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Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods

Research output: Contribution to journalArticle

Original languageEnglish
Article numbere0228951
Number of pages19
JournalPLoS ONE
Volume15
Issue number2
DOIs
DateAccepted/In press - 26 Jan 2020
DatePublished (current) - 19 Feb 2020

Abstract

Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.

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    Rights statement: This is the final published version of the article (version of record). It first appeared online via PLOS at https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228951. Please refer to any applicable terms of use of the publisher.

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