Genetic and genomic resources to study natural variation in Brassica rapa

Ping Lou, Scott Woody, Kathleen Greenham, Robert VanBuren, Marivi Colle, Patrick P. Edger, Ryan Sartor, Yakun Zheng, Nathan Levendoski, Jan Lim, Calvin So, Brian Stoveken, Timothy Woody, Jianjun Zhao, Shuxing Shen, Richard M. Amasino, C. Robertson McClung

Research output: Contribution to journalArticlepeer-review

Abstract

The globally important crop Brassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history of B. rapa domestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress-tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation toward the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation in B. rapa, we constructed an Advanced Intercross Recombinant Inbred Line (AI-RIL) population using B. rapa subsp. trilocularis (Yellow Sarson) R500 and the B. rapa subsp. parachinensis (Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and future B. rapa genomic resources, we generated a de novo genome assembly of the B. rapa subsp. trilocularis (Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using this de novo genome was used to map Quantitative Trait Loci (QTL) for seed coat color and revealed the improved mapping resolution afforded by this new assembly.

Original languageEnglish (US)
Article numbere00285
JournalPlant Direct
Volume4
Issue number12
DOIs
StatePublished - Dec 2020

Bibliographical note

Funding Information:
We thank Guusje Bonnema for the doubled haploid line L58. This work was supported by National Science Foundation grants IOS‐1202779 to K.G., IOS‐1711662 to R.S., and IOS‐1547796, IOS‐1547796 to R.M.A. and C.R.M., and by the Rural Development Administration, Republic of Korea Next Generation BioGreen 21 grant number SSACPJ01327306 to C.R.M. Brassica rapa

Publisher Copyright:
© 2020 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.

Keywords

  • Advanced-Intercross Recombinant Inbred Lines
  • Brassica rapa
  • Quantitative Trait Loci
  • natural variation
  • seed coat color

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