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Article

Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study

1
Department of Horticulture, Washington State University, Pullman, WA 99164, USA
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Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA
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USDA-ARS Plant Germplasm Introduction and Testing Unit, Washington State University, Pullman, WA 99164, USA
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USDA-ARS Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
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Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
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Breeder Seed Production Center, Bangladesh Agricultural Research Institute, Debiganj-5020, Panchagarh, Bangladesh
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Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan
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USDA-ARS Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(6), 2129; https://doi.org/10.3390/ijms21062129
Received: 5 March 2020 / Revised: 13 March 2020 / Accepted: 16 March 2020 / Published: 20 March 2020
(This article belongs to the Section Molecular Genetics and Genomics)
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. View Full-Text
Keywords: Aphanomyces euteiches; candidate genes; GBS; GWAS; lentil; linkage disequilibrium (LD); QTL mapping; root rot; SNP Aphanomyces euteiches; candidate genes; GBS; GWAS; lentil; linkage disequilibrium (LD); QTL mapping; root rot; SNP
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MDPI and ACS Style

Ma, Y.; Marzougui, A.; Coyne, C.J.; Sankaran, S.; Main, D.; Porter, L.D.; Mugabe, D.; Smitchger, J.A.; Zhang, C.; Amin, M.N.; Rasheed, N.; Ficklin, S.P.; McGee, R.J. Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study. Int. J. Mol. Sci. 2020, 21, 2129. https://doi.org/10.3390/ijms21062129

AMA Style

Ma Y, Marzougui A, Coyne CJ, Sankaran S, Main D, Porter LD, Mugabe D, Smitchger JA, Zhang C, Amin MN, Rasheed N, Ficklin SP, McGee RJ. Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study. International Journal of Molecular Sciences. 2020; 21(6):2129. https://doi.org/10.3390/ijms21062129

Chicago/Turabian Style

Ma, Yu, Afef Marzougui, Clarice J. Coyne, Sindhuja Sankaran, Dorrie Main, Lyndon D. Porter, Deus Mugabe, Jamin A. Smitchger, Chongyuan Zhang, Md. N. Amin, Naser Rasheed, Stephen P. Ficklin, and Rebecca J. McGee 2020. "Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study" International Journal of Molecular Sciences 21, no. 6: 2129. https://doi.org/10.3390/ijms21062129

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