Open AccessSegregation distortion: Utilizing simulated genotyping data to evaluate statistical methods
Author(s) -
Alexander Coulton,
Alexandra M. PrzewieslikAllen,
Amanda Burridge,
Daniel S. Shaw,
Keith J. Edwards,
Gary Barker
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0228951
Subject(s) - bonferroni correction , replicate , distortion (music) , false discovery rate , multiple comparisons problem , statistical hypothesis testing , biology , linkage (software) , population , computational biology , genetics , computer science , statistics , mathematics , gene , amplifier , computer network , bandwidth (computing) , demography , sociology
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.