Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

Journal name:
Nature Genetics
Year published:
Published online


Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

At a glance


  1. Phylogenetic tree of 199 B. rapa and 119 B. oleracea accessions.
    Figure 1: Phylogenetic tree of 199 B. rapa and 119 B. oleracea accessions.

    The tree was constructed using 6,707 SNP loci selected from gene pairs that were syntenic in the B. rapa and B. oleracea genomes. Different branches of the tree are highlighted by different colors. For B. rapa accessions (left), colors correspond to groups as follows: light blue, turnip; dark blue, sarson; pink, turnip rape; yellow, Japanese group; green, pak choi, wutacai, caixin, zicaitai and taicai; red, late-diverging Chinese cabbage (heading B. rapa, BrH group). For B. oleracea accessions (right), colors correspond to groups as follows: black, wild B. oleracea; blue, kohlrabi; yellow, Chinese kale; light green, cauliflower; green, broccoli; light green, Brussels sprouts; purple, kale; red, heading cabbage (heading B. oleracea, BoH group). Pictures placed beside each clade show typical morphotypes for the corresponding groups.

  2. Genomic signatures of selection in genomes of Chinese cabbage and cabbage.
    Figure 2: Genomic signatures of selection in genomes of Chinese cabbage and cabbage.

    (a) ROD and PiHS values were normalized as z scores for B. rapa. A 200-kb sliding window with an increment of 5 kb was used to calculate these values; each point represents a value in a 200-kb window. The horizontal dashed lines show the empirical threshold of α = 0.01 (z = 2.33). (b) The distributions of normalized values for ROD, π and PiHS. The rightward tails of z (ROD) and z (PiHS) indicate the existence of highly differentiated regions in the BrH genome as compared to the BrNH genome that have been positively selected. The leftward tail of z (π) reflects the existence of genomic regions with low diversity in the BrH group. μ, mean; σ, sigma. (c) A Venn diagram showing unique and shared outlier regions detected by ROD, π and PiHS for B. rapa. (d) Normalized ROD and PiHS z scores for B. oleracea. (e) The distributions of normalized ROD, π and PiHS values for B. oleracea, with the same interpretations as in b. (f) A Venn diagram of the outlier regions detected by ROD, π and PiHS for B. oleracea.

  3. Parallel subgenomic selection among subgenomes from leaf-heading morphotypes of B. rapa and B. oleracea.
    Figure 3: Parallel subgenomic selection among subgenomes from leaf-heading morphotypes of B. rapa and B. oleracea.

    The LF, MF1 and MF2 subgenomes were constructed using diploid chromosomes from the Brassica ancestor tPCK9. The z scores of PiHS values were then plotted against the six B. rapa and B. oleracea subgenomes. The red vertical lines show the empirical threshold of α = 0.01 (z = 2.33). The red horizontal lines encompass regions of subgenomic parallel selection among the six subgenomes, and the light blue horizontal lines encompass loci that harbor candidate genes for the leaf-heading trait on one of the subgenomes. Blue arrows indicate subgenomic parallel selection among the three B. rapa (left) or B. oleracea (right) subgenomes, and green arrows indicate parallel or convergent selection between the B. rapa and B. oleracea subgenomes. The light blue circles show the location of retained candidate paralogs, and circles with red crosses denote gene copies lost in the corresponding subgenomes. Numerical suffixes to the gene names denote the location of the gene on the LF (1), MF1 (2) or MF2 (3) subgenome, respectively.

  4. Selection signals detected in the BrARF3.1 gene.
    Figure 4: Selection signals detected in the BrARF3.1 gene.

    (a) PiHS analysis identifies recent positive selection for the haplotype harboring BrARF3.1; the red star denotes the location of a core SNP in the genic region of BrARF3.1. (b) High FST and ROD values and low π values around the BrARF3.1 gene. Measures were calculated for individual SNPs located in the genomic region between the two vertical dashed lines in a. (c) Haplotypes extending from the core SNP located in the BrARF3.1 gene region for the B. rapa accessions. (d) Extent of haplotype conservation in the BrH and BrNH groups of B. rapa. EHH denotes extended haplotype homozygosity21. (e) BrARF3.1 gene model. A nonsynonymous mutation (G>C) was detected in coding exon 9, which causes an amino acid change from glutamine to histidine. (f) In a larger B. rapa collection of 806 accessions, the C genotype at the core SNP referred to in e strongly associates with the BrH trait.

