BMC Genomics最新文献

{"title":"Transcriptomic analysis of wild Cannabis sativa: insights into tissue- and stage-specific expression and secondary metabolic regulation.","authors":"Jinyuan Hu, Zishi Wang, He Xu, Zhenlong Wang, Ning Li, Rui Feng, Jianyu Yin, Fangru Liu, Baishi Wang","doi":"10.1186/s12864-025-11697-5","DOIUrl":"10.1186/s12864-025-11697-5","url":null,"abstract":"<p><p>Cannabis sativa is a medicinally and economically significant plant known for its production of cannabinoids, terpenoids, and other secondary metabolites. This study presents a transcriptomic analysis to elucidate tissue-specific expression and regulatory mechanisms across leaves, stems, and roots. A total of 2,530 differentially expressed genes (DEGs) were identified, with key genes such as terpene synthase (TPS) and phenylalanine ammonia-lyase (PAL) exhibiting elevated expression in leaf tissues, emphasizing their roles in terpenoid and phenylpropanoid biosynthesis. Alternative splicing (AS) analysis revealed 8,729 distinct events, dominated by exon skipping, contributing to transcriptomic diversity. Long non-coding RNA (lncRNA) prediction identified 3,245 candidates, many of which displayed tissue-specific expression patterns and co-expression with metabolic genes, suggesting regulatory roles in secondary metabolism. Additionally, 12,314 SNPs and 2,786 INDELs were detected, with notable enrichment in genes associated with secondary metabolite biosynthesis, particularly in leaf tissues. These findings advance the understanding of molecular mechanisms governing secondary metabolism and genetic diversity in C. sativa, providing valuable insights for future metabolic engineering and breeding strategies to enhance cannabinoid production.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"528"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and functional characterization of LBD gene family in four Cymbidium species (Orchidaceae) and potential regulatory role of CsiLBD27 in floral development of Cymbidium sinense.","authors":"Yonglu Wei, Zengyu Lin, Jianpeng Jin, Wei Zhu, Jie Gao, Jie Li, Qi Xie, Chuqiao Lu, Genfa Zhu, Fengxi Yang","doi":"10.1186/s12864-025-11701-y","DOIUrl":"10.1186/s12864-025-11701-y","url":null,"abstract":"<p><strong>Background: </strong>The Lateral Organ Boundaries Domain (LBD) gene family, encompassing plant-specific LOB domain proteins, plays essential roles in various aspects of plant growth and development, and has continuously diversified its functions across numerous species. However, studies on LBD genes in the Orchidaceae family remain limited. To our knowledge, this is the first systematic investigation of the LBD gene family in Cymbidium, a genus that exhibits remarkable species and trait diversity within the Orchidaceae.</p><p><strong>Results: </strong>In this study, we identified 122 LBD genes within the genomes of four Cymbidium species, distributed on 20 chromosomes. These genes were classified into class I (109 members, including 16 in subclass Ic/d) and class II (13 members), with protein lengths ranging from 94-477 amino acids. Promoter sequences of CymLBD genes revealed various cis-elements significant for light, hormonal, biotic, and abiotic stress responses. Transcriptomic analysis revealed tissue- and stage-specific expression of CymLBD genes in Cymbidium, and RT-qPCR and yeast one-hybrid assays indicated that CsiLBD27 may regulate floral patterning by directly binding to the CsiSEP3 promoter and activating its transcription. Under ABA treatment, the genes CsiLBD13, CsiLBD19, and CsiLBD21 displayed tissue-specific expression changes, suggesting hormone-responsive regulation. In Cymbidium ensifolium, 16 CenLBD genes were differentially expressed, while in Cymbidium mannii, 9 CmaLBD gene expression exist obvious circadian rhythm. GO and KEGG enrichment of 1074 and 399 predicted target genes, respectively, indicating a diverse range of functions for LBDs.</p><p><strong>Conclusions: </strong>Collectively, this study provides the first comprehensive insight into the evolutionary dynamics, regulatory mechanisms, and functional roles of LBD genes in Cymbidium. These findings offer a valuable genetic resource for understanding floral and vegetative development in Orchidaceae and uncover potential novel functions of LBD genes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"536"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Mg²⁺-dependent high-yield method for extracting high-molecular-weight genomic DNA from a single planarian specimen.","authors":"Ao Li, Bingrui Sun, Ying Zhang, Ping Yu, Jicheng Qu, Hongkuan Deng, Qiuxiang Pang, Fengtang Yang","doi":"10.1186/s12864-025-11731-6","DOIUrl":"10.1186/s12864-025-11731-6","url":null,"abstract":"<p><strong>Background: </strong>The isolation of intact, high-molecular-weight genomic DNA (HMW gDNA) is essential for achieving complete genome assemblies. However, extracting HMW gDNA from a single individual of Dugesia japonica remains a technical challenge using the standard protocol, probably due to the presence of abundant polysaccharides and nucleases.