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Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain


Breeding to increase β-carotene levels in cereal grains, termed provitamin A biofortification, is an economical approach to address dietary vitamin A deficiency in the developing world. Experimental evidence from association and linkage populations in maize (Zea mays L.) demonstrate that the gene encoding β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with β-carotene concentration and conversion in maize kernels. crtRB1 alleles associated with reduced transcript expression correlate with higher β-carotene concentrations. Genetic variation at crtRB1 also affects hydroxylation efficiency among encoded allozymes, as observed by resultant carotenoid profiles in recombinant expression assays. The most favorable crtRB1 alleles, rare in frequency and unique to temperate germplasm, are being introgressed via inexpensive PCR marker-assisted selection into tropical maize germplasm adapted to developing countries, where it is most needed for human health.

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Figure 1: Carotenoid biosynthetic pathway and Zea mays crtRB1 gene structure.
Figure 2: Mean carotenoid concentration (μg g−1 dry weight, DW) for crtRB1 allele classes across three F2:3 populations.
Figure 3: Allele-specific crtRB1 effects on biochemical activity and transcriptional expression.

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  1. Tanumihardjo, S.A., Bouis, H., Hotz, C., Meenakshi, J.V. & McClafferty, B. Biofortification of staple crops: an emerging strategy to combat hidden hunger. Compr. Rev. Food Sci. Food Safety 7, 329–334 (2008).

    Google Scholar 

  2. Pfeiffer, W.H. & McClafferty, B. HarvestPlus: breeding crops for better nutrition. Crop Sci. 47, S88–S105 (2007).

    Article  Google Scholar 

  3. Fierce, Y. et al. In vitro and in vivo characterization of retinoid synthesis from β-carotene. Arch. Biochem. Biophys. 472, 126–138 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Harjes, C.E. et al. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319, 330–333 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Sun, Z.R., Gantt, E. & Cunningham, F.X. Cloning and functional analysis of the β-carotene hydroxylase of Arabidopsis thaliana. J. Biol. Chem. 271, 24349–24352 (1996).

    Article  CAS  PubMed  Google Scholar 

  6. Tian, L. & DellaPenna, D. Characterization of a second carotenoid β-hydroxylase gene from Arabidopsis and its relationship to the LUT1 locus. Plant Mol. Biol. 47, 379–388 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Bai, L., Kim, E., DellaPenna, D. & Brutnell, T.P. Novel lycopene epsilon cyclase activities in maize revealed through perturbation of carotenoid biosynthesis. Plant J. 59, 588–599 (2009).

    Article  CAS  PubMed  Google Scholar 

  8. Aluru, M. et al. Generation of transgenic maize with enhanced provitamin A content. J. Exp. Bot. 59, 3551–3562 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Vallabhaneni, R. et al. Metabolite sorting of a germplasm collection reveals the hydroxylase3 locus as a new target for maize provitamin A biofortification. Plant Physiol. 151, 1635–1645 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cunningham, F.X. Jr., Lee, H. & Gantt, E. Carotenoid biosynthesis in the primitive red alga Cyanidioschyzon merolae. Eukaryot. Cell 6, 533–545 (2007).

    Article  CAS  PubMed  Google Scholar 

  11. Vallabhaneni, R. & Wurtzel, E.T. Timing and biosynthetic potential for carotenoid accumulation in genetically diverse germplasm of maize. Plant Physiol. 150, 562–572 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Li, F., Murillo, C. & Wurtzel, E.T. Maize Y9 encodes a product essential for 15-cis-zeta-carotene isomerization. Plant Physiol. 144, 1181–1189 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Matthews, P.D. & Wurtzel, E.T in Food Colorants: Chemical and Functional Properties (ed. Sociaciu, C.) 361–368 (CRC Press, Boca Raton, Florida, USA, 2007).

  14. Kurilich, A.C. & Juvik, J.A. Quantification of carotenoid and tocopherol antioxidants in Zea mays. J. Agric. Food Chem. 47, 1948–1955 (1999).

    Article  CAS  PubMed  Google Scholar 

  15. Chander, S. et al. Using molecular markers to identify two major loci controlling carotenoid contents in maize grain. Theor. Appl. Genet. 116, 223–233 (2008).

    Article  CAS  PubMed  Google Scholar 

  16. Yu, J.M. et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203–208 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Hardy, O.J. & Vekemans, X. SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2, 618–620 (2002).

    Article  Google Scholar 

  19. Fu, Y. et al. Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl. Acad. Sci. USA 102, 12282–12287 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wang, S., Basten, C.J. & Zeng, Z. Windows QTL Cartographer 2.5 (North Carolina State University, Raleigh, North Carolina, USA, 2005).

  21. Ooijen, J.W.V. & Voorrips, R.E. JOINMAP version 3.0, Software for the Calculation of Genetic Linkage Maps (Plant Research International, Wageningen, The Netherlands, 2001).

  22. Kandianis, C. Genetic Dissection of Carotenoid Concentration and Compositional Traits in Maize Grain Doctoral dissertation, University of Illinois, Urbana-Champaign. 〈〉 (December 2009).

  23. Utz, H.F. & Melchinger, A.E. PLABQTL: A Computer Program to Map QTL, Version 1.2 (1993).<>

  24. SAS Institute. SAS/STAT User's Guide Version 9.2 (SAS Institute, Cary, North Carolina, USA, 2008).

  25. Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).

    Article  CAS  PubMed  Google Scholar 

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We thank K. Pixley and J. Chandler for seed and field experiment coordination and W. White, P. Bermudez, S. Islam, C. Paul, W. Liu, S. Xu and Y. Zhou for carotenoid HPLC profiling. Helpful comments on the manuscript from J. Wilkinson and J. Yu are appreciated. This research was supported by the US Agency for International Development (T.R.), HarvestPlus (T.R., D.D.P., J.Y., J.L., M.L.W.), National Science Foundation (NSF) DBI-0321467, DBI-0820619 (E.S.B.), NSF DBI-0604923 (T.R.), USDA-ARS (E.S.B.), NSF DBI-0501713 (T.B.), TRIAD Foundation (T.B.), China NSF-30821140352 (J.L., J.Y.), China Scholarship Fund (Y.F.) and JBT Fellowship-UIUC (C.B.K.).

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C.E.H. and J.Y. identified the gene. X.Y., Z.F., Y.F., R.B., C.B.K., J.Y., M.G.S.F., M.Z. and S.M. carried out the sequencing and genotyping. L.B., E.-H.K. and X.Y. carried out the transcript expression and biochemical assays. J.Y. and D.J.S. developed the crtRB1 molecular markers. R.B. and J.Y. supervised the field testing. C.B.K., Z.F., Q.L. and N.P. carried out the carotenoid profiling. C.B.K. and X.Y. completed the genetic mapping and QTL analyses. J.Y. and C.B.K. carried out the association and genetic analyses. The study was designed and supervised by J.Y., J.L., D.D.P., T.B., E.S.B., M.L.W. and T.R. The manuscript was prepared by J.Y., C.B.K., D.J.S., M.L.W. and T.R. and was edited by D.D.P., T.B. and E.S.B.

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Correspondence to Marilyn L Warburton or Torbert Rocheford.

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The authors declare no competing financial interests.

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Supplementary Figures 1–5 and Supplementary Tables 1–20 (PDF 2955 kb)

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Yan, J., Kandianis, C., Harjes, C. et al. Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nat Genet 42, 322–327 (2010).

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