Jayakumar Sivalingam, R.P. Athe, T. Bhattacharya, R. Chatterjee, U. R. Kumar, S. P. Yadav, K. R. Ravindra, M. Balakrishnan, M.V. Chaudhari
{"title":"Complete Chromosome Wise Identification of SSRs in the Two Published Chicken Genome Assemblies","authors":"Jayakumar Sivalingam, R.P. Athe, T. Bhattacharya, R. Chatterjee, U. R. Kumar, S. P. Yadav, K. R. Ravindra, M. Balakrishnan, M.V. Chaudhari","doi":"10.18805/ijar.b-5254","DOIUrl":null,"url":null,"abstract":"Background: Microsatellites are short repeat motifs consisting 1-6 base pair (bp) and have a high degree of length polymorphism and are useful to study the genetic diversity. In Chicken, no micro satellite markers were demarcated to different chromosomes, viz., 29, 34, 35, 36, 37, 38 and 39 in the genome. In the present study, we carried out chromosome-wise identification of SSRs that will be of great use in diversity and gene mapping studies in chicken. Methods: The perl script of MISA tool was used to screen the polymorphic microsatellites with different thresholds level. Result: We identified a total of 397877 SSRs from the latest chicken genome assembly (GRCg7b), of which mononucleotides, dinucleotides, trinucleotides, tetranucleotides, pentanucleotides and hexanucleotides composed of 307453 (77.27%), 40991 (10.30%), 23059 (5.79%), 16723 (4.20%), 8127 (2.04%) and 1524 (0.38%), respectively.\n","PeriodicalId":507727,"journal":{"name":"Indian Journal of Animal Research","volume":"12 4","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Indian Journal of Animal Research","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.18805/ijar.b-5254","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Background: Microsatellites are short repeat motifs consisting 1-6 base pair (bp) and have a high degree of length polymorphism and are useful to study the genetic diversity. In Chicken, no micro satellite markers were demarcated to different chromosomes, viz., 29, 34, 35, 36, 37, 38 and 39 in the genome. In the present study, we carried out chromosome-wise identification of SSRs that will be of great use in diversity and gene mapping studies in chicken. Methods: The perl script of MISA tool was used to screen the polymorphic microsatellites with different thresholds level. Result: We identified a total of 397877 SSRs from the latest chicken genome assembly (GRCg7b), of which mononucleotides, dinucleotides, trinucleotides, tetranucleotides, pentanucleotides and hexanucleotides composed of 307453 (77.27%), 40991 (10.30%), 23059 (5.79%), 16723 (4.20%), 8127 (2.04%) and 1524 (0.38%), respectively.
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