Abstract
Epicuticular wax (bloom) plays important roles in protecting the tissues of sorghum (Sorghum bicolor (L.) Moench) plants from abiotic stresses. However, reducing wax content provides resistance to greenbug and sheath blight—a useful trait in agricultural crops. We generated a sorghum bloomless (bm) mutant by gamma irradiation. One bm population segregated for individuals with and without epicuticular wax at a frequency of 72:22, suggesting that the bm mutation was under the control of a single recessive nuclear gene. Genes differentially expressed in the wild-type and the bm mutant were identified by RNA-seq technology. Of the 31 downregulated genes, Sb06g023280 was the most differentially expressed and was similar to WBC11, which encodes an ABC transporter responsible for wax secretion in Arabidopsis. An inversion of about 1.4 Mb was present in the region upstream of the Sb06g023280 gene in the bm mutant; it is likely that this inversion changed the promoter sequence of the Sb06g023280 gene. Using genomic PCR, we confirmed that six independent F2 bm mutant-phenotype plants carried the same inversion. Therefore, we concluded that the inversion involving the Sb06g023280 gene inhibited wax secretion in the bloomless sorghum.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- Bm :
-
Bloomless
- BLMC :
-
Bloom-cuticle
- WBC:
-
White-brown complex
- CER:
-
Eceriferum
- FATB:
-
Fatty acyl-ACP thioesterase
- KCS:
-
β-Ketoacyl-CoA synthase condensing enzyme
- ECR:
-
Enoyl-CoA reductase
- ABC transporter:
-
ATP binding cassette (ABC) transporter
- qRT-PCR:
-
Quantitative reverse transcription-PCR
- FPKM:
-
Fragments per kilobase of exon per million fragments
References
Bird D, Beisson F, Brigham A, Shin J, Greer S, Jetter R, Kunst L, Wu XW, Yephremov A, Samuels L (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J 52:485–498
Bonaventure G, Ba XM, Ohlrogge J, Pollard M (2004) Metabolic responses to the reduction in palmitate caused by disruption of the FATB gene in Arabidopsis. Plant Physiol 135:1269–1279
Burow GB, Franks CD, Acosta-Martinez V, Xin ZG (2009) Molecular mapping and characterization of BLMC, a locus for profuse wax (bloom) and enhanced cuticular features of Sorghum (Sorghum bicolor (L.) Moench.). Theor Appl Genet 118:423–431
Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE (2011) Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics 12:514
Fiebig A, Mayfield JA, Miley NL, Chau S, Fischer RL, Preuss D (2000) Alterations in CER6, a gene identical to CUT1, differentially affect long-chain lipid content on the surface of pollen and stems. Plant Cell 12:2001–2008
Jenks MA, Joly RJ, Peters PJ, Rich PJ, Axtell JD, Ashworth EN (1994) Chemically-induced cuticle mutation affecting epidermal conductance to water-vapor and disease susceptibility in Sorghum bicolor (L) moench. Plant Physiol 105:1239–1245
Jordan WR, Monk RL, Miller FR, Rosenow DT, Clark LE, Shouse PJ (1983) Environmental physiology of Sorghum.1. Environmental and genetic-control of epicuticular wax load. Crop Sci 23:552–558
Kasuga S, Inoue N, Kaidai H, Watanabe H (2001) Effects of brown midrib and bloomless genes on the resistance to sheath blight (Rhizoctonia solani Kuehn) in sorghum. Grassl Sci 47:256–261
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Mcnevin JP, Woodward W, Hannoufa A, Feldmann KA, Lemieux B (1993) Isolation and characterization of eceriferum (Cer) mutants induced by T-DNA insertions in Arabidopsis thaliana. Genome 36:610–618
Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T (2010) Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics 11:683
Mizuno H, Kawahigashi H, Kawahara Y, Kanamori H, Ogata J, Minami H, Itoh T, Matsumoto T (2012) Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interaction. BMC Plant Biol 12:121
