BMC Genomics最新文献

{"title":"Gonadal transcriptome analysis reveals MAG participates in ovarian suppression of intersex red claw crayfish (Cherax quadricarinatus).","authors":"Honglin Chen, Miaofeng Ouyang, Huan Zhou, Fangfang Liu, Huiyi Cai, Bao Lou","doi":"10.1186/s12864-025-11249-x","DOIUrl":"10.1186/s12864-025-11249-x","url":null,"abstract":"<p><strong>Background: </strong>The red claw crayfish (Cherax quadricarinatus) is a commercially and ecologically significant species that displays a unique intersex model with an ovotestis gonad and was identified to have functional testes and a vestigial ovary, which was inhibited by insulin-like androgenic gland hormone (IAG), but the underlying molecular mechanisms are still unclear.</p><p><strong>Results: </strong>In this study, the structure and transcriptomic profiles of ovotestis and female and male gonad was analysis and compared, 406 differentially expressed genes were identified, among which membrane-anchored AG-specific factor (MAG) exhibited significantly greater expression in ovotestis gonads than in male or female gonads. The localization of MAG in type I or II cells of androgenic gland revealed its potential function of IAG hormone synthesis. Furthermore, the analyses of gene regulation relationship revealed that IAG positively regulates MAG expression, while MAG negatively regulates vitellogenin gene (VTG) expression.</p><p><strong>Conclusions: </strong>Our research suggesting MAG participates in the IAG regulated ovarian suppression in the intersex red claw crayfish, which provides important information on the regulatory mechanism of the ovarian dysplasia in the ovotestis of intersex red claw crayfish. These results will enhance the knowledge of IAG-related pathways in the female reproductive axis, as well as the mechanisms of sexual differentiation in crustaceans.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"134"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11816507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398023","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":"The interactions between monocarboxylate transporter genes MCT1, MCT2, and MCT4 and the kinetics of blood lactate production and removal after high-intensity efforts in elite males: a cross-sectional study.","authors":"Ewelina Maculewicz, Andrzej Mastalerz, Aleksandra Garbacz, Anna Mróz, Petr Stastny, Miroslav Petr, Dominik Kolinger, Pavlina Vostatková, Aleksandra Bojarczuk","doi":"10.1186/s12864-025-11307-4","DOIUrl":"10.1186/s12864-025-11307-4","url":null,"abstract":"<p><strong>Background: </strong>This cross-sectional study investigated the relationship between genetic variations in monocarboxylate transporter genes and blood lactate production and removal after high-intensity efforts in humans. The study was conducted to explore how genetic variations in the MCT1, MCT2, and MCT4 genes influenced lactate dynamics and to advance the field of sports genetics by pinpointing critical genetic markers that can enhance athletic performance and recovery.</p><p><strong>Methods: </strong>337 male athletes from Poland and the Czech Republic underwent two intermittent all-out Wingate tests. Before the tests, DNA samples were taken from each participant, and SNP (single nucleotide polymorphism) analysis was carried out. Two intermittent all-out tests were implemented, and lactate concentrations were assessed before and after these tests.</p><p><strong>Results: </strong>Sprinters more frequently exhibited the haplotype TAC in the MCT2 gene, which was associated with an increase in the difference between maximum lactate and final lactate concentration. Additionally, this haplotype was linked to higher maximum lactate concentration and was more frequently observed in sprinters. The genotypic interactions AG/T- and GGxT- (MCT1 rs3789592 x MCT4 rs11323780), TTxTT (MCT1 rs12028967 x MCT2 rs3763979), and MCT1 rs7556664 x MCT4 rs11323780 were all associated with an increase in the difference between maximum lactate concentration and final lactate concentration. Conversely, the AGxGG (MCT1 rs3789592 x MCT2 rs995343) interaction was linked to a decrease in this difference. The relationship between maximum lactate concentration and genotypic interactions can be observed as follows: when ATxTT (MCT2 rs3763980 x MCT4 rs11323780) or CTxCT (MCT1 rs10857983 x MCT2 rs3763979) genotypic combinations are present, it leads to a decrease in maximum lactate concentration. Similarly, the combination of CTxCT (MCT1 rs4301628 x MCT2 rs3763979), CT x TT (MCT1 rs4301628 x MCT4 rs11323780), and CTxTT (MCT1 rs4301628 x MCT2 rs3763979) results in decreased maximum lactate concentration.