</p><p><strong>Results: </strong>In this study, we have developed a more robust protocol for preparing HMM gDNA, with high yields and quality, from a single D. japonica. The key step in our protocol involves the use of a Mg²⁺-dependent lysis buffer, rather than using metal cation chelation to block the activities of DNase I as in the standard protocol. Using this approach were able to achieve a yield of about 10-15 µg of HWM gDNA per worm. Our method showed species- and region-specific effectiveness, with optimal results observed at 20 mM Mg²⁺ for our local D. japonica specimens. The extracted HMW gDNA is fully compatible with advanced long-read sequencing platforms such as PacBio HiFi and Oxford Nanopore. However, when applied to Schmidtea mediterranea and D. japonica specimens from Beijing, the method was ineffective and led to progressive gDNA degradation.</p><p><strong>Conclusions: </strong>This protocol offers a simple and high-yield solution for isolating HMW gDNA from D. japonica. It also provides an alternative for organisms whose gDNA consistently exhibits unexplained degradation using established protocols.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"532"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity analysis and DNA fingerprinting of different populations of largemouth bass (Micropterus salmoides) in China with fluorescence-labeled microsatellite markers.","authors":"Jinxing Du, Tao Zhu, Taihang Tian, Hongmei Song, Caixia Lei, Jing Tian, Linqiang Han, Shengjie Li","doi":"10.1186/s12864-025-11721-8","DOIUrl":"10.1186/s12864-025-11721-8","url":null,"abstract":"<p><strong>Background: </strong>Largemouth bass (Micropterus salmoides, LMB) is an economic fish in China, which has developed into many different cultured populations in the past decades. These populations exhibit different growth rates, morphological traits, stress resistance, and genetic diversity. Analyzing genetic diversity and molecular identification of these populations is crucial for conserving and utilizing germplasm resources, as well as for breeding new varieties.</p><p><strong>Result: </strong>In this study, ten distinct LMB populations from China were collected and examined using fluorescence-labeled microsatellite markers. A total of 53 alleles were identified using seven microsatellite primer pairs, with allele counts ranging from 5 to 11 and an average of 7.571. The observed heterozygosity among the ten LMB populations varied from 0.210 to 0.967, while expected heterozygosity ranged from 0.204 to 0.651, and the polymorphism information content was between 0.175 and 0.597. Genetic distance varied from 0.019 to 0.457, the genetic differentiation index ranged from 0.013 to 0.258, and the number of effective migrants (Nm) was between 0.719 and 18.981. The genetic structure analysis indicated that the ten LMB populations could be classified into two or four groups. The analysis of molecular variance (AMOVA) revealed that 83.77% of genetic variation was found within individuals, with only 16.23% attributed to differences among populations. Through construction of DNA fingerprinting, we discovered unique fragments at several loci were detected in the populations such as the reintroduced Northern LMB population, \"Youlu No.3\" population, and the hybrid populations. Additionally, we also created digital DNA fingerprint maps of these LMB populations. Through analysis the digital DNA fingerprints from four candidate LMB populations, three known populations corresponded with the populations collected in this study. These results indicated high identification efficiencies of the digital DNA fingerprinting created in this study.</p><p><strong>Conclusion: </strong>We established a method to distinguish 10 different LMB populations in China, which will assist in identification, traceability management, protection, and intellectual property rights of LMB in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"531"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of single nucleotide polymorphisms (SNPs) associated with heat stress and milk production traits in Chinese holstein cows.","authors":"Jingyi Xu, Lirong Hu, Jingyang Ning, Fan Zhang, Qing Xu, Yachun Wang","doi":"10.1186/s12864-025-11716-5","DOIUrl":"10.1186/s12864-025-11716-5","url":null,"abstract":"<p><strong>Background: </strong>Heat stress (HS) poses a significant challenge to the dairy industry, affecting both the health and productivity of dairy cows. Identifying candidate genes and single nucleotide polymorphisms (SNPs) associated with HS is critical to improving heat tolerance of dairy cows. In our previous work, the eukaryotic translation initiation factor 4E (EIF4E), heat shock protein family A member 4 (HSPA4), and inositol 1,4,5-trisphosphate receptor type 2 (ITPR2) genes were found to play critical roles in the HS response of dairy cows.