International Journal of Genomics最新文献

{"title":"QTL Mapping of Traits Associated with Dual Resistance to the African Stem Borer (<i>Busseola fusca</i>) and Spotted Stem Borer (<i>Chilo partellus</i>) in Sorghum (<i>Sorghum bicolor</i>).","authors":"Phyllis W Muturi, Mary Mgonja, Patrick Rubaihayo, James K Mwololo","doi":"10.1155/2021/7016712","DOIUrl":"10.1155/2021/7016712","url":null,"abstract":"<p><p>Sorghum (<i>Sorghum bicolor</i> (L.) Moench) is an important food crop in semi-arid tropics. The crop grain yield ranges from 0.5 t/ha to 0.8 t/ha compared to potential yields of 10 t/ha. The African stem borer <i>Busseola fusca</i> Fuller (Noctuidae) and the spotted stem borer <i>Chilo partellus</i> Swinhoe (Crambidae), are among the most economically important insect pests of sorghum. The two borers can cause 15% - 80% grain yield loss in sorghum. Mapping of QTLs associated with resistance traits to the two stem borers is important towards marker-assisted breeding. The objective of this study was to map QTLs associated with resistance traits to <i>B. fusca</i> and <i>C. partellus</i> in sorghum. 243 F_9:10 sorghum RILs derived from ICSV 745 (S) and PB 15520-1 (R) were selected for the study with 4,955 SNP markers. The RILs were evaluated in three sites. Data was collected on leaf feeding, deadheart, exit holes, stem tunnels, leaf toughness, seedling vigour, bloom waxiness, and leaf glossiness. ANOVA for all the traits was done using Genstat statistical software. Insect damage traits and morphological traits were correlated using Pearson's correlation coefficients. Genetic mapping was done using JoinMap 4 software, while QTL analysis was done using PLABQTL software. A likelihood odds ratio (LOD) score of 3.0 was used to declare linkage. Joint analyses across borer species and sites revealed 4 QTLs controlling deadheart formation; 6 controlling leaf feeding damage; 5 controlling exit holes and stem tunneling damages; 2 controlling bloom waxiness, leaf glossiness, and seedling vigour; 4 conditioning trichome density; and 6 conditioning leaf toughness. Joint analyses for <i>B. fusca</i> and <i>C. partellus</i> further revealed that marker <i>CS132-2</i> colocalised for leaf toughness and stem tunneling traits on QTLs 1 and 2, respectively; thus, the two traits can be improved using the same linked marker. This study recommended further studies to identify gene(s) underlying the mapped QTLs.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"7016712"},"PeriodicalIF":2.9,"publicationDate":"2021-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7834829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25324976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LAPTM5 Plays a Key Role in the Diagnosis and Prognosis of Testicular Germ Cell Tumors.","authors":"Xiunan Li,&nbsp;Yu Su,&nbsp;Jiayao Zhang,&nbsp;Ye Zhu,&nbsp;Yingkun Xu,&nbsp;Guangzhen Wu","doi":"10.1155/2021/8816456","DOIUrl":"https://doi.org/10.1155/2021/8816456","url":null,"abstract":"<p><strong>Objective: </strong>Testicular germ cell tumors (TGCT) are a serious malignant tumor with low early diagnosis rates and high mortality.</p><p><strong>Methods: </strong>To investigate novel biomarkers to predict the diagnosis and prognosis of this cancer, bioinformatics analysis was used as an accurate, efficient, and economical method.</p><p><strong>Results: </strong>Our study detected 39 upregulated and 589 downregulated differentially expressed genes (DEGs) using the GEO and TCGA databases. To identify the function of DEGs, GO functional analysis, three pathway analysis (KEGG, REACTOME, and PANTHER), and protein-protein interaction network were performed using the KOBAS website, as well as the String database. After a series of analyses in GEPIA and TIMER, including differential expression, we found one candidate gene related to the prognosis and diagnosis of TGCT. LAPTM5 was also associated with CD8+ T cell and PDCD1 expression, which suggests that it may affect immune infiltration.</p><p><strong>Conclusions: </strong>LAPTM5 was identified as a hub gene, which could be used as a potential biomarker for TGCT diagnosis and prognosis.