Accession codes

Primary accessions


Sequence Read Archive


  1. Nagaharu, U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 7, 389452 (1935).
  2. Zhao, J. et al. Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor. Appl. Genet. 110, 13011314 (2005).
  3. Cheng, F., Wu, J. & Wang, X. Genome triplication drove the diversification of Brassica plants. Hortic. Res. 1, 14024 (2014).
  4. Lenser, T. & Theißen, G. Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci. 18, 704714 (2013).
  5. Vavilov, N.I. The law of homologous series in variation. J. Genet. 12, 4789 (1922).
  6. Hovav, R., Chaudhary, B., Udall, J.A., Flagel, L. & Wendel, J.F. Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genetics 179, 17251733 (2008).
  7. Fuller, D.Q. et al. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc. Natl. Acad. Sci. USA 111, 61476152 (2014).
  8. Wang, M. et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46, 982988 (2014).
  9. Cheng, F. et al. Deciphering the diploid ancestral genome of the mesohexaploid Brassica rapa. Plant Cell 25, 15411554 (2013).
  10. Wang, X. et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 10351039 (2011).
  11. Liu, S. et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat. Commun. 5, 3930 (2014).
  12. Cheng, F. et al. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 7, e36442 (2012).
  13. Tang, H. et al. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190, 15631574 (2012).
  14. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945959 (2000).
  15. Prakash, S.H.K. Taxonomy, cytogenetics and origin of crop brassicas, a review. Opera Bot. 55, 157 (1980).
  16. Arias, T., Beilstein, M.A., Tang, M., McKain, M.R. & Pires, J.C. Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. Am. J. Bot. 101, 8691 (2014).
  17. Bonnema, G., Carpio, D.P.D. & Zhao, J. in Genetics, Genomics and Breeding of Vegetable Brassicas 1st edn. (eds. Sadowski, J. & Kole, C.) 81124 (Science Publishers, 2011).
  18. Boswell, V.R. in Our Vegetable Travelers 1st edn, Vol. 96 (ed. Boswell, V.R.) 145217 (National Geographic Magazine, 1949).
  19. Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437460 (1983).
  20. Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105111 (2012).
  21. Voight, B.F., Kudaravalli, S., Wen, X. & Pritchard, J.K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).
  22. Axelsson, E. et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495, 360364 (2013).
  23. Stamm, P. & Kumar, P.P. The phytohormone signal network regulating elongation growth during shade avoidance. J. Exp. Bot. 61, 28892903 (2010).
  24. Santner, A. & Estelle, M. Recent advances and emerging trends in plant hormone signalling. Nature 459, 10711078 (2009).
  25. Gazzarrini, S. & McCourt, P. Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us. Ann. Bot. 91, 605612 (2003).
  26. Manju, R.V., Abida, P.S., Sudarshana, L., Nataraja, K.N. & Sashidhar, V.R. Unusual discrimination against carrier protein antibodies during partial purification of hapten-protein polyclonal antibodies to plant stress hormones. Indian J. Exp. Biol. 33, 15 (1995).
  27. Wang, J., Guo, H., Jin, D., Wang, X. & Paterson, A.H. in The Brassica rapa Genome (ed. Wang, X.) 121130 (Springer, 2015).
  28. Hake, S. et al. The role of knox genes in plant development. Annu. Rev. Cell Dev. Biol. 20, 125151 (2004).
  29. Kidner, C.A. & Timmermans, M.C. Mixing and matching pathways in leaf polarity. Curr. Opin. Plant Biol. 10, 1320 (2007).
  30. Husbands, A.Y., Chitwood, D.H., Plavskin, Y. & Timmermans, M.C. Signals and prepatterns: new insights into organ polarity in plants. Genes Dev. 23, 19861997 (2009).
  31. Byrne, M.E. Networks in leaf development. Curr. Opin. Plant Biol. 8, 5966 (2005).
  32. Bowman, J.L., Eshed, Y. & Baum, S.F. Establishment of polarity in angiosperm lateral organs. Trends Genet. 18, 134141 (2002).
  33. Eshed, Y., Baum, S.F., Perea, J.V. & Bowman, J.L. Establishment of polarity in lateral organs of plants. Curr. Biol. 11, 12511260 (2001).
  34. Izhaki, A. & Bowman, J.L. KANADI and class III HD-Zip gene families regulate embryo patterning and modulate auxin flow during embryogenesis in Arabidopsis. Plant Cell 19, 495508 (2007).
  35. Wu, G. et al. KANADI1 regulates adaxial–abaxial polarity in Arabidopsis by directly repressing the transcription of ASYMMETRIC LEAVES2. Proc. Natl. Acad. Sci. USA 105, 1639216397 (2008).
  36. Liu, Z., Jia, L., Wang, H. & He, Y. HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways. J. Exp. Bot. 62, 43674381 (2011).
