R Markdown documents can also include footnotes and citations, with support for a wide variety of bibliography formats and output styles.
To define the bibliography and citation styles for a document you include a bibliography and citation style (csl) file in the same directory as your R Markdown document and then add corresponding fields to the document's metadata. For example:
--- title: "Crop Analysis Q3 2013" bibliography: crop-analysis.bib csl: chicago-author-date.csl ---
For pdf_document and beamer_presentation you can also use bibtex or natbib for bibliographies. In this case you can also include the following fields in metadata:
biblio-styleLaTeX bibliography style (used with natbib option)
biblio-filesBibliography files to use in LaTeX (used with natbib or biblatex options)
You can find more information on the markdown syntax for citations within the pandoc documentation on citations and footnotes.