Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation

PloS One
Waltram Second RavelombolaSenyu Chen

Abstract

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to...Continue Reading

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Citations

Apr 13, 2021·Frontiers in Plant Science·Ulrike GartnerVivian C Blok

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Datasets Mentioned

BETA
M97305077
M98332108

Methods Mentioned

BETA
Chips
protein folding

Software Mentioned

rrBLUP
kernlab
gBLUP LASSO
GAPIT
TASSEL
BGLR
SAS
gBLUP
R
randomForest

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