Abstract
Key message
This study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines.
Abstract
Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum.
Similar content being viewed by others
References
Aarts M, Keijzer CJ, Stiekema WJ, Pereira A (1995) Molecular characterization of the CER1 gene of arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. Plant Cell 7:2115–2127
Akinsanmi O, Mitter V, Simpfendorfer S, Backhouse D, Chakraborty S (2004) Identity and pathogenicity of Fusarium spp. isolated from wheat fields in Queensland and northern New South Wales. Crop Pasture Sci 55:97–107
Bai Z, Liu C (2015) Histological evidence for different spread of Fusarium crown rot in barley genotypes with different heights. J Phytopathol 163:91–97
Barrero JM, Cavanagh C, Verbyla KL, Tibbits JF, Verbyla AP, Huang BE, Rosewarne GM, Stephen S, Wang P, Whan A (2015) Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL. Genome Biol 16:93
Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23:1379–1386
Bozkurt TO, Richardson A, Dagdas YF, Mongrand S, Kamoun S, Raffaele S (2014) The plant membrane-associated REMORIN1.3 accumulates in discrete perihaustorial domains and enhances susceptibility to phytophthora infestans. Plant Physiol 165(3):1005–1018
Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci 110:8057–8062
Chakraborty S, Liu C, Mitter V, Scott J, Akinsanmi O, Ali S, Dill-Macky R, Nicol J, Backhouse D, Simpfendorfer S (2006) Pathogen population structure and epidemiology are keys to wheat crown rot and Fusarium head blight management. Australas Plant Pathol 35:643–655
Chen G, Liu Y, Ma J, Zheng Z, Wei Y, McIntyre CL, Zheng Y-L, Liu C (2013a) A novel and major quantitative trait locus for Fusarium crown rot resistance in a genotype of wild barley (Hordeum spontaneum L.). PLoS One 8:e58040
Chen G, Liu Y, Wei Y, McIntyre C, Zhou M, Zheng Y-L, Liu C (2013b) Major QTL for Fusarium crown rot resistance in a barley landrace. Theor Appl Genet 126:2511–2520
Chen G, Yan W, Liu Y, Wei Y, Zhou M, Zheng Y-L, Manners JM, Liu C (2014) The non-gibberellic acid-responsive semi-dwarfing gene uzu affects Fusarium crown rot resistance in barley. BMC Plant Biol 14(1):22
Chen G, Habib A, Wei Y, Zheng Y-L, Shabala S, Zhou M, Liu C (2015) Enhancing Fusarium crown rot resistance by pyramiding large-effect QTL in barley. Mol Breed 35:1–8
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Desmond OJ, Manners JM, Schenk PM, Maclean DJ, Kazan K (2008) Gene expression analysis of the wheat response to infection by Fusarium pseudograminearum. Physiol Mol Plant Pathol 73(1–3):40–47
Ding L, Xu H, Yi H, Yang L, Kong Z, Zhang L, Xue S, Jia H, Ma Z (2011) Resistance to hemi-biotrophic F. graminearum infection is associated with coordinated and ordered expression of diverse defense signaling pathways. PLoS One 6:e19008
Gardiner DM, McDonald MC, Covarelli L, Solomon PS, Rusu AG, Marshall M, Kazan K, Chakraborty S, McDonald BA, Manners JM (2012) Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLoS Pathog 8:e1002952
Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM (2017) Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC Plant Biol 17:123
Habib A, Shabala S, Shabala L, Zhou M, Liu C (2016) Near-isogenic lines developed for a major QTL on chromosome arm 4HL conferring Fusarium crown rot resistance in barley. Euphytica 209:555–563
Hofstad AN, Nussbaumer T, Akhunov E, Shin S, Kugler KG, Kistler HC, Mayer KF, Muehlbauer GJ (2016) Examining the transcriptional response in wheat near-isogenic lines to infection and deoxynivalenol treatment. Plant Genome. https://doi.org/10.3835/plantgenome2015.05.0032