</p><p><strong>Results: </strong>In this study, we further validated the gene expression patterns and genetic effects of the three candidate genes on HS response and milk production in Chinese Holstein cows. A total of 21 SNPs were identified by sequencing the exon and 2000 bp flanking region of the EIF4E (4 SNPs), HSPA4 (8 SNPs), and ITPR2 (9 SNPs) in pooled DNA samples from 70 Holstein bulls. Among these, two SNPs (g.44653172A > G and g.44660065C > T) were located in the coding exon and the 3' untranslated region of the HSPA4 gene, respectively. Association analyses were conducted between identified SNPs and three HS traits and six milk production traits in a population of 1,160 Chinese Holstein cows. The SNP-based association analysis identified significant associations between ten SNPs and HS traits (P < 0.05), as well as eight SNPs and milk production traits (P < 0.05). In the HSPA4 gene, five SNPs (g.44618036G > A, g.44624256 A > C, g.44624428T > C, g.44653172 A > G, and g.44660065 C > T) were significantly associated with rectal temperature (RT; P < 0.05). Notably, no SNPs were associated with milk production traits. Haplotype blocks containing g.44,653,172 A > G and g.44,660,065 C > T also showed significant associations with RT (P < 0.05). Further analysis suggests that g.44,660,065 C > T affects the stability of the mRNA secondary structure, microRNA and transcription factor binding, thereby potentially influencing the gene expression of HSPA4.</p><p><strong>Conclusion: </strong>In conclusion, we demonstrated that these three genes had significant genetic effects on HS and milk production traits. And g.44,660,065 C > T in the HSPA4 gene could be used as functional molecular markers for the genetic selection of dairy cows for improving heat tolerance without compromising their high milk performance.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"534"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preservation of milk in liquid nitrogen during sample collection does not affect the RNA quality for RNA-seq analysis.","authors":"Lucía Jiménez-Montenegro, Leopoldo Alfonso, Beatriz Soret, José A Mendizabal, Olaia Urrutia","doi":"10.1186/s12864-025-11707-6","DOIUrl":"10.1186/s12864-025-11707-6","url":null,"abstract":"<p><strong>Background: </strong>Standard procedures for milk sample collection for transcriptome analysis use ice as preservation method, which can affect the RNA stability and requires immediate sample processing. These problems would be eased if the milk samples could be snap-frozen in liquid nitrogen. This study describes the applicability of a new method for milk sample collection and subsequent RNA extraction from milk fat globules, determining whether the quality, integrity and quantity of the RNA extracts met the minimum requirements for downstream RNA-seq.</p><p><strong>Results: </strong>The quality of the extracts measured by A_260/280 ratio and the Integrity and Quality (IQ) values obtained fulfilled the reference values of 1.9 - 2.1 (P1 < 0.05 and P2 < 0.05) and ≥ 9 (P < 0.05), respectively. However, the RNA Integrity Number (RIN), based on rRNA 18S and 28S analysis, was 3.59 (P > 0.05) and failed to meet the RIN ≥ 7 benchmark for RNA-seq (P > 0.05). Milk fat globules contain low molecular-weight RNA fragments and minimal 18S and 28S rRNA, suggesting low RIN values were inherent to sample type. Likewise, the RNA concentration from milk fat globules were generally low (120.43 ± 22.27 ng/µL, 102.87 ± 15.64 ng/µL and 109.43 ± 22.69 ng/µL, measured by Nanodrop, Qubit HS and QuanTI Ribogreen, respectively). Nevertheless, RNA-seq yielded 52.7 million paired-end reads per sample. The raw reads passed all quality control parameters having the same sequence-read lengths (151 bp), 100% base-coverage, 49% GC base content, and base quality scores of 36, enabling successful transcriptome profiling. Moreover, milk proteins were identified as the most abundant transcripts in MFG in the analysis of the most expressed genes, indicating that the sequenced reads would accurately reflect the transcriptome of this milk fraction.