The Effect of microsatellite number and motif type on estimation of population parameters in genetic diversity studies i

Hashemi, Mona, Rahimi Mianji, Godrat, Hossein Banabazi, Mohammad, Orozco ter-Wengel, Pablo ORCID: https://orcid.org/0000-0002-7951-4148 and Biscarini, Filippo 2021. The Effect of microsatellite number and motif type on estimation of population parameters in genetic diversity studies i. Journal of Ruminant Research 8 (4) , pp. 39-54. 10.22069/EJRR.2021.17558.1732

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Abstract

Abstract1 Background and objective: Microsatellites are repetitive regions in DNA including a homogeneous array of mono, di-, tri-, tetra-, penta-, and hexa-nucleotides with a length of less than 1 Kbp which are non-randomly distributed in the genome. The number and density of microsatellites are varying within species even in very close species such as humans and chimpanzees. The frequency of microsatellite motifs and their mutation rate are reported differently in various organisms. Di-nucleotide microsatellites are the most abundant motifs followed by mono and tetra microsatellite motifs in mammalian genomes. Tri-nucleotide microsatellites are more frequent in plants. However, the effect of different microsatellite motifs on genetic diversity or population structural parameters is a topic that has received less attention. Material and methods: In the present study, using the 36 VCf file of microsatellite markers extracted from the whole genome of Iranian sheep “Ovis aries and Ovis orientalis” by NGS, the total number of 163973 microsatellite markers were detected. The distribution of Ovis aries samples is from the north-west part of Iran and Ovis orientalis samples belongs to the central part and north-west of Iran. After rearrangement and filtration on the data file using Samtools and VCFtools software, we classified the whole markers on four different motif types including di- tri- and tetra-nucleotide microsatellites and a file include all three microsatellite types. Several subsets including 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400 and 500 markers were generated from each microsatellite motif types using an R script. Six common genetic diversity parameters including observed and expected heterozygosity, Nei diversity index, Shanon index, Allelic richness, and FIS were calculated for each different subset of number and motif type of microsatellites in MSA (V.4.05) software. 10 replications were considered for each parameter. The mean and variance were calculated among 10 replications and results were represented by boxplots using R (v.3.3.3). The statistical investigation of parameter estimation differences using different microsatellite number and motif types were analyzed using ANOVA for testing the hypothesis of equality of means in R (v.3.3.3). Results: Estimation of all six parameters revealed various results using a different number of loci as well as motif types. Additionally, the results revealed higher values for parameters estimated with di microsatellite motifs compared to others. In addition, the highest and lowest values for most parameters were obtained by 40-di and 10-tri/tetra microsatellites respectively. The statistical significance on findings of parameter values using different number/motif of microsatellite markers were analyzed using ANOVA in R (v.3.3.3). In cases where the implication of the model showed significant results, Tukey Honestly Significant Difference test was used to test pairwise contrasts between different subsets. Conclusion: Our results propose a better application of di microsatellites for genetic diversity studies in sheep populations. Moreover, results showed that for stable estimation of population parameters in genetic diversity studies a minimum of 50 microsatellite loci are needed.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
ISSN:	2345-4253
Date of First Compliant Deposit:	11 January 2021
Date of Acceptance:	28 December 2020
Last Modified:	22 Feb 2023 19:16
URI:	https://orca.cardiff.ac.uk/id/eprint/137544

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