QTL mapping and GWAS for identification of loci conferring partial resistance to Pythium sylvaticum in soybean ( Glycine
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QTL mapping and GWAS for identification of loci conferring partial resistance to Pythium sylvaticum in soybean (Glycine max (L.) Merr) Feng Lin & Shabir H. Wani & 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
Received: 8 May 2019 / Accepted: 6 May 2020 # Springer Nature B.V. 2020
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-
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11032-020-01133-9) contains supplementary material, which is available to authorized users. F. Lin : P. J. Collins : Z. Wen : W. Li : N. Zhang : A. G. McCoy : Y. Bi : R. Tan : S. Zhang : C. Gu : M. I. Chilvers : D. Wang (*) Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI 48824-1325, USA e-mail: [email protected]
R. Tan e-mail: [email protected] S. Zhang e-mail: [email protected] C. Gu e-mail: [email protected]
F. Lin e-mail: [email protected] P. J. Collins e-mail: [email protected] Z. Wen e-mail: [email protected] W. Li e-mail: [email protected] N. Zhang e-mail: [email protected] A. G. McCoy e-mail: [email protected] Y. Bi e-mail: [email protected]
M. I. Chilvers e-mail: [email protected] S. H. Wani 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 e-mail: [email protected] W. Li College of Agronomy, Agricultural University of Hebei, Baoding, China Y. Bi Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Road, Harbin, China
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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 and q10.2), 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 ( 5% and a missing data rate of < 20% were used for genome-wide association analysis in this study. All of the SNPs were used to estimate the genetic relatedness and correct the
Mol Breeding
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population stratification between individuals by principal component analysis (PCA) using TASSEL 5.0 (Bradbury et al. 2007; Price et al. 2006). Nei’s genetic distance (Nei and Ta
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