Genome wide association study identifies novel single nucleotide polymorphic loci and candidate genes involved in soybean sudden death syndrome resistance

PloS One
Sivakumar SwaminathanMadan K Bhattacharyya

Abstract

Fusarium virguliforme is a soil borne root pathogen that causes sudden death syndrome (SDS) in soybean [Glycine max (L.) Merrill]. Once the fungus invades the root xylem tissues, the pathogen secretes toxins that cause chlorosis and necrosis in foliar tissues leading to defoliation, flower and pod drop and eventually death of plants. Resistance to F. virguliforme in soybean is partial and governed by over 80 quantitative trait loci (QTL). We have conducted genome-wide association study (GWAS) for a group of 254 plant introductions lines using a panel of approximately 30,000 SNPs and identified 19 single nucleotide polymorphic loci (SNPL) that are associated with 14 genomic regions encoding foliar SDS and eight SNPL associated with seven genomic regions for root rot resistance. Of the identified 27 SNPL, six SNPL for foliar SDS resistance and two SNPL for root rot resistance co-mapped to previously identified QTL for SDS resistance. This study identified 13 SNPL associated with eight novel genomic regions containing foliar SDS resistance genes and six SNPL with five novel regions for root-rot resistance. This study identified five genes carrying nonsynonymous mutations: (i) three of which mapped to previously identified QTL for ...Continue Reading

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Citations

Jul 25, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Liuping ZhangShiming Liu
Jun 30, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shiming LiuDeliang Peng

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Datasets Mentioned

BETA
GAU22154.1

Methods Mentioned

BETA
PCA

Software Mentioned

R
R lem4 package
R package
R package car
R package agricolae
R fBasics
Tassel
BEAGLE
genome assessment and prediction integrated tools ( GAPIT )

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