Genes & genomics最新文献

{"title":"Genetic diversity and structure of Persicaria amphibia (Polygonaceae) in South Korea using genotyping by sequencing.","authors":"KyoungSu Choi, Yong Hwang, Jeong-Ki Hong, So Young Park","doi":"10.1007/s13258-024-01571-1","DOIUrl":"https://doi.org/10.1007/s13258-024-01571-1","url":null,"abstract":"<p><strong>Background: </strong>Persicaria amphibia, a member of the Polygonaceae family, exists both aquatic and terrestrial forms. It is native to North America, Asia, Europe, and some parts of Africa.</p><p><strong>Objective: </strong>This study aimed to determine the genetic diversity within and among populations of P. amphibia and the distribution characteristics of each population to investigate insights into the genetic structure and conservation of P. amphibia.</p><p><strong>Methods: </strong>In this study, the genetic diversity and structure of 84 P. amphibia individuals from 7 populations in South Korea were analyzed using genotyping-by-sequencing (GBS). We used 2,469 single nucleotide polymorphisms (SNPs) to analyze genetic diversity, principal components, structure, and phylogeny.</p><p><strong>Results: </strong>Our results showed a mean observed heterozygosity and mean expected heterozygosity of 0.34409 and 0.34082, respectively. Genetic diversity analysis indicated that the variation among populations (60.08%) was greater than that within populations (39.92%). Fixation index values, principal components analysis, structure, and phylogeny analyses showed that the population in Gyodongdo, Ganghwa Island was highly different.</p><p><strong>Conclusion: </strong>These results provide important insights for better understand the population history and genetic structure of P. amphibia.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression profiling of the Wnt gene family in three abalone species.","authors":"Qian Zhang, Yangtao Fu, Yanyan Zhang, Hourong Liu","doi":"10.1007/s13258-024-01579-7","DOIUrl":"https://doi.org/10.1007/s13258-024-01579-7","url":null,"abstract":"<p><strong>Background: </strong>The Wnt gene family plays pivotal roles in a variety of biological processes including cell proliferation and differentiation, apoptosis, and embryonic development. Identifying the Wnt signaling pathway in abalone could provide a basis for elucidating growth and development mechanisms and improving quality.</p><p><strong>Objective: </strong>To identify the number, protein physicochemical properties, gene structure, phylogenetic analysis, and expression profiles of the Wnt gene family in abalone.</p><p><strong>Methods: </strong>A comprehensive genome-wide analysis was performed to identify the Wnt gene family in the genomes of three abalone species (Haliotis discus hannai, H. rubra, and H. rufescens).</p><p><strong>Results: </strong>Ten single-copy Wnt genes were identified in each abalone species, suggesting that the number of Wnt genes was relatively conserved in Haliotis. Eight Wnt gene subfamilies, including Wnt1, Wnt4, Wnt5, Wnt6, Wnt7, Wnt10, Wnt16, and WntA, are present in all three species. Each abalone species contains two species-specific subfamilies (Wnt9 and Wnt11 in H. discus hannai, Wnt2 and Wnt11 in H. rubra, and Wnt2 and Wnt9 in H. rufescens), reflecting polymorphisms of the Wnt genes in Haliotis. Interestingly, gastropods are characterised by the loss of Wnt8, suggesting a potential evolutionary specificity in gastropods. As expected, Wnt3 is absent in all protostomes, including the abalone. In addition, spatio-temporal expression profiling revealed differential expression levels of the Wnt genes at different developmental stages and in different tissues of H. discus hannai. HdWnt5 and HdWntA might participate in several processes during larval development stages, including germ layer formation and body axis elongation. HdWnt5 may be involved in eye and tentacle development. HdWnt10 may be related to muscle development, and HdWnt6 may be involved in shell formation in abalone.</p><p><strong>Conclusion: </strong>To our knowledge, the results of this study, which is the first genome-wide investigation of the Wnt gene family in abalone, lay the groundwork for future research on the evolution and function of the Wnt gene family in Gastropoda.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated analysis of single-cell RNA-seq and bulk RNA-seq revealed key genes for bone metastasis and chemoresistance in prostate cancer.","authors":"Hongai Bai, Zhenyue Li, Yueyue Weng, Facai Cui, Wenpu Chen","doi":"10.1007/s13258-024-01575-x","DOIUrl":"https://doi.org/10.1007/s13258-024-01575-x","url":null,"abstract":"<p><strong>Background: </strong>Prostate cancer (PCa) is a serious malignancy. The main causes of PCa aggravation and death are unexplained resistance to chemotherapy and bone metastases.