Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Xinshuai Qi, Hong An, Aaron P. Ragsdale, Tara E. Hall, Ryan N Gutenkunst, J. Chris Pires, Michael S Barker

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European–Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400–4,100 years ago, and that Chinese cabbage originated 1,200–2,100 years ago via admixture of pak choi and European–Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.

Original languageEnglish (US)
Pages (from-to)3373-3388
Number of pages16
JournalMolecular Ecology
Volume26
Issue number13
DOIs
StatePublished - Jul 1 2017

Fingerprint

Brassica rapa
domestication
genomics
demographic statistics
Demography
Brassica rapa subsp. chinensis
crop
Chinese cabbage
Brassica
crops
subspecies
Single Nucleotide Polymorphism
Brassica rapa subsp. dichotoma
Brassica rapa subsp. trilocularis
Founder Effect
Metagenomics
founder effect
historical record
Transcriptome
transcriptome

Keywords

  • Brassica rapa
  • crop improvement
  • domestication
  • genetic structure
  • population genomics
  • transcriptome

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Genomic inferences of domestication events are corroborated by written records in Brassica rapa. / Qi, Xinshuai; An, Hong; Ragsdale, Aaron P.; Hall, Tara E.; Gutenkunst, Ryan N; Chris Pires, J.; Barker, Michael S.

In: Molecular Ecology, Vol. 26, No. 13, 01.07.2017, p. 3373-3388.

Research output: Contribution to journalArticle

Qi, Xinshuai ; An, Hong ; Ragsdale, Aaron P. ; Hall, Tara E. ; Gutenkunst, Ryan N ; Chris Pires, J. ; Barker, Michael S. / Genomic inferences of domestication events are corroborated by written records in Brassica rapa. In: Molecular Ecology. 2017 ; Vol. 26, No. 13. pp. 3373-3388.
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