A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL
- 756 Downloads
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.
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.
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.
- 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 110:8057–8062CrossRefPubMedPubMedCentralGoogle Scholar
- 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:e1002952CrossRefPubMedPubMedCentralGoogle Scholar
- 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 175:891–905CrossRefPubMedPubMedCentralGoogle Scholar
- 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 14:1CrossRefGoogle Scholar
- 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 88:82–94CrossRefPubMedGoogle Scholar
- 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 119:853–867PubMedGoogle Scholar
- 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
- 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 28:511–515CrossRefPubMedPubMedCentralGoogle Scholar