Huang Y, Li L, Smith KP, Muehlbauer GJ (2016) Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance. BMC Genom 17:387
Kazan K, Gardiner DM (2017) Transcriptomics of cereal-Fusarium graminearum interactions: what we have learned so far. Mol Plant Pathol. https://doi.org/10.1111/mpp.12561
Keurentjes JJ, Bentsink L, Alonso-Blanco C, Hanhart CJ, Blankestijn-De Vries H, Effgen S, Vreugdenhil D, Koornneef M (2007) Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics 175:891–905
Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363
Kugler KG, Siegwart G, Nussbaumer T, Ametz C, Spannagl M, Steiner B, Lemmens M, Mayer KF, Buerstmayr H, Schweiger W (2013) Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.). BMC Genom 14:1
Lefebvre B, Timmers T, Mbengue M, Moreau S, Hervé C, Tóth K, Bittencourt-Silvestre J, Klaus D, Deslandes L, Godiard L (2010) A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proc Natl Acad Sci 107:2343–2348
Li X, Liu C, Chakraborty S, Manners JM, Kazan K (2008) A simple method for the assessment of crown rot disease severity in wheat seedlings inoculated with Fusarium pseudograminearum. J Phytopathol 156:751–754
Li H, Zhou M, Liu C (2009) A major QTL conferring crown rot resistance in barley and its association with plant height. Theor Appl Genet 118:903–910
Liu Y, Yang X, Ma J, Wei Y, Zheng Y, Ma H, Yao J, Yan G, Wang Y, Manners J (2010) Plant height affects Fusarium crown rot severity in wheat. Phytopathology 100:1276–1281
Liu Y, Ma J, Yan W, Yan G, Zhou M, Wei Y, Zheng Y, Liu C (2012) Different tolerance in bread wheat, durum wheat and barley to Fusarium crown rot disease caused by Fusarium pseudograminearum. J Phytopathol 160:412–417
Liu C, Zhou Q, Dong L, Wang H, Liu F, Weng J, Li X, Xie C (2016a) Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing. BMC Genom 17:915
Liu D, Zhang J, Liu X, Wang W, Liu D, Teng Z, Fang X, Tan Z, Tang S, Yang J (2016b) Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T 1 region in upland cotton. BMC Genom 17:295
Ma J, Yan G, Liu C (2012) Development of near-isogenic lines for a major QTL on 3BL conferring Fusarium crown rot resistance in hexaploid wheat. Euphytica 183:147–152
Ma J, Jiang Q-T, Zhang X-W, Lan X-J, Pu Z-E, Wei Y-M, Liu C, Lu Z-X, Zheng Y-L (2013a) Structure and expression of barley starch phosphorylase genes. Planta 238:1081–1093
Ma J, Jiang Q-T, Zhao Q-Z, Zhao S, Lan X-J, Dai S-F, Lu Z-X, Liu C, Wei Y-M, Zheng Y-L (2013b) Characterization and expression analysis of waxy alleles in barley accessions. Genetica 141:227–238
Ma J, Stiller J, Zhao Q, Feng Q, Cavanagh C, Wang P, Gardiner D, Choulet F, Feuillet C, Zheng Y-L (2014) Transcriptome and allele specificity associated with a 3BL locus for fusarium crown rot resistance in bread wheat. PLoS One 9:e113309
Makandar R, Nalam VJ, Lee H, Trick HN, Dong Y, Shah J (2012) Salicylic acid regulates basal resistance to Fusarium head blight in wheat. MPMI 25:431–439
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Murray GM, Brennan JP (2009) Estimating disease losses to the Australian wheat industry. Australas Plant Pathol 38:558–570
Murray G, Brennan J (2010) Estimating disease losses to the Australian barley industry. Australas Plant Pathol 39:85–96
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4326
Nagel R, Berasategui A, Paetz C, Gershenzon J, Schmidt A (2014) Overexpression of an isoprenyl diphosphate synthase in spruce leads to unexpected terpene diversion products that function in plant defense. Plant Phys 164:555–569
