Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study
Open Access
- 19 March 2020
- journal article
- research article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 21 (6), 2129
- https://doi.org/10.3390/ijms21062129
Abstract
Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.Funding Information
- Washington State Department of Agriculture (K1983)
This publication has 71 references indexed in Scilit:
- QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteichesin four sources of resistance in peaBMC Plant Biology, 2013
- The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristemBMC Plant Biology, 2013
- Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentilBMC Genomics, 2013
- The variant call format and VCFtoolsBioinformatics, 2011
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Overexpression of Pectin Methylesterase Inhibitors in Arabidopsis Restricts Fungal Infection by Botrytis cinereaPlant Physiology, 2007
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004
- Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT MethodMethods, 2001
- THE ESTIMATION OF MAP DISTANCES FROM RECOMBINATION VALUESAnnals of Eugenics, 1943