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"8816456"},"PeriodicalIF":2.9,"publicationDate":"2021-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25316331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Bioinformatic Analysis Identifies Networks and Promising Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma.","authors":"Yun Ji,&nbsp;Yue Yin,&nbsp;Weizhen Zhang","doi":"10.1155/2020/2061024","DOIUrl":"https://doi.org/10.1155/2020/2061024","url":null,"abstract":"<p><p>Chronic infection with hepatitis B virus (HBV) has long been recognized as a dominant hazard factor for hepatocellular carcinoma (HCC) and accounts for at least half of HCC instances globally. However, the underlying molecular mechanism of HBV-linked HCC has not been completely elucidated. Here, three microarray datasets, totally containing 170 tumoral samples and 181 adjacent normal tissues from the liver of patients suffering from HBV-related HCC assembled from the Gene Expression Omnibus (GEO) database, were subjected to integrated analysis of differentially expressed genes (DEGs). Subsequently, the analysis of function and pathway enrichment as well as the protein-protein interaction network (PPI) was performed. The ten hub genes screened out from the PPI network were further subjected to expression profile and survival analysis. Overall, 329 DEGs (67 upregulated and 262 downregulated) were identified. Ten DEGs with the highest degree of connectivity included cyclin-dependent kinase 1 (CDK1), cyclin B1 (CCNB1), cyclin B2 (CCNB2), PDZ-binding kinase (PBK), abnormal spindle microtubule assembly (ASPM), nuclear division cycle 80 (NDC80), aurora kinase A (AURKA), targeting protein for xenopus kinesin-like protein 2 (TPX2), kinesin family member 2C (KIF2C), and centromere protein F (CENPF). Kaplan-Meier analysis unveiled that overexpression levels of KIF2C and TPX2 were relevant to both the poor overall survival and relapse-free survival. In summary, the hub genes validated in the present study may provide promising targets for the diagnosis, prognosis, and therapy of HBV-associated HCC. Additionally, our work uncovers various crucial biological components (e.g., extracellular exosome) and signaling pathways that participate in the progression of HCC induced by HBV, serving comprehensive knowledge of the mechanisms regarding HBV-related HCC.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2020 ","pages":"2061024"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2020/2061024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10299718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Metabolome and Transcriptome Analysis Uncovers the Role of Anthocyanin Metabolism in Michelia maudiae","authors":"Xiaoan Lang, Na Li, Lingfei Li, Shouzhou Zhang","doi":"10.1155/2019/4393905","DOIUrl":"https://doi.org/10.1155/2019/4393905","url":null,"abstract":"Michelia maudiae Dunn is one of the important ornamental plants in the Magnoliaceae family, and the color of its flowers usually appears naturally pure white. The discovery of a rubellis flower named M. maudiae Dunn var. rubicunda provides an opportunity to reveal the metabolism of the flavonoids and anthocyanins of this “early angiosperm” plant. Combined metabolome and transcriptome analyses were applied using white and rubellis mutant tepals. Seven stages have been divided for flower development, and forty-eight differentially altered metabolites were identified between white and rubellis tepals at a later stage. The major anthocyanins including peonidin O-hexoside, cyanidin O-syringic acid, cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and pelargonidin 3-O-glucoside were upregulated over 157-fold in the mutant. Conversely, the highly significant accumulation of the colorless procyanidin or the slightly yellow epicatechin and catechin was found in white flowers. Putative homologues of color-related genes involved in the phenylpropanoid and flavonoid biosynthesis pathway were identified in the transcriptome. The increasing expression of dihydroflavonol 4-reductase (DFR) might play an important role in the occurrence of rubellis pigments, while the overexpression of anthocyanidin reductase (ANR) in white flowers may promote the biosynthesis of proanthocyanidins. Additionally, several coloration-related repressor R2R3-MYB transcription factors showed different expression levels in the tepals of the rubellis mutant. This study provides a comprehensive analysis relating color compounds to gene expression profiles of the Magnoliids plant M. maudiae. The newly generated information will provide a profound effect on horticultural applications of Magnoliaceae.