Panikashvili D, Savaldi-Goldstein S, Mandel T, Yifhar T, Franke RB, Hofer R, Schreiber L, Chory J, Aharoni A (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol 145:1345–1360
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboobur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Peiretti RA, Amini I, Weibel DE, Starks KJ, Mcnew RW (1980) Relationship of bloomless (bm-bm) sorghum to greenbug resistance. Crop Sci 20:173–176
Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6:S22–S32
Peterson GC, Suksayretrup K, Weibel DE (1982) Inheritance of some bloomless and sparse-bloom mutants in sorghum. Crop Sci 22:63–67
Pighin JA, Zheng HQ, Balakshin LJ, Goodman IP, Western TL, Jetter R, Kunst L, Samuels AL (2004) Plant cuticular lipid export requires an ABC transporter. Science 306:702–704
Samuels L, Kunst L, Jetter R (2008) Sealing plant surfaces: cuticular wax formation by epidermal cells. Annu Rev Plant Biol 59:683–707
Shih CH, Chu IK, Yip WK, Lo C (2006) Differential expression of two flavonoid 3′-hydroxylase cDNAs involved in biosynthesis of anthocyanin pigments and 3-deoxyanthocyanidin phytoalexins in sorghum. Plant Cell Physiol 47:1412–1419
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515
Tsuchiya T, Kameya N, Nakamura I (2009) Straight walk: a modified method of ligation-mediated genome walking for plant species with large genomes. Anal Biochem 388:158–160
Ukitsu H, Kuromori T, Toyooka K, Goto Y, Matsuoka K, Sakuradani E, Shimizu S, Kamiya A, Imura Y, Yuguchi M, Wada T, Hirayama T, Shinozaki K (2007) Cytological and biochemical analysis of COF1, an Arabidopsis mutant of an ABC transporter gene. Plant Cell Physiol 48:1524–1533
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
Weibel DE, Starks KJ (1986) Greenbug nonpreference for bloomless sorghum. Crop Sci 26:1151–1153
Zheng HQ, Rowland O, Kunst L (2005) Disruptions of the Arabidopsis enoyl-CoA reductase gene reveal an essential role for very-long-chain fatty acid synthesis in cell expansion during plant morphogenesis. Plant Cell 17:1467–1481
Acknowledgments
The authors thank Dr. Takeshi Itoh, Dr. Yoshihiro Kawahara, Takayuki Yazawa and Dr. Yuichi Katayose for their valuable suggestions and technical assistance for bioinformatics. This work was supported by a Grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics for Agricultural Innovation, SOR-0006).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by R. Snowdon.
H. Mizuno and H. Kawahigashi contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
122_2013_2069_MOESM3_ESM.pdf
Supplementary Fig. 1 bloomless (bm) mutant-phenotype plants commonly carry a genomic inversion including the Sb06g023280 gene. (A) Primer design. Primers were designed to flank the upstream or downstream junction, respectively, and mixed for amplification of relevant junction sequences (Online Resource: Supplementary Table 1). (B) Genomic PCR. Genomic DNAs of wild-type (wt) phenotype plants (wt2, wt3, wt5, wt6, wt8, wt9) and bm mutant-phenotype plants (bm1, bm4, bm7, bm14, bm18, bm23) were subjected to genomic PCR analysis. Among the wt-phenotype plants, two lines (wt2 and wt5) had homozygous alleles and four lines (wt3, wt6, wt8, wt9) had heterozygous alleles. Supplementary material 3 (PDF 42 kb)
Rights and permissions
About this article
Cite this article
Mizuno, H., Kawahigashi, H., Ogata, J. et al. Genomic inversion caused by gamma irradiation contributes to downregulation of a WBC11 homolog in bloomless sorghum. Theor Appl Genet 126, 1513–1520 (2013). https://doi.org/10.1007/s00122-013-2069-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-013-2069-x