To cite R/qtl2 in publications use:

  Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell
  BS, Churchill GA (2019) R/qtl2: software for mapping quantitative
  trait loci with high-dimensional data and multi-parent populations.
  Genetics 211:495-502 doi:10.1534/genetics.118.301595

A BibTeX entry for LaTeX users is

  @Article{Broman2019,
    title = {R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations.},
    author = {Karl W. Broman and Daniel M. Gatti and Petr Simecek and Nicholas A. Furlotte and Pjotr Prins and Śaunak Sen and Brian S. Yandell and Gary A. Churchill},
    journal = {Genetics},
    doi = {10.1534/genetics.118.301595},
    year = {2019},
    volume = {211},
    pages = {495-502},
    url = {https://doi.org/10.1534/genetics.118.301595},
    eprint = {https://academic.oup.com/genetics/article-pdf/211/2/495/37817017/genetics0495.pdf},
  }