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A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL

Citation

Habib, A and Powell, JJ and Stiller, J and Liu, M and Shabala, S and Zhou, M and Gardiner, DM and Liu, C, A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL, Theoretical and Applied Genetics, 131, (3) pp. 613-624. ISSN 0040-5752 (2018) [Refereed Article]

Copyright Statement

Copyright 2017 Springer-Verlag GmbH Germany, part of Springer Nature

DOI: doi:10.1007/s00122-017-3023-0

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.

Item Details

Item Type:Refereed Article
Keywords:barley, crown rot, fungi, genes, plants, RNA
Research Division:Agricultural and Veterinary Sciences
Research Group:Crop and Pasture Production
Research Field:Crop and Pasture Improvement (Selection and Breeding)
Objective Division:Plant Production and Plant Primary Products
Objective Group:Winter Grains and Oilseeds
Objective Field:Barley
UTAS Author:Habib, A (Mr Ahsan Habib)
UTAS Author:Shabala, S (Professor Sergey Shabala)
UTAS Author:Zhou, M (Professor Meixue Zhou)
ID Code:125786
Year Published:2018
Web of Science® Times Cited:4
Deposited By:TIA - Research Institute
Deposited On:2018-05-05
Last Modified:2019-03-20
Downloads:0

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