</p><p><strong>Conclusions: </strong>The TAC haplotype (rs3763980, rs995343, rs3763979) in the MCT2 gene is associated with altered lactate clearance in sprinters, potentially affecting performance and recovery by elevating post-exercise lactate concentrations. While MCT4 rs11323780 is also identified as a significant variant in lactate metabolism, suggesting its role as a biomarker for sprinting performance, further investigation is necessary to clarify underlying mechanisms and consider additional factors. Based on elite male athletes from Poland and the Czech Republic, the study may not generalize to all sprinters or diverse athletic populations. Although genetic variants show promise as biomarkers for sprinting success, athletic performance is influenced by a complex interplay of genetics, environment, and training extending beyond MCT genes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"133"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11817040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398029","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":"Predicting substrates for orphan solute carrier proteins using multi-omics datasets.","authors":"Y Zhang, S Newstead, P Sarkies","doi":"10.1186/s12864-025-11330-5","DOIUrl":"10.1186/s12864-025-11330-5","url":null,"abstract":"<p><p>Solute carriers (SLC) are integral membrane proteins responsible for transporting a wide variety of metabolites, signaling molecules and drugs across cellular membranes. Despite key roles in metabolism, signaling and pharmacology, around one third of SLC proteins are 'orphans' whose substrates are unknown. Experimental determination of SLC substrates is technically challenging, given the wide range of possible physiological candidates. Here, we develop a predictive algorithm to identify correlations between SLC expression levels and intracellular metabolite concentrations by leveraging existing cancer multi-omics datasets. Our predictions recovered known SLC-substrate pairs with high sensitivity and specificity compared to simulated random pairs. CRISPR-Cas9 dependency screen data and metabolic pathway adjacency data further improved the performance of our algorithm. In parallel, we combined drug sensitivity data with SLC expression profiles to predict new SLC-drug interactions. Together, we provide a novel bioinformatic pipeline to predict new substrate predictions for SLCs, offering new opportunities to de-orphanise SLCs with important implications for understanding their roles in health and disease.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"130"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390002","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":"Transcriptome and WGCNA reveals the potential genetic basis of photoperiod-sensitive male sterility in soybean.","authors":"Yuhua Yang, Suqin He, Lihong Xu, Minggui Wang, Shuichun Chen, Zhiyuan Bai, Tingting Yang, Bo Zhao, Lixiang Wang, Haiping Zhang, Jiangjiang Zhang, Ruijun Zhang","doi":"10.1186/s12864-025-11314-5","DOIUrl":"10.1186/s12864-025-11314-5","url":null,"abstract":"<p><strong>Background: </strong>Soybean (Glycine max (L.) Merr.) is a crucial crop due to its high plant protein and oil content. Previous studies have shown that soybeans exhibit significant heterosis in terms of yield and protein content However, the practical application of soybean heterosis remains difficult, as the molecular mechanisms underlying photoperiod-sensitive genic male sterile (PGMS) is still unclear.</p><p><strong>Results: </strong>This study characterized the PGMS line 88-428BY, which is sterile under short-day (SD) conditions and fertile under long-day (LD) conditions. To elucidate the genetic basis for this trait, we collected anthers, from 88-428BY under SD and LD conditions at three developmental stages, resulting in the identification of differentially expressed genes (DEGs) (2333, 2727 and 7282 DEGs, respectively) using Illumina transcriptome analysis. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, we fund that among the DEGs, enriched genes were associated with photoperiod stress, light stimulus, oxidation-reduction processes, multicellular organism development and protein phosphorylation. Additionally, weighted correlation network analysis identified four modules (blue, brown, red, and yellow) that were significantly correlated with PGMS, revealing co-expressed hub genes with potential regulatory roles. Functional annotation of 224 DEGs with|KME| >0.9 across the four modules in seven databases highlighted their involvement in light stimulus, oxidation-reduction processes, multicellular organism development, and protein phosphorylation, suggesting their importance in soybean PGMS. By integrating fertility-related genes previously identified by other studies with the DEGs from our analysis, we identified eight candidate genes associated with the photosensitive sterility in soybeans.