  37. Wu, F. et al. The N-terminal double-stranded RNA binding domains of Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing. Plant Cell 19, 914925 (2007).
  38. Yu, X. et al. Cloning and structural and expressional characterization of BcpLH gene preferentially expressed in folding leaf of Chinese cabbage. Sci. China C Life Sci. 43, 321329 (2000).
  39. Townsley, B.T. & Sinha, N.R. A new development: evolving concepts in leaf ontogeny. Annu. Rev. Plant Biol. 63, 535562 (2012).
  40. Barkoulas, M., Galinha, C., Grigg, S.P. & Tsiantis, M. From genes to shape: regulatory interactions in leaf development. Curr. Opin. Plant Biol. 10, 660666 (2007).
  41. Piazza, P., Jasinski, S. & Tsiantis, M. Evolution of leaf developmental mechanisms. New Phytol. 167, 693710 (2005).
  42. Braybrook, S.A. & Kuhlemeier, C. How a plant builds leaves. Plant Cell 22, 10061018 (2010).
  43. Kelley, D.R., Arreola, A., Gallagher, T.L. & Gasser, C.S. ETTIN (ARF3) physically interacts with KANADI proteins to form a functional complex essential for integument development and polarity determination in Arabidopsis. Development 139, 11051109 (2012).
  44. Pekker, I., Alvarez, J.P. & Eshed, Y. Auxin response factors mediate Arabidopsis organ asymmetry via modulation of KANADI activity. Plant Cell 17, 28992910 (2005).
  45. Beuchat, J. et al. BRX promotes Arabidopsis shoot growth. New Phytol. 188, 2329 (2010).
  46. Santuari, L. et al. Positional information by differential endocytosis splits auxin response to drive Arabidopsis root meristem growth. Curr. Biol. 21, 19181923 (2011).
  47. Li, J. et al. BREVIS RADIX is involved in cytokinin-mediated inhibition of lateral root initiation in Arabidopsis. Planta 229, 593603 (2009).
  48. Mouchel, C.F., Osmont, K.S. & Hardtke, C.S. BRX mediates feedback between brassinosteroid levels and auxin signalling in root growth. Nature 443, 458461 (2006).
  49. Scacchi, E. et al. Dynamic, auxin-responsive plasma membrane–to-nucleus movement of Arabidopsis BRX. Development 136, 20592067 (2009).
  50. Zhang, N. et al. Morphology, carbohydrate composition and vernalization response in a genetically diverse collection of Asian and European turnips (Brassica rapa subsp. rapa). PLoS One 9, e114241 (2014).
  51. Gepts, P. The contribution of genetic and genomic approaches to plant domestication studies. Curr. Opin. Plant Biol. 18, 5159 (2014).
  52. Kwak, M., Toro, O., Debouck, D.G. & Gepts, P. Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris). Ann. Bot. 110, 15731580 (2012).
  53. Lin, Z. et al. Parallel domestication of the Shattering1 genes in cereals. Nat. Genet. 44, 720724 (2012).
  54. Li, W. & Gill, B.S. Multiple genetic pathways for seed shattering in the grasses. Funct. Integr. Genomics 6, 300309 (2006).
  55. Tang, H. et al. Seed shattering in a wild sorghum is conferred by a locus unrelated to domestication. Proc. Natl. Acad. Sci. USA 110, 1582415829 (2013).
  56. Bancroft, I. et al. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat. Biotechnol. 29, 762766 (2011).
  57. Cheng, F. et al. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 11, 136 (2011).
  58. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 17541760 (2009).
  59. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 20782079 (2009).
  60. Yu, X. et al. QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa. PLoS One 8, e76059 (2013).
  61. Cheng, F., Wu, J., Fang, L. & Wang, X. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front. Plant Sci. 3, 198 (2012).
  62. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 17921797 (2004).
  63. Retief, J.D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132, 243258 (2000).
  64. Akey, J.M., Zhang, G., Zhang, K., Jin, L. & Shriver, M.D. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12, 18051814 (2002).
  65. Sabeti, P.C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832837 (2002).
  66. Berardini, T.Z. et al. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135, 745755 (2004).
  67. Wang, X. et al. Linkage mapping of a dominant male sterility gene Ms-cd1 in Brassica oleracea. Genome 48, 848854 (2005).
  68. Morrissy, A.S. et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res. 19, 18251835 (2009).
  69. Xue, J. et al. Transcriptome analysis of the brown planthopper Nilaparvata lugens. PLoS One 5, e14233 (2010).
  70. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 19661967 (2009).
  71. Zhang, Z. et al. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4, 259263 (2006).
  72. Schnable, J.C., Springer, N.M. & Freeling, M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108, 40694074 (2011).