</p><p><strong>Objective: </strong>This study aimed to investigate the molecular mechanisms associated with the dynamic processes of progression, bone metastasis, and chemoresistance in PCa.</p><p><strong>Methods: </strong>Through comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data, Gene Expression Omnibus (GEO) tumor progression and metastasis-related genes were identified. These genes were subjected to lasso regression modeling using the Cancer Genome Atlas (TCGA) database. Tartrate-resistant acid phosphatase (TRAP) staining and real-time quantitative PCR (RT-qPCR) were used to evaluate osteoclast differentiation. CellMiner was used to confirm the effect of LDHA on chemoresistance. Finally, the relationship between LDHA and chemoresistance was verified using doxorubicin-resistant PCa cell lines.</p><p><strong>Results: </strong>7928 genes were identified as genes related to tumor progression and metastasis. Of these, 7 genes were found to be associated with PCa prognosis. The scRNA-seq and TCGA data showed that the expression of LDHA was higher in tumors and associated with poor prognosis of PCa. In addition, upregulation of LDHA in PCa cells induces osteoclast differentiation. Additionally, high LDHA expression was associated with resistance to Epirubicin, Elliptinium acetate, and doxorubicin. Cellular experiments demonstrated that LDHA knockdown inhibited doxorubicin resistance in PCa cells.</p><p><strong>Conclusions: </strong>LDHA may play a potential contributory role in PCa initiation and development, bone metastasis, and chemoresistance. LDHA is a key target for the treatment of PCa.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GVAF: generalized, flexible filtering software for annotated variant files.","authors":"Sora Kim, Sungwon Jung","doi":"10.1007/s13258-024-01580-0","DOIUrl":"https://doi.org/10.1007/s13258-024-01580-0","url":null,"abstract":"<p><strong>Background: </strong>In the rapidly advancing field of genomics, many tools have been developed to interpret genetic variants using next-generation sequencing (NGS) data. However, these tools often produce annotated variant files in different formats, which require specific software or programming skills to filter and analyze.</p><p><strong>Objective: </strong>To provide a filtering tool that can be used with diverse variant annotation tools without requiring specific software or programming skills.</p><p><strong>Methods: </strong>We developed Germline Variant Annotation and Filtering (GVAF), a command-line software tool that can handle annotated variant files in any table-shaped format. GVAF offers powerful filtering operations without the need for additional software or programming expertise.</p><p><strong>Results: </strong>Built on the Java framework and bash scripts, it provides extensive features, including flexible filtering rules, recognition of genotype-related fields from variant call format (VCF) files, and customizable result generation. GVAF also integrates easily into existing data analysis pipelines. Compared to other tools, GVAF offers a broader range of functionalities, making it more flexible and intuitive for managing annotated variant files.</p><p><strong>Conclusion: </strong>This GVAF software and online manual is publicly available at https://www.sysbiolab.org/gvaf for academic users and is designed to streamline the variant interpretation process, aiding researchers in producing meaningful results.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Weighted gene co-expression network analysis and identification of ginsenoside biosynthesis candidate genes for ginseng adventitious roots under MeJA treatment.","authors":"Xiangzhu Li, Yongjun Zheng, Mingming Liu, Kangyu Wang, Hong Chen","doi":"10.1007/s13258-024-01577-9","DOIUrl":"https://doi.org/10.1007/s13258-024-01577-9","url":null,"abstract":"<p><strong>Background: </strong>Ginseng (Panax ginseng) is an herb with a long history and a wide range of applications. Ginsenoside is one of the most representative and active ginseng compounds, with various pharmacological effects. Therefore, the development of bioreactors using methyl jasmonate (MeJA) as an inducer for targeted ginsenoside production is of great commercial value. Combined with transcriptomic research tools, screenings to obtain candidate genes involved in ginsenoside biosynthesis are crucial for future discoveries about the molecular mechanism of MeJA-regulated ginsenoside biosynthesis.</p><p><strong>Objective and methods: </strong>In our study, the ginsenoside content of ginseng adventitious roots treated with MeJA at different times was analyzed. Transcriptome analysis was performed to investigate the effects of MeJA on changes in ginsenoside content in ginseng adventitious roots.</p><p><strong>Results: </strong>The MeJA could significantly increase changes in the content of pro-ginsenodiol ginsenosides as well as pro-triol ginsenosides Rg3, Re, and Rf in ginseng adventitious roots. Differential gene expression analysis showed that a total of 14,009 differentially expressed genes were obtained from the screening of the present study. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that differentially expressed genes were mainly enriched under GO terms in response to stimuli, metabolic processes, and the regulation of biological processes, with significant annotation to the metabolic terms of terpenoids and polyketides. Two expression modules of genes highly related to ginsenoside biosynthesis were obtained via WGCNA.</p><p><strong>Conclusions: </strong>Our study provides a reference system for the targeted ginsenoside production using MeJA as an inducer, and also provides genetic and gene resources for subsequently validating genes related to the regulation of ginsenoside biosynthesis using weighted gene co-expression network analysis (WGCNA).</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Units containing telomeric repeats are prevalent in subtelomeric regions of a Mesorhabditis isolate collected from the Republic of Korea.","authors":"Seoyeon Kim, Jun Kim","doi":"10.1007/s13258-024-01576-w","DOIUrl":"https://doi.org/10.1007/s13258-024-01576-w","url":null,"abstract":"<p><strong>Background: </strong>Mesorhabditis is known for its somatic genome being only a small portion of the germline genome due to programmed DNA elimination. This phenotype may be associated with the maintenance of telomeres at the ends of fragmented somatic chromosomes.</p><p><strong>Objective: </strong>To comprehensively investigate the telomeric regions of Mesorhabditis nematodes at the sequence level, we endeavored to collect a Mesorhabditis nematode in the Republic of Korea and acquire its highly contiguous genome sequences.</p><p><strong>Methods: </strong>We isolated a Mesorhabditis nematode and assembled its 108-Mb draft genome using both 6.3 Gb (53 ×) of short-read and 3.0 Gb (25 × , N50 = 5.7 kb) of nanopore-based long-read sequencing data. Our genome assembly exhibits comparable quality to the public genome of Mesorhabditis belari in terms of contiguity and evolutionary conserved genes.</p><p><strong>Results: </strong>Unexpectedly, our Mesorhabditis genome has many more interstitial telomeric sequences (ITSs), specifically subtelomeric ones, compared to the genomes of Caenorhabditis elegans and M. belari. Moreover, several subtelomeric sequences containing ITSs had 4-26 homologous sequences, implying they are highly repetitive. Based on this highly repetitive nature, we hypothesize that subtelomeric ITSs might have accumulated through the action of transposable elements containing ITSs.</p><p><strong>Conclusions: </strong>It still remains elusive whether these ITS-containing units are associated with programmed DNA elimination, but they may facilitate new telomere formation after DNA elimination. Our genomic resources for Mesorhabditis can aid in understanding how its distinct phenotypes have evolved.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical report and genetic analysis of a Chinese family with retinitis pigmentosa 79 caused by a novel loss-of-function HK1 variant.","authors":"Xin Luo, Lu Wang, Daxi Xue","doi":"10.1007/s13258-024-01574-y","DOIUrl":"https://doi.org/10.1007/s13258-024-01574-y","url":null,"abstract":"<p><strong>Background: </strong>Retinitis pigmentosa (RP) is a genetically heterogeneous disease. RP 79 has been associated with heterozygous variants of hexokinase 1 (HK1). Only two missense HK1 variants have been reported in 11 families.</p><p><strong>Objective: </strong>To discover the molecular pathogenic mechanism of RP and validate the biological harm of HK1 through in vitro experiments.</p><p><strong>Methods: </strong>We conducted a genetic analysis of a 3-year-old female patient with RP and her family. We also evaluated the ocular phenotypes caused by HK1 (the identified variant). Peripheral blood samples were collected from the patient, her parents, and her brother, and trio whole-exome sequencing was performed. A protein structure analysis was performed to assess the functional impact of the variant, and a mutant plasmid was constructed for the quantitative polymerase chain reaction (qPCR) and western blot (WB) analysis of the effects of the variant on transcription and protein translation.</p><p><strong>Results: </strong>The patient harbored the NM_000188.3: c.613del (p.Ala205Leufs*3) variant, which is a heterozygous variant of HK1. Sanger sequencing confirmed the presence of this variant in the patient; however, the patient's parents and brother had the wild-type variant. The protein structure analysis indicated that the variant resulted in a truncated protein caused by premature termination of amino acid coding. The qPCR results indicated that the variant may not have affected the transcription process. However, the WB analysis demonstrated that the mutant HK-1 protein was not expressed and that the wild-type group exhibited normal expression.