Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions
Open Access
- 20 March 2020
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 15 (3), e0227710
- https://doi.org/10.1371/journal.pone.0227710
Abstract
Phytophthora sojae is one of the costliest soybean pathogens in the US. Quantitative disease resistance (QDR) is a vital part of Phytophthora disease management. In this study, QDR was measured in 478 and 495 plant introductions (PIs) towards P. sojae isolates OH.121 and C2.S1, respectively, in genome-wide association (GWA) analyses to identify genetic markers linked to QDR loci (QDRL). Populations were generated by sampling PIs from the US, the Republic of Korea, and the full collection of PIs maintained by the USDA. Additionally, a meta-analysis of QDRL reported from bi-parental studies was done to compare past and present findings. Twenty-four significant marker-trait associations were identified from the 478 PIs phenotyped with OH.121, and an additional 24 marker-trait associations were identified from the 495 PIs phenotyped with C2.S1. In total, 48 significant markers were distributed across 16 chromosomes and based on linkage analysis, represent a total of 44 QDRL. The majority of QDRL were identified with only one of the two isolates, and only a region on chromosome 13 was consistently identified. Regions on chromosomes 3, 13, and 17 were identified in previous GWA-analyses and were re-identified in this study. Five QDRL co-localized with P. sojae meta-QDRL identified from QDRL reported in previous biparental mapping studies. The remaining regions represent novel QDRL, in the soybean P. sojae pathosystem and were primarily identified in germplasm from the Republic of Korea. Overall, the number of loci identified in this study highlights the complexity of QDR to P. sojae.This publication has 100 references indexed in Scilit:
- Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)BMC Genomics, 2013
- Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841Theoretical and Applied Genetics, 2013
- BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithmsBioinformatics, 2012
- Genome-wide association studies in diverse populationsNature Reviews Genetics, 2010
- Mixed linear model approach adapted for genome-wide association studiesNature Genetics, 2010
- SoyBase, the USDA-ARS soybean genetics and genomics databaseNucleic Acids Research, 2009
- Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in RiceScience, 2009
- Complex genetic networks underlying the defensive system of rice ( Oryza sativa L.) to Xanthomonas oryzae pv. oryzaeProceedings of the National Academy of Sciences of the United States of America, 2006
- A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic PhaseAmerican Journal of Human Genetics, 2006
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004