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United States Department of Agriculture

Agricultural Research Service

Research Project: Management of Genetic Resources and Associated Information for Selected Vegetable Crops

Location: Plant Genetic Resources Research

Title: Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L

Author
item Bird, Kevin
item An, Hong
item Gazave, Elodie
item Gore, Michael
item Pires, Joseph
item Robertson, Larry
item Labate, Joanne

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2017
Publication Date: 3/12/2017
Citation: Bird, K., An, H., Gazave, E., Gore, M., Pires, J., Robertson, L., Labate, J.A. 2017. Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Frontiers in Plant Science. 8:321.

Interpretive Summary: The crop Brassica rapa L. is very diverse in its usage. It can be consumed as a raw or cooked leafy green (mizuna, Chinese cabbage, bok choy, tatsoi, choy sum, komatsuna), a spice or condiment (brown sarson, yellow sarson), a root vegetable also used as animal fodder (turnip), or a cooking oil (oilseed rape). The genetic relationships among these various types (morphotypes) is not well understood but a deeper understanding would be beneficial for crop conservation and improvement. We sequenced portions of the genomes of 333 diverse accessions of B. rapa from the USDA National Plant Germplasm System (NPGS) that originated from the Americas, Europe, East Asia, South Asia/Middle East, and Australia and included all ten of the above mentioned morphotypes. Our results indicated that both morphotype and geography contributed to the global genetic patterns of B. rapa. We identified four distinct groups (turnip, oilseed, Chinese cabbage, and bok choy) and separated turnips by geographic origin (European vs. East Asian). These results emphasized the importance of morphotype on genetic diversity but also indicated that there exists significant differences between the same morphotypes that are related to geographic origin. These differences may have arisen through different domestication histories, breeding histories, or extensive geographic isolation. The results provided enhanced resolution to the genetic relationships of morphotypes within the species B. rapa. Understanding of these relationships is key to future breeding and scientific work in B. rapa.

Technical Abstract: The crop species Brassica rapa L. has significant economic importance around the globe. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption and fodder for livestock. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. We used genotyping-by-sequencing (GBS) to simultaneously identify and score 18,272 single-nucleotide polymorphism (SNP) markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System (NPGS) accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses revealed five subpopulations that were largely reflective of morphotype and geography. Additionally, for some accessions we found evidence of incongruence between the subspecies designations proposed by breeders and/or curators and population structure assignments, particularly for oilseed morphotypes and turnips. The results of this study have provided unprecedented resolution to the genetic and evolutionary relationships of subspecies within the species B. rapa. Understanding of these relationships is key to future breeding and scientific work in B. rapa.

Last Modified: 10/19/2017
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