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/4393905","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45740241","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":"Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties","authors":"Rabiatul-Adawiah Zainal-Abidin, N. Abu-Bakar, Y. Sew, Sanimah Simoh, Z. Mohamed-Hussein","doi":"10.1155/2019/4168045","DOIUrl":"https://doi.org/10.1155/2019/4168045","url":null,"abstract":"Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/4168045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49064498","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":"Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop","authors":"F. Al-Qurainy, Aref Alshameri, A. Gaafar, Salim Khan, M. Nadeem, A. Alameri, M. Tarroum, M. Ashraf","doi":"10.1155/2019/7295859","DOIUrl":"https://doi.org/10.1155/2019/7295859","url":null,"abstract":"The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2 × 100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/7295859","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44182747","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":"Florfenicol Resistance in Enterobacteriaceae and Whole-Genome Sequence Analysis of Florfenicol-Resistant Leclercia adecarboxylata Strain R25","authors":"Yuanyuan Ying, Fei Wu, Chongyang Wu, Yi Jiang, Min Yin, Wangxiao Zhou, Xinyi Zhu, Cong Cheng, Licheng Zhu, Kewei Li, Junwan Lu, Teng Xu, Qiyu Bao","doi":"10.1155/2019/9828504","DOIUrl":"https://doi.org/10.1155/2019/9828504","url":null,"abstract":"Due to inappropriate use, florfenicol resistance is becoming increasingly serious among animal respiratory tract and gut bacteria. To detect the florfenicol resistance mechanism among Enterobacteriaceae bacteria, 292 isolates from animal feces were examined. The agar dilution method was conducted to determine the minimum inhibitory concentration (MIC) for florfenicol, and polymerase chain reaction (PCR) was performed to detect florfenicol resistance genes. To further explore the molecular mechanism of florfenicol resistance, the whole-genome Leclercia adecarboxylata R25 was sequenced. Of the strains tested, 61.6% (180/292) were resistant to florfenicol, 64.4% (188/292) were positive for floR, and 1.0% (3/292) for cfr. The whole-genome sequence analysis of L. adecarboxylata R25 revealed that the floR gene is carried by a transposon and located on a plasmid (pLA-64). Seven other resistance genes are also encoded on pLA-64, all of which were found to be related to mobile genetic elements. The sequences sharing the greatest similarities to pLA-64 are the plasmids p02085-tetA of Citrobacter freundii and p234 and p388, both from Enterobacter cloacae. The resistance gene-related mobile genetic elements also share homologous sequences from different species or genera of bacteria. These findings indicate that floR mainly contributes to the high rate of florfenicol resistance among Enterobacteriaceae. The resistance gene-related mobile genetic elements encoded by pLA-64 may be transferred among bacteria of different species or genera, resulting in resistance dissemination.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/9828504","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42526936","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":"Computational Identification of Metabolic Pathways of <i>Plasmodium falciparum</i> using the <i>k</i>-Shortest Path Algorithm.","authors":"Jelili Oyelade, Itunuoluwa Isewon, Olufemi Aromolaran, Efosa Uwoghiren, Titilope Dokunmu, Solomon Rotimi, Oluwadurotimi Aworunse, Olawole Obembe, Ezekiel Adebiyi","doi":"10.1155/2019/1750291","DOIUrl":"10.1155/2019/1750291","url":null,"abstract":"<p><p><i>Plasmodium falciparum</i>, a malaria pathogen, has shown substantial resistance to treatment coupled with poor response to some vaccines thereby requiring urgent, holistic, and broad approach to prevent this endemic disease. Understanding the biology of the malaria parasite has been identified as a vital approach to overcome the threat of malaria. This study is aimed at identifying essential proteins unique to malaria parasites using a reconstructed <i>iPfa</i> genome-scale metabolic model (GEM) of the 3D7 strain of <i>Plasmodium falciparum</i> by filling gaps in the model with nineteen (19) metabolites and twenty-three (23) reactions obtained from the MetaCyc database. Twenty (20) currency metabolites were removed from the network because they have been identified to produce shortcuts that are biologically infeasible. The resulting modified <i>iPfa</i> GEM was a model using the <i>k</i>-shortest path algorithm to identify possible alternative metabolic pathways in glycolysis and pentose phosphate pathways of <i>Plasmodium falciparum</i>. Heuristic function was introduced for the optimal performance of the algorithm. To validate the prediction, the essentiality of the reactions in the reconstructed network was evaluated using betweenness centrality measure, which was applied to every reaction within the pathways considered in this study. Thirty-two (32) essential reactions were predicted among which our method validated fourteen (14) enzymes already predicted in the literature. The enzymatic proteins that catalyze these essential reactions were checked for homology with the host genome, and two (2) showed insignificant similarity, making them possible drug targets. In conclusion, the application of the intelligent search technique to the metabolic network of <i>P. falciparum</i> predicts potential biologically relevant alternative pathways using graph theory-based approach.