</p><p><strong>Conclusions: </strong>Our patient had a loss-of-function (LoF) variant of HK1, which may be the genetic cause of typical features of RP that are observed at an early age. These findings expand the spectrum of HK1 variants and phenotypes and suggest that LoF variants of HK1 may represent a specific pathogenic mechanism of RP.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into ACO genes across Rosaceae: evolution, expression, and regulatory networks in fruit development.","authors":"Yuxin Zhang, Yirong Zhang, Ze Yu, Hanyu Wang, Boya Ping, Yunxiao Liu, Jiakai Liang, Fengwang Ma, Yangjun Zou, Tao Zhao","doi":"10.1007/s13258-024-01551-5","DOIUrl":"10.1007/s13258-024-01551-5","url":null,"abstract":"<p><strong>Background: </strong>ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development.</p><p><strong>Objective: </strong>This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development.</p><p><strong>Methods: </strong>we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits.</p><p><strong>Results: </strong>Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits.</p><p><strong>Conclusion: </strong>The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance.","authors":"Maoni Chao, Qiufang Zhang, Ling Huang, Li Wang, Jie Dong, Shibo Kou, Weifeng Song, Tiegu Wang","doi":"10.1007/s13258-024-01558-y","DOIUrl":"10.1007/s13258-024-01558-y","url":null,"abstract":"<p><strong>Background: </strong>ADP-glucose pyrophosphorylase (AGPase) is the key rate-limiting enzyme in starch biosynthesis pathway, and has been identified as a potential target for manipulation strategies aimed at improving crop yield and quality.</p><p><strong>Objective: </strong>To identify the AGPase gene family members in soybean, and explore the potential implications of GmAGPS2 in drought stress tolerance.</p><p><strong>Methods: </strong>The genome-wide identification and sequence analysis of soybean AGPase gene family was carried out by bioinformatics methods. The GmAGP gene expression was analyzed using transcriptome data and quantitative real-time PCR (qRT-PCR). Furthermore, transgenic yeast strains overexpressing GmAGPS2 were generated, and their growth was observed under drought stress.</p><p><strong>Results: </strong>In this study, we searched for AGPase genes (GmAGP) in the soybean genome and identified a total of 14 GmAGP genes. The GmAGP proteins had a unique conserved NTP_transferase domain and were mainly located in the chloroplast and cytosol. Evolutionarily, the GmAGP proteins can be clustered into two distinct subgroups; within the same subgroup, they displayed a similar distribution pattern of conserved motifs. The GmAGP genes exhibited an uneven distribution on 10 chromosomes, and segmental duplication contributed to AGPase gene family expansion in soybean. The GmAGP genes presented different tissue expression pattern, in which GmAGPL6, GmAGPL9, and GmAGPL10 mainly exhibited tissue-specific expression pattern. The promoter of GmAGP genes had multiple cis-acting elements related to phytohormones and stress responses, and 8 GmAGP genes contained drought-responsive cis-acting elements. qRT‒PCR analysis demonstrated a significant upregulation expression of GmAGPL6, GmAGPL10, and GmAGPS2 in response to drought stress. Further functional analysis indicated that GmAGPS2 gene could improve yeast growth under drought stress conditions and enhance the drought tolerance of yeast.</p><p><strong>Conclusion: </strong>These results will contribute to further elucidation of the function of GmAGP genes, and offer important candidate genes for the genetic improvement of starch and yield-related traits and the breeding of high drought stress tolerance varieties in soybean.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds.","authors":"Trifan Budi, Anh Huynh Luu, Worapong Singchat, Wongsathit Wongloet, Juniman Rey, Nichakorn Kumnan, Piangjai Chalermwong, Chien Phuoc Tran Nguyen, Thitipong Panthum, Nivit Tanglertpaibul, Thanyapat Thong, Hina Ali, Kanithaporn Vangnai, Aingorn Chaiyes, Chotika Yokthongwattana, Chomdao Sinthuvanich, Kyudong Han, Agostinho Antunes, Narongrit Muangmai, Prateep Duengkae, Kornsorn Srikulnath","doi":"10.1007/s13258-024-01561-3","DOIUrl":"10.1007/s13258-024-01561-3","url":null,"abstract":"<p><strong>Background: </strong>Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear.</p><p><strong>Objective: </strong>To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption.</p><p><strong>Methods: </strong>Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from \"The Siam Chicken Bioresource Project\" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals.</p><p><strong>Result: </strong>The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks.</p><p><strong>Conclusion: </strong>Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}