</p><p><strong>Conclusions: </strong>This study enhances the understanding of PGMS in soybean and establishes the genetic basis for a two-line hybrid seed production system in soybean.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"131"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11816801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398033","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":"Full-length transcriptome assembly and RNA-Seq integration of diploid and tetraploid ryegrass to investigate differences in cd uptake and accumulation among ryegrass with different ploidy levels.","authors":"Xunzhe Yang, Xia Wang, Xuan Zhang, Dandan Wu, Yiran Cheng, Yi Wang, Lina Sha, Jian Zeng, Houyang Kang, Xing Fan, Linkai Huang, Yinglong Chen, Yonghong Zhou, Haiqin Zhang","doi":"10.1186/s12864-025-11325-2","DOIUrl":"10.1186/s12864-025-11325-2","url":null,"abstract":"<p><strong>Background: </strong>The accumulation of cadmium (Cd) in ryegrass (Lolium multiflorum Lamk.) as a widely used pasture plant poses a serious risk to food safety. This study aimed to investigate the differences in phenotypes, physiology, and expression of metal transporters between four ryegrass genotypes (diploid/tetraploid and Cd-tolerant/sensitive).</p><p><strong>Results: </strong>The diploid/Cd-sensitive genotypes were found to uptake, accumulate, and translocate more Cd compared to the tetraploid/Cd-tolerant genotypes. Cd with more soluble components facilitated the transfer of Cd from root to shoot in the sensitive genotypes. Tetraploid and Cd-tolerant Chuansi No.1 accumulated less Cd in shoots but higher ratio in root cell wall, making it a promising model for studying the mechanisms of plant resistance to Cd stress. The complex regulatory system and dilution effect contributed to the lower uptake and accumulation of Cd in tetraploid genotypes. Moreover, tetraploid genotypes exhibited higher expression of genes that promoted Cd efflux, which could contribute to their lower Cd accumulation.</p><p><strong>Conclusions: </strong>Overall, this study sheds light on the physiological and transcriptional mechanisms of Cd uptake and accumulation by different polyploids, providing guidance for ryegrass breeding and soil improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"128"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389919","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 analysis of the FKBP gene family and the potential role of GhFKBP 13 in chloroplast biogenesis in upland cotton.","authors":"Jianguang Liu, Zhao Geng, Guiyuan Zhao, Mengzhe Li, Zetong An, Hanshuang Zhang, Yongqiang Wang","doi":"10.1186/s12864-025-11293-7","DOIUrl":"10.1186/s12864-025-11293-7","url":null,"abstract":"<p><strong>Background: </strong>In plants, FK506-binding proteins (FKBPs) have been shown to participate in various biological processes such as photosynthetic system reaction, stress response, and growth and development. However, the roles of FKBPs in cotton are less well known.</p><p><strong>Results: </strong>In this study, we investigated FKBP family genes on a genome-wide scale in four Gossypium species. A total of 147 FKBP genes were identified from these four Gossypium species and placed into three classes based on phylogenetic analysis. Collinearity analysis indicated that whole-genome duplication events and segmental duplication events were the main sources of gene amplification during the evolution of FKBP genes. Conserved motif, expression profiles and cis-acting elements prediction of the GhFKBPs analysis revealed that GhFKBPs were differentially expressed in different tissues and under abiotic stress. qRT-PCR analysis showed that some GhFKBPs were predominantly expressed in leaves. The analysis of cis-acting elements prediction revealed that MYB, MYC and ERE related binding sites in the promoters of GhFKBP genes were the most abundant. Furthermore, the composition and distribution of these cis-acting elements exhibited differences between homologous GhFKBP gene pairs. Silencing of GhFKBP13 in cotton resulted in disruption of chloroplast structure and starch metabolism disorders.