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2019 1","pages":"1750291"},"PeriodicalIF":2.9,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/1750291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64741895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Analysis of TIFY Transcription Factors and Their Expression Profiles under Jasmonic Acid and Abiotic Stresses in Watermelon","authors":"Youxin Yang, G. Ahammed, Chunpeng Wan, Haoju Liu, Rongrong Chen, Yong Zhou","doi":"10.1155/2019/6813086","DOIUrl":"https://doi.org/10.1155/2019/6813086","url":null,"abstract":"The TIFY gene family is plant-specific and encodes proteins involved in the regulation of multiple biological processes. Here, we identified 15 TIFY genes in the watermelon genome, which were divided into four subfamilies (eight JAZs, four ZMLs, two TIFYs, and one PPD) in the phylogenetic tree. The ClTIFY genes were unevenly located on eight chromosomes, and three segmental duplication events and one tandem duplication event were identified, suggesting that gene duplication plays a vital role in the expansion of the TIFY gene family in watermelon. Further analysis of the protein architectures, conserved domains, and gene structures provided additional clues for understanding the putative functions of the TIFY family members. Analysis of qRT-PCR and RNA-seq data revealed that the detected ClTIFY genes had preferential expression in specific tissues. qRT-PCR analysis revealed that nine selected TIFY genes were responsive to jasmonic acid (JA) and abiotic stresses including salt and drought. JA activated eight genes and suppressed one gene, among which ClJAZ1 and ClJAZ7 were the most significantly induced. Salt and drought stress activated nearly all the detected genes to different degrees. These results lay a foundation for further functional characterization of TIFY family genes in Citrullus lanatus.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"351 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/6813086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41258145","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":"Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses","authors":"M. Singer-Berk, K. E. Knickelbein, Z. Lounsberry, Margo Crausaz, S. Vig, Nikhil A. Joshi, M. Britton, M. Settles, C. Reilly, E. Bentley, C. Nunnery, A. Dwyer, M. Lassaline, R. Bellone","doi":"10.1155/2019/3610965","DOIUrl":"https://doi.org/10.1155/2019/3610965","url":null,"abstract":"Squamous cell carcinoma (SCC) is the most common periocular cancer in horses and the second most common tumor of the horse overall. A missense mutation in damage-specific DNA-binding protein 2 (DDB2, c.1012 C>T, p.Thr338Met) was previously found to be strongly associated with ocular SCC in Haflinger and Belgian horses, explaining 76% of cases across both breeds. To determine if this same variant in DDB2 contributes to risk for ocular SCC in the Arabian, Appaloosa, and Percheron breeds and to determine if the variant contributes to risk for oral or urogenital SCC, histologically confirmed SCC cases were genotyped for the DDB2 variant and associations were investigated. Horses with urogenital SCC that were heterozygous for the DDB2 risk allele were identified in the Appaloosa breed, but a significant association between the DDB2 variant and SCC occurring at any location in this breed was not detected. The risk allele was not identified in Arabians, and no Percherons were homozygous for the risk allele. High-throughput sequencing data from six Haflingers were analyzed to ascertain if any other variant from the previously associated 483 kb locus on ECA12 was more concordant with the SCC phenotype than the DDB2 variant. Sixty polymorphisms were prioritized for evaluation, and no other variant from this locus explained the genetic risk better than the DDB2 allele (P = 3.39 × 10−17, n = 118). These data provide further support of the DDB2 variant contributing to risk for ocular SCC, specifically in the Haflinger and Belgian breeds.","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2019-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/3610965","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44637793","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}