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Author information

  1. These authors contributed equally to this work.

    • Feng Cheng,
    • Rifei Sun,
    • Xilin Hou,
    • Hongkun Zheng &
    • Fenglan Zhang


  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.

    • Feng Cheng,
    • Rifei Sun,
    • Yangyong Zhang,
    • Bo Liu,
    • Jianli Liang,
    • Mu Zhuang,
    • Yunxia Liu,
    • Xiaobo Wang,
    • Pingxia Li,
    • Yumei Liu,
    • Yan Wang,
    • Hui Wang,
    • Jie Deng,
    • Yongcui Liao,
    • Keyun Wei,
    • Xueming Zhang,
    • Lixia Fu,
    • Yunyan Hu,
    • Jisheng Liu,
    • Chengcheng Cai,
    • Shujiang Zhang,
    • Shifan Zhang,
    • Fei Li,
    • Hui Zhang,
    • Jifang Zhang,
    • Ning Guo,
    • Zhiyuan Liu,
    • Jin Liu,
    • Chao Sun,
    • Yuan Ma,
    • Haijiao Zhang,
    • Yang Cui,
    • Guusje Bonnema,
    • Jian Wu &
    • Xiaowu Wang
  2. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang, Nanjing, China.

    • Xilin Hou
  3. Biomarker Technologies Corporation, Beijing, China.

    • Hongkun Zheng &
    • Dongyuan Liu
  4. Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing Vegetable Research Center (BVRC), Beijing, China.

    • Fenglan Zhang
  5. Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.

    • Ke Lin,
    • Johan Bucher,
    • Ningwen Zhang,
    • Theo Borm &
    • Guusje Bonnema
  6. Department of Plant and Microbial Biology, University of California, Berkeley, Berkley, California, USA.

    • Micheal R Freeling


Xiaowu Wang, F.C., G.B. and J.W. conceived and designed the experiments. J.W., G.B., Y.Z., M.Z., Yunxia Liu, Yumei Liu, T.B., X.Z., L.F., Y.H., Shujiang Zhang, Shifan Zhang, F.L., Hui Zhang, J.Z., N.G., Z.L., Jin Liu, Y.M., Haijiao Zhang, J.B. and Y.C. contributed materials. Y.W., H.W., N.Z., J.D., Y. Liao and K.W. contributed to phenotyping. N.Z. performed QTL analysis for the RIL populations. R.S., G.B., T.B., H. Zheng, X.H., F.Z., K.L., B.L., D.L., Xiaobo Wang, Jisheng Liu and C.S. contributed to resequencing. F.C., B.L., C.C. and T.B. analyzed the data and performed statistical analysis. P.L., J. Liang and L.F. performed the experiments. F.C. and Xiaowu Wang wrote the manuscript, with help from J. Liang, M.R.F., J.W., G.B., T.B. and P.L.

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