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QTL mapping and GWAS for identification of loci conferring partial resistance to Pythium sylvaticum in soybean (Glycine max (L.) Merr)

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Abstract

Pythium sylvaticum is one of the most prevalent and aggressive Pythium species causing seedling and root rot of soybean. In this study, two recombinant inbred line populations (POP1 and POP2) and a genome-wide association study (GWAS) panel were used for mapping loci conferring partial resistance to P. sylvaticum in soybean using a greenhouse assay. POP1 (“E09014” × “E05226-T”) and POP2 (“E05226-T” × ‘E09088”) each contains 113 and 79 lines, respectively, and all lines were genotyped using the SoySNP6K BeadChip. QTL mapping using composite interval mapping (CIM) identified 5 QTL on soybean chromosomes of 10 (q10.1 andq10.2), 18 (q18.1 and q18.2), and 20 (q20.1), and each QTL explained 9.7–16.6% of phenotypic variation. The GWAS panel consisted of 214 soybean lines and was genotyped using the SoySNP50K BeadChip. A total of 7 significant SNP markers were identified on chromosomes 10, 18, and 20. Markers Gm10_42965189_G_T, Gm10_42975806_T_C, and Gm10_43004105_A_C were closely linked with q10.1 (<50 kb). Marker Gm18_7898429_A_C was co-localized with q18.2 and was located within the coding region of Glyma.18 g081700. Further investigation revealed that Gm20_2245263_G_A co-localized with qRRW20, a QTL previously identified for partial resistance to P. irregulare. All of the QTL identified in this study can be incorporated into soybean lines to improve enduring partial resistance to Pythium diseases using marker assisted breeding.

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Acknowledgment

We thank Janette Jacobs, Randy Laurenz, John Boyse, Robert Stoutenburg, and Dr. Wenyan Du for the help in conducting this research. We are also thankful to University Grants Commission (UGC), India, for providing Raman Postdoctoral Fellowship (5–20/2016(IC)) to SHW.

Funding

We thank the funding support from Michigan Soybean Promotion Committee, USDA National Institute of Food and Agriculture (Hatch project 1011788) and AgBioResearch at Michigan State University (Project No. MICL02013).

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Authors and Affiliations

  1. Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA

    Feng Lin, Paul J. Collins, Zixiang Wen, Wenlong Li, Na Zhang, Austin G. McCoy, Yingdong Bi, Ruijuan Tan, Shichen Zhang, Cuihua Gu, Martin I. Chilvers & Dechun Wang

  2. Mountain Research Centre for Field Crops, Khudwani, Anantnag-192 101, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu, Jammu and Kashmir, India

    Shabir H. Wani

  3. College of Agronomy, Agricultural University of Hebei, Baoding, China

    Wenlong Li

  4. Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Road, Harbin, China

    Yingdong Bi

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  1. Feng Lin
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Supplementary Figure 1

Population structures of soybean lines in GWAS panel. A: Neighbor-joining tree of 214 soybean accessions. B: PCA plots of the first two components of 214 soybean accessions. Subgroup 1 (Coser et al. 2017) contained mainly landraces from China, Japan, and Korea. Subgroup 2 (green) contained improved lines from Michigan State University and other places in the United States. Subgroup 3 (blue) mainly consisted of improved lines from Michigan State University (Supplementary Table 1). (JPG 138 kb)

Supplementary Figure 2

Genome-wide average LD decay estimated in GWAS panel. The position of euchromatin and heterochromatin of each chromosome were based on Wm82.a2 (Gmax2.0). The LD decay rate indicated by r2 was dropped to 0.2 at 354 kb and 7500 kb in euchromatic and heterochromatic regions, respectively. This result was similar with the mean LD estimated by Hwang et al. (2014) using the same method (360 kb and 9600 kb in euchromatic and heterochromatic regions, respectively). On whole chromosome level, r2 was dropped to half its maximum value at 395 kb, which was similar with the LD decay of improved lines (370 kb) reported by Wen et al. (2018) (JPG 38 kb)

Supplementary Figure 3

Genome-wide association study of partial resistance to P. sylvaticum in soybean. A: Manhattan plots for RRW-BLUP in GWAS panel. The -log10(P) values from a genome-wide scan were plotted against the position on each of the 20 chromosomes. The horizontal red line indicated the genome-wide significance threshold (FDR < 0.05).B: Quantile-quantile plot in the GWAS panel. (JPG 145 kb)

Supplementary Table 1

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Lin, F., Wani, S.H., Collins, P.J. et al. QTL mapping and GWAS for identification of loci conferring partial resistance to Pythium sylvaticum in soybean (Glycine max (L.) Merr). Mol Breeding 40, 54 (2020). https://doi.org/10.1007/s11032-020-01133-9

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