Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions

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. OPEN ACCESS Citation: Rolling W, Lake R, Dorrance AE, McHale LK (2020) Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions. PLoS ONE 15(3): e0227710. https:// development, including saturated soils and temperatures around 25˚C [2 -4]. Under these conditions, zoospores of P. sojae chemotactically swim towards soybean roots [5,6]. Successful infection of susceptible plants results in seed rot and damping off at early growth stages, and wilting, stem lesions, and plant death at later growth stages. Genetic resistance is considered the most effective strategy for preventing or reducing the impact of Phytophthora diseases [4,7].Soybean-breeding programs have relied on resistance conferred by single, dominantly inherited Resistance to Phytophthora sojae (Rps)-genes. More than 30 Rps-genes/alleles have been mapped (S1 Table) [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25]. The effectiveness of Rps-mediated resistance is limited as these genes only confer immunity towards specific races of P. sojae. Over time this results in selection within pathogen populations, leading to adaptation [3,4] and limited Rps-gene lifespans of 8-20 years [26]. A recent survey completed in the North Central region of the US demonstrated that none of the deployed Rps-genes confer resistance to all P. sojae isolates, with field populations having complex virule...

Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean

“…Many known Rps genes are not effective towards all populations of P. sojae (Anderson et al., 2012; Costamilan et al., 2013; Dorrance et al., 2016; Kaitany et al., 2001; Ryley et al., 1998; Yan & Nelson, 2019; Yang et al., 2019), yet a wealth of data exits for the resistance reaction of PIs to various isolates with complex pathotypes (Matthiesen et al., 2016; Rolling et al., 2020; USDA GRIN database). Thus, the purpose of our study was to identify novel P. sojae resistance loci via GWA analyses from panels of soybean PIs with available P. sojae reaction data, especially with several isolates of complex pathotypes.…”

“…A total of 429 (Panel 3) and 460 (Panel 4) G. max accessions were phenotyped for resistance against the complex P. sojae isolates, OH.121 and C2.S1, respectively (Rolling et al., 2020). In Panel 3 and Panel 4, 46 and 22 G. max lines showed resistance to OH.121 (10.7%) and C2.S1 (4.8%), respectively (Table 1).…”

“…1a, 1b, 1d, 1k, 2, 3a, 3c, 4, 5, 6, 7, 8) and PT2004 C2.S1 (vir. 1a, 1b, 1c, 1d, 1k, 2, 3a, 3c, 4, 5, 6, 7, 8) (Supplemental Table S2), as described in Rolling et al (2020) by the hypocotyl assay tested in the greenhouse. For GWA analyses, susceptible phenotype was assigned as "0," and resistance phenotype was assigned as "1".…”

“…First, we used 448 G. max and 520 G. soja , known as a good source for genetic improvement in cultivated soybean (Hyten et al., 2006), accessions evaluated with a pool of three P. sojae isolates (Matthiesen et al., 2016). Secondly, we used two panels of 429 and 460 G. max PIs, examined with two highly virulent P. sojae isolates, respectively (Rolling, Schneider, Dorrance, & McHale, 2020). Finally, we collected publicly available data from USDA GRIN on the resistance phenotypes of G. max accessions against twelve races of P. sojae (Dorrance & Schmitthenner, 2000; Kyle, Nickell, Nelson, & Pedersen, 1998; Lohnes, Nickell, & Schmitthenner, 1996).…”

Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies

“…When available, MQTLs can be anchored to a reference genome, and relevant candidate genes could be proposed. A number of studies since 2009 are reported in crops for meta-QTL analysis of resistance against fungi and viruses, in order to propose valuable QTL to perform MAS, in particular in Theobroma cacao [ 78 ], barley [ 79 ], tetraploid cotton [ 80 , 81 ], pea [ 82 ], wheat [ 83 , 84 ], maize [ 85 ], peanut [ 86 ], grapevine [ 87 ], and soybean [ 88 ]. A study carried out in maize on the response to stem borers and storage pests feeding on leaves, stems, and kernels, from geographically diverse environments, pointed out the presence of a total of 104 resistance meta-QTLs from 382 individual QTLs, many of which were involved in several insect species, therefore generating a significant interest for multiple-insect resistance breeding [ 89 ].…”