</p><p><strong>Conclusions: </strong>Milk preservation in liquid nitrogen is a suitable sample collection method that overcomes the limitations of immediate sample processing required if ice is used. Thus, this procedure, together with the subsequent RNA isolation from milk fat globules and its sequencing by RNA-seq, would provide a practical and a non-invasive method for measuring the mammary epithelial cell transcriptome, improving the feasibility of conducting studies related to mammary gland and lactation physiology.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"525"},"PeriodicalIF":3.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and expression analysis of N⁶-methyltransferase and demethylase in rapeseed (Brassica napus L.).","authors":"Xiaoyu Chen, Yu Kang, Shun Li, Bo Yang, Xiaoyan Xia, Zhonghua Wang, Lunwen Qian, Xinhua Xiong, Lei Kang, Xin He","doi":"10.1186/s12864-025-11695-7","DOIUrl":"10.1186/s12864-025-11695-7","url":null,"abstract":"<p><strong>Background: </strong>N⁶-methyladenosine (m⁶A) modification involves the addition of a methyl group to the nitrogen atom at position six of adenine in RNA. It is the most prevalent type of dynamic internal RNA methylation modification, plays an important role in plant development and abiotic stress. The m⁶A modification is facilitated by m⁶A writers (m⁶A methyltransferases), m⁶A erasers (m⁶A demethylation enzymes), and m⁶A readers (m⁶A methylated reading proteins).</p><p><strong>Results: </strong>In order to study the characterization and expression of m⁶A methyltransferases and demethylases in Brassica napus (rapeseed), we used five methyltransferases and two demethylases from Arabidopsis thaliana as reference sequences. A total of 34 methyltransferases and 12 demethylases were identified in B. napus, B. oleracea, and B. rapa. We analyzed the physicochemical properties, gene structures, conserved domains, chromosome localization, and expression pattern across all tissues, as well as the effects of hormone and stress treatments on B. napus. Our findings revealed that the methyltransferase BnaHAKAI was highly expressed during the late stages of seed development. It may be related to the synthesis of oil content and seed size in the later stage of seed growth. In contrast, the demethylase BnaALKBH10B exhibited high expression primarily in the petals, followed by the pods, buds. This expression pattern may be associated with flower development and the timing of flowering. Furthermore, BnaALKBH10B primarily responded to abiotic stresses such as salinity, drought, osmotic, cold, and freezing, as well as to hormones like jasmonic acid and gibberellins. The qRT-PCR results showed that BnaALKBH10B responded to freezing and salt stress.</p><p><strong>Conclusions: </strong>In summary, a total of 34 methyltransferases and 12 demethylases genes were identified in B. napus, B. oleracea, and B. rapa, and their phylogenetic relationships, structural domains, and expression patterns in tissues and under abiotic stress were comprehensively analyzed. This research will serve as a foundation for future studies on m⁶A in B. napus.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"526"},"PeriodicalIF":3.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture.","authors":"Livia Beccacece, Stefano Pallotti, Yiyun Li, Jie Huang, Leonardo Pasotti, Valerio Napolioni","doi":"10.1186/s12864-025-11702-x","DOIUrl":"10.1186/s12864-025-11702-x","url":null,"abstract":"<p><strong>Background: </strong>The Anterior Cruciate Ligament (ACL) plays a critical role in maintaining the musculoskeletal stability of the knee. Its injury has been linked to an increased risk of developing osteoarthritis. This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. Differential gene expression analysis was performed for each dataset, producing a genome-wide transcriptional signature of fold-change significance for individual genes. Stouffer's method was used to integrate the results, identifying genes significantly deregulated across all species. Additionally, gene-set enrichment analysis revealed pathways that were consistently upregulated or downregulated.</p><p><strong>Results: </strong>A positive correlation in expression was observed between human and the other three species (r² = 0.177-0.305, p-value ≤ 2.7 × 10^- 113), identifying 210 genes as the most consistently up- and down-regulated in response to ACL rupture (p-adjusted ≤ 1.27 × 10^- 23). These genes are primarily involved in cellular mitosis, collagen pathways, and cartilage development. Furthermore, 60 pathways were found to be significantly up- or down-regulated across all species (p-adjusted ≤ 4.57 × 10^- 4). Among these, the upregulation of inhibition of bone mineralization (p-adjusted ≤ 2.99 × 10^- 6) aligns with previous findings on the reduction of subchondral bone mineral density following ACL rupture.