</p><p><strong>Conclusions: </strong>Taken together, 147 FKBP family genes in four Gossypium species are comprehensively characterized, and GhFKBP13 play a critical role in chloroplast biogenesis in upland cotton.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"125"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11809014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389938","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":"Gene-based Hardy-Weinberg equilibrium test using genotype count data: application to six types of cancers.","authors":"Jo Nishino, Fuyuki Miya, Mamoru Kato","doi":"10.1186/s12864-025-11321-6","DOIUrl":"10.1186/s12864-025-11321-6","url":null,"abstract":"<p><strong>Background: </strong>An alternative approach to investigate associations between genetic variants and disease is to examine deviations from the Hardy-Weinberg equilibrium (HWE) in genotype frequencies within a case population, instead of case-control association analysis. The HWE analysis requires disease cases and demonstrates a notable ability in mapping recessive variants. Allelic heterogeneity is a common phenomenon in diseases. While gene-based case-control association analysis successfully incorporates this heterogeneity, there are no such approaches for HWE analysis. Therefore, we proposed a gene-based HWE test (gene-HWT) by aggregating single-nucleotide polymorphism (SNP)-level HWE test statistics in a gene to address allelic heterogeneity.</p><p><strong>Results: </strong>This method used only genotype count data and publicly available linkage disequilibrium information and has a very low computational cost. Extensive simulations demonstrated that gene-HWT effectively controls the type I error at a low significance level and outperforms SNP-level HWE test in power when there are multiple causal variants within a gene. Using gene-HWT, we analyzed genotype count data from a genome-wide association study of six cancer types in Japanese individuals and suggest DGKE and ANO3 as potential germline factors in colorectal cancer. Furthermore, FSTL4 was suggested through a combined analysis across the six cancer types, with particularly notable associations observed in colorectal and prostate cancers.</p><p><strong>Conclusions: </strong>These findings indicate the potential of gene-HWT to elucidate the genetic basis of complex diseases, including cancer.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"124"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11809088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389930","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":"Whole-genome relaxed selection and molecular constraints in Triplophysa under adapted Qinghai-Tibetan Plateau.","authors":"Qingyuan Zhao, Fei Xie, Qiuyue He, Lulu Wang, Kenan Guo, Cong Zhang, Yong Wang","doi":"10.1186/s12864-025-11290-w","DOIUrl":"10.1186/s12864-025-11290-w","url":null,"abstract":"<p><p>High-altitude environments are inhospitable, but Triplophysa, the largest taxon among the three major fish groups in the Qinghai-Tibetan Plateau (QTP), is an exception. However, the evolutionary profiling of the common ancestor and its contribution to the adaptation of existing QTP native species is unclear.We researched the comparative genomics of Triplophysa species and found that the genome-wide genes of Triplophysa and its ancestry have the characteristics of rapid evolution.Moreover, the rapid evolution of the ancestral genes was caused by relaxed selection. Natural selection analysis showed that more ancestral relaxed selection genes were under strongly purifying selection and showed higher expression in QTP endemic Triplophysa species.The change in natural selection might be associated with the adaptation to QTP. It should be noted that SPT5 homolog, DSIF elongation factor subunit (supt5h) experienced relaxed selection in common ancestral populations of Triplophysa but under purifying selection in extant species, which might be related to hypoxia adaptation of QTP. In summary, the extant species in different environments were used to infer the evolutionary profile of the common ancestor and to identify candidate genes based on changes in natural selection. Our work might provide new clues for understanding adaptation to extreme environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"123"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381462","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":"Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.).","authors":"Javier Belinchon-Moreno, Aurélie Berard, Aurélie Canaguier, Véronique Chovelon, Corinne Cruaud, Stéfan Engelen, Rafael Feriche-Linares, Isabelle Le-Clainche, William Marande, Vincent Rittener-Ruff, Jacques Lagnel, Damien Hinsinger, Nathalie Boissot, Patricia Faivre-Rampant","doi":"10.1186/s12864-025-11295-5","DOIUrl":"10.1186/s12864-025-11295-5","url":null,"abstract":"<p><strong>Background: </strong>Nanopore adaptive sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Here we designed and validated an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept.</p><p><strong>Results: </strong>Using the same reference to guide read acceptance or rejection with NAS, we successfully and accurately reconstructed the 15 regions in two newly assembled ssp. melo genomes and in a third ssp. agrestis cultivar. We obtained fourfold enrichment regardless of the tested samples, but with some variations according to the enriched regions. The accuracy of our assembly was further confirmed by PCR in the agrestis cultivar. We discussed parameters that could influence the enrichment and accuracy of NAS generated assemblies.</p><p><strong>Conclusions: </strong>Overall, we demonstrated that NAS is a simple and efficient approach for exploring complex genomic regions, such as clusters of Nucleotide-binding site leucine-rich repeat (NLR) resistance genes. These regions are characterized by containing a high number of copy number variations, presence-absence polymorphisms and repetitive elements. These features make accurate assembly challenging but are crucial to study due to their central role in plant immunity and disease resistance. This approach facilitates resistance gene characterization in a large number of individuals, as required when breeding new cultivars suitable for the agroecological transition.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"126"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390000","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":"Effects of a transient lack of dietary mineral phosphorus on renal gene expression and plasma metabolites in two high-yielding laying hen strains.","authors":"Hiba Qasir, Henry Reyer, Michael Oster, Siriluck Ponsuksili, Nares Trakooljul, Vera Sommerfeld, Markus Rodehutscord, Klaus Wimmers","doi":"10.1186/s12864-025-11294-6","DOIUrl":"10.1186/s12864-025-11294-6","url":null,"abstract":"<p><strong>Background: </strong>There is an emerging body of evidence that current poultry feed is formulated in excess for phosphorus (P), which results in unnecessarily high P excretions. Sustainable concepts for agricultural P flows should trigger animal-intrinsic mechanisms for efficient P utilization. In the current study, Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) laying hens were fed either a high P diet (P+) with 1 g/kg mineral P supplement or a low P diet (P-) with 0 g/kg mineral P supplement for a period of 4 weeks prior to sampling. Before and after onset of laying, i.e., at 19 and 24 weeks of life, kidney and plasma samples were collected to investigate the endogenous P utilization in response to restricted dietary P, laying hen strain, and sexual maturation.</p><p><strong>Results: </strong>Plasma analyses of minerals and metabolites confirmed the response to a low P diet, which was characterized by a significant reduction in plasma P levels at week 19 in both strains. The plasma calcium (Ca) levels were tightly regulated throughout the entire experimental period. Notably, there was a numerical trend of increased plasma calcitriol levels in P- fed birds of both strains compared to the P + group, which might have mediated a substantial role regarding the adaptive responses to low P supply. At week 19, RNA sequencing of kidney identified 1,114 and 556 differentially expressed genes (DEGs) unique to the LB and LSL strains, respectively. The number of DEGs declined with increasing maturity of the hens culminating in 90 and 146 DEGs for LB and LSL strains at week 24. Analyses revealed an enrichment of pathways related to energy metabolism and cell cycle, particularly at week 19 in both strains. The diet-specific expression of target genes involved in P homeostasis highlighted transcripts related to active (SLC34A1, SLC20A2) and passive mineral transport (CLDN14, CLDN16), Ca utilization (STC1, CALB1), and acid-base balance (CA2, SLC4A1).</p><p><strong>Conclusions: </strong>Results suggest that both laying hen strains adapted to the lack of mineral P supplements and achieved a physiological Ca: P-ratio in body compartments through endogenous regulation as evidenced via the endocrine profile.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"129"},"PeriodicalIF":3.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389913","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}