Selection of Genetic Markers to Determine Diversity in Theileria annulata Populations after Recombination

• Published in: Türkiye parazitolojii dergisi Vol. 41; no. 1; pp. 9 - 18
• Main Authors: Bilgiç, Hüseyin Bilgin, Ünlü, Ahmet Hakan, Aksulu, Ayça, Bakırcı, Serkan, Hacılarlıoğlu, Selin, Eren, Hasan, Weir, William, Karagenç, Tülin
• Format: Journal Article
• Language: English
• Published: Turkey 01.03.2017
• Subjects: DNA Primers; Genetic Markers; Genetic Variation; Microsatellite Repeats; Minisatellite Repeats; Polymorphism, Genetic; Recombination, Genetic; Software; Theileria annulata - classification; Theileria annulata - genetics
• ISSN: 1300-6320; 2146-3077
• DOI: 10.5152/tpd.2017.4970

Selecting polymorphic mini- and microsatellite markers to determine genetic diversity and chromosomal regions exhibiting elevated rates of recombination in Theileria annulata populations after recombination. The Unipro UGENE software was used to select markers. A score at which 10 times more tandem repeats (TRs) were identified in the real DNA sequence than those in the scrambled sequences of T. annulata was used as the cutoff. TRs containing minimum three nucleotides in length for microsatellite and six nucleotides for minisatellite regions and having a repeat motif identity between 96%-100% with the unit size repeated minimum three times were screened through the whole genome using the suffix array algorithm. A total of 359 minisatellites and 8973 microsatellites were identified. TRs were screened one by one through the whole genome; mini- and microsatellites representing a single region and having suitable regions for primer design were selected based on their localization on T. annulata chromosomes, their repeat motif identity (>96%), and their repeat length (<1500 bp). The primers used to amplify selected candidates were designed, and each primer was used to check 27 different isolates of T. annulata. In the present study, a total of 13 polymorphic mini- and microsatellite markers located on the different chromosomes were selected to determine the population diversity of T. annulata.