Locating the sex determining region of linkage group 12 of guppy (Poecilia reticulata)

Deborah Charlesworth*, R Bergero, Chay Graham, Jim Gardner, Lengxob Yong

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)


Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals' sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species' male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.
Original languageEnglish
Pages (from-to)3639-3649
Number of pages11
JournalG3: Genes, Genomes, Genetics
Issue number10
Early online date4 Aug 2020
Publication statusPrint publication - 5 Oct 2020
Externally publishedYes

Bibliographical note

Copyright © The Author(s) 2020. Published by the Genetics Society of America.


  • Duplication
  • Genome assembly
  • Linkage disequilibrium
  • Partial sex linkage


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