Pankratov I, McQuinn R, Schwartz J, Bar E, Fei Z, Lewinsohn E, Zamir D, Giovannoni JJ, Hirschberg J (2016) Fruit carotenoid-deficient mutants in tomato reveal a function of the plastidial isopentenyl diphosphate isomerase (IDI1) in carotenoid biosynthesis. Plant J 88:82–94
Powell JJ, Fitzgerald TL, Stiller J, Berkman PJ, Gardiner DM, Manners JM, Henry RJ, Kazan K (2016) The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias. Plant Biotechnol J 15:533–543
Powell JJ, Carere J, Fitzgerald T, Stiller J, Covarelli L, Xu Q, Gubler F, Colgrave ML, Gardiner DM, Manners J, Henry RJ, Kazan K (2017) The Fusarium crown rot pathogen Fusarium pseudograminearum triggers a suite of transcriptional and metabolic changes in bread wheat (Triticum aestivum L.). Ann Bot 119:853–867
Qi P-F, Johnston A, Balcerzak M, Rocheleau H, Harris LJ, Long X-Y, Wei Y-M, Zheng Y-L, Ouellet T (2012) Effect of salicylic acid on Fusarium graminearum, the major causal agent of fusarium head blight in wheat. Fungal Biol 116:413–426
Raffaele S, Bayer E, Lafarge D, Cluzet S, Retana SG, Boubekeur T, Leborgne-Castel N, Carde J-P, Lherminier J, Noirot E (2009) Remorin, a solanaceae protein resident in membrane rafts and plasmodesmata, impairs potato virus X movement. Plant Cell 21:1541–1555
Roberts A, Pimentel H, Trapnell C, Pachter L (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27:2325–2329
Sablok G, Powell JJ, Kazan K (2017) Emerging roles and landscape of translating mRNAs in plants. Front Plant Sci. https://doi.org/10.3389/fpls.2017.01443
Samad-Zamini M, Schweiger W, Nussbaumer T, Mayer KF, Buerstmayr H (2017) Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum. Plant Biotechnol J. https://doi.org/10.1111/pbi.12729
Smiley RW, Gourlie JA, Easley SA, Patterson L-M, Whittaker RG (2005) Crop damage estimates for crown rot of wheat and barley in the Pacific Northwest. Plant Dis 89:595–604
Steiner B, Kurz H, Lemmens M, Buerstmayr H (2009) Differential gene expression of related wheat lines with contrasting levels of head blight resistance after Fusarium graminearum inoculation. Theor Appl Genet 118:753–764
Stephen S, Cullerne D, Spriggs A, Helliwell C, Lovell D, Taylor J (2012) Biokanga: a suite of high performance bioinformatics applications. https://github.com/csiro-crop-informatics/biokanga. Accessed 15 Sept 2017
Swanson-Wagner RA, DeCook R, Jia Y, Bancroft T, Ji T, Zhao X, Nettleton D, Schnable PS (2009) Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science 326(5956):118–1120
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
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
West MAL, Kim K, Kliebenstein DJ, van Leeuwen H, Michelmore RW, Doerge RW, St. Clair DA (2007) Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175:1441–1450
Xiao J, Jin X, Jia X, Wang H, Cao A, Zhao W, Pei H, Xue Z, He L, Chen Q (2013) Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai. BMC Genom 14:1
Ye J, Yang Y, Chen B, Shi J, Luo M, Zhan J, Wang X, Liu G, Wang H (2017) An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.). BMC Genom 18:71
Acknowledgements
Work reported in this publication was partially funded by the Grains Research and Development Corporation, Australia (Project no. CFF00010). AH is grateful to University of Tasmania, Australia, and Khulna University, Bangladesh, for financial supports during the tenure of his Ph.D. studentship.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by Hermann Buerstmayr.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Habib, A., Powell, J.J., Stiller, J. et al. A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL. Theor Appl Genet 131, 613–624 (2018). https://doi.org/10.1007/s00122-017-3023-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-017-3023-0