analysis revealed that the upstream regulatory regions of ZmTALE genes were enriched in light-responsive, phytohormone-responsive, and abiotic stress-related cis-acting regulatory elements, implying their potential involvement in multiple developmental and stress-responsive pathways. Expression profiling under LP conditions revealed pronounced genotype-dependent transcriptional responses among different maize inbred lines. Notably, ZmTALE1/5/12/14/18/30/31/33/36 were significantly induced by LP stress, whereas ZmTALE10 and ZmTALE37 were markedly repressed. These differentially expressed genes represent promising candidates for further functional investigation of phosphorus-deficiency tolerance in maize. Furthermore, ZmTALE10, ZmTALE14, and ZmTALE31 are nuclear-localized transcriptional activators. Taken together, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize TALE gene family and offer candidate genes for developing phosphorus-efficient maize cultivars through molecular breeding.
Xianting Huang, Shuang Li, Litao Yi et al.· Plants· 0 citations
Functional characterization demonstrated that transgenic tobacco plants overexpressing AsGRF17 displayed significantly enhanced drought tolerance compared with wild-type plants, and this study provides new insights into the molecular mechanisms underlying AsGRF17 -mediated drought tolerance in oat.
Jingyan Li, Shi Tong, Kailian Li et al.· 0 citations
Simple Summary Cotton is one of the world’s most important fiber and oil crops, but drought and salty soils strongly reduce its growth and yield. Enzymes of the BXL family help remodel plant cell walls and are thought to contribute to a plant’s ability to cope with environmental stress. In this study, we searched the cotton genome and identified 25 BXL genes, and we examined their evolutionary relationships, gene structures, and the regulatory regions that control their activity. We then tested how these genes respond when cotton seedlings are exposed to drought-like and salt-like conditions. Several BXL genes were strongly activated under both treatments, and three in particular were identified as central “hub” genes within networks of stress-responsive genes. These results indicate that specific BXL genes may help cotton survive dry or salty conditions, and they provide candidate targets for future efforts to improve cotton’s tolerance to drought and salinity. Such improvements could help stabilize cotton production under increasingly challenging environmental conditions.
Zhenzhen Wei, An-Xing Zhu, Yang Liu et al.· Biology· 0 citations
