Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance
Open Access
- 21 January 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Plant Biology
- Vol. 21 (1), 1-14
- https://doi.org/10.1186/s12870-021-02824-x
Abstract
Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.Funding Information
- Global Innovation Linkage program (GIL53853)
This publication has 75 references indexed in Scilit:
- Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in ArabidopsisProceedings of the National Academy of Sciences of the United States of America, 2013
- DNA-binding specificity changes in the evolution of forkhead transcription factorsProceedings of the National Academy of Sciences of the United States of America, 2013
- Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regionsNucleic Acids Research, 2013
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Dormancy cycling in Arabidopsis seeds is controlled by seasonally distinct hormone-signaling pathwaysProceedings of the National Academy of Sciences of the United States of America, 2011
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genomeBMC Bioinformatics, 2011
- DEGseq: an R package for identifying differentially expressed genes from RNA-seq dataBioinformatics, 2009
- The evolution of Fox genes and their role in development and diseaseNature Reviews Genetics, 2009
- DAWDLE, a Forkhead-Associated Domain Gene, Regulates Multiple Aspects of Plant DevelopmentPlant Physiology, 2006
- Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT MethodMethods, 2001