</p><p><strong>Conclusions: </strong>This study highlights that distinct species exhibit common molecular responses to ACL rupture, underscoring the value of mice, dogs, and rabbits as potential translational model organisms for ACL rupture research. Furthermore, the identified genes and pathways highlight the molecular mechanisms underlying ACL rupture.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"524"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-wide association study reveals that DgFH18 and DgCMO-like are associated with flowering time in orchardgrass (Dactylis glomerata).","authors":"Miaoli Wang, Guangyan Feng, Zhongfu Yang, Lei Cao, Gang Nie, Xiaoheng Xu, Feixiang Hao, Linkai Huang, Xinquan Zhang","doi":"10.1186/s12864-025-11708-5","DOIUrl":"10.1186/s12864-025-11708-5","url":null,"abstract":"<p><strong>Background: </strong>Flowering is a tightly regulated process influencing yield and promoting plant genetic diversity and conservation. Orchardgrass (Dactylis glomerata) exhibits excellent yield traits and stress resistance, making it ideal for animal husbandry and ecological restoration. However, the molecular regulatory factors of the flowering time of orchardgrass are still unknown, limiting its molecular breeding.</p><p><strong>Results: </strong>To speed up molecular breeding to enhance flowering traits in orchardgrass, we conducted a genome-wide association study (GWAS). A diverse panel of 249 orchardgrass accessions was phenotyped for heading stage and flowering time. GWAS analysis identified 359 candidate genes that overlapped or were adjacent to effective single-nucleotide polymorphisms (SNPs), which were considered potential flowering time-related genes. Furthermore, we validated that formin-like protein 18 (DgFH18) and choline monooxygenase (DgCMO-like) was two important flowering candidate genes by overexpressing them in Arabidopsis to unravel their potential functions. Overexpression of DgFH18 and DgCMO-like positively regulated flowering time by inducing the expression of flowering-related genes. Moreover, sucrose treatment could significantly promote the expression of flavonoid pathway genes and enhance the content of total flavonoids and anthocyanins in the DgCMO-like-overexpressing lines compared to the wild type.</p><p><strong>Conclusion: </strong>These results provide valuable resources for future orchardgrass breeding programs and broaden the current comprehension of flowering time regulation in perennial grasses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"522"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-Seq uncovers endogenous NO-induced hormone signal transduction and carbon metabolism in response to PEG stress in alfalfa.","authors":"Ying Zhao, Xiaofang Zhang, Yizhen Wang, Qian Ruan, Baoqiang Wang, Xiaoyue Wen, Xiaohong Wei","doi":"10.1186/s12864-025-11706-7","DOIUrl":"10.1186/s12864-025-11706-7","url":null,"abstract":"<p><strong>Background: </strong>Alfalfa (Medicago sativa L.) has the benefits of high yield and nutritional value as a sustainable forage. However, the water deficit significantly limits its growth and yield performance. Nitric oxide (NO) is a signal molecule that can enhance plant tolerance. The majority of previous studies focus on the role of exogenous NO in plant tolerance. However, the underlying mechanism of endogenous NO in alfalfa drought tolerance remains largely unexplored.</p><p><strong>Results: </strong>To explore the mechanism of the endogenous NO-mediated water deficit resistance in the alfalfa, seedlings were exposed to polyethylene glycol 6000 (PEG) and NO scavenger (cPTIO). Results showed that PEG treatment significantly augmented alfalfa endogenous NO, MDA, O₂^·-, and H₂O₂ levels. In parallel, eliminating endogenous NO under PEG stress (PEG-NO) significantly diminished NO level, exacerbated MDA and reactive oxygen species accumulation, and decreased the activities of key enzymes involved in carbon fixation and TCA cycle, such as Rubisco, FBA, PDH, α-KGDH, and SDH, as well as reduced ABA and IAA content in alfalfa leaves. RNA-Seq and bioinformatics analysis suggested that endogenous NO-responsive DEGs primarily relate to carbon metabolism and hormone signal transduction. In further studies of these DEGs, we speculated that GH3, SAUR, SnRK2, and ABF genes and FBA, GAPDH, SBP, and CS are critical genes in response to endogenous NO under PEG stress.</p><p><strong>Conclusions: </strong>In summary, our study innovatively proposes a mechanism model of how endogenous NO enhances alfalfa tolerance to water deficiency at the physiological and molecular levels. The novel candidate genes can give genetic resources for the subsequent molecular-assisted breeding of drought-resistant alfalfa crops.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"523"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}