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

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 foliar SDS resistance and (ii) two mapped to two novel regions containing root rot resistance genes. Of the three genes mapped to QTL for foliar SDS resistance genes, two encode LRR-receptors and third one encodes a novel protein with unknown function. Of the two genes governing root rot resistance, Glyma.01g222900.1 encodes a soybean-specific LEA protein and Glyma.10g058700.1 encodes a heparan-alpha-glucosaminide N-acetyltransferase. In the LEA protein, a conserved serine residue was substituted with asparagine; and in the heparan-alpha-glucosaminide N-acetyltransferase, a conserved histidine residue was substituted with an arginine residue. Such changes are expected to alter functions of these two proteins regulated through phosphorylation. The five genes with nonsynonymous mutations could be considered candidate SDS resistance genes and should be suitable molecular markers for breeding SDS resistance in soybean. The study also reports desirable plant introduction lines and novel genomic regions for enhancing SDS resistance in soybean.

Fig 1. Foliar responses of 254 PI lines to F. virguliforme.

(A) The foliar disease symptoms were scored 35 days following infection with F. virguliforme. Arrows indicate the disease scores of the SDS resistant cultivars, MN1606 and Ripley, and susceptible cultivar, Spencer. Phenotypic evaluation was conducted five times, each with three replications. The values are means of fifteen biological replications. (B) Distribution of foliar SDS scores among the 254 PI that are lines presented in (A).

Fig 2. Root responses of 254 PI lines to F. virguliforme.

(A) The root rot symptoms were scored 37 days following infection with F. virguliforme. Arrows indicate the disease scores of the SDS resistant cultivars, MN1606 and Ripley, and susceptible cultivar, Spencer. Phenotypic evaluation was conducted five times, each with three replications. The values are means of fifteen biological replications. (B) Distribution of root rot symptoms among the 254 PI lines that are presented in (A).

Fig 3. Segregation of foliar and root responses of 25 PI lines F. virguliforme.

(A) Root responses of 25 most foliar SDS resistant PI lines to F. virguliforme. (B) Foliar responses of 25 most root rot resistant PI lines to F. virguliforme. The values are means and standard errors calculated from five independent experiments. The Scott-Knott statistical significance difference of the PI lines are provided in S1 Table.

Fig 4. Manhattan plot of the SNPs associated with the foliar SDS scores of the 254 PI lines.

The − log10 p-values from a genome-wide scan are plotted against the positions of each of the SNPs on 20 chromosomes. The horizontal blue line indicates the genome-wide significance threshold (FDR < 0.05). SNPs in Manhattan plot were placed in kb unit.

Fig 5. Manhattan plot of the SNPs associated with the root rot severities of 254 PI lines.

The − log10 p-values from a genome-wide scan are plotted against the positions of each of the SNPs on 20 chromosomes. The horizontal blue line indicates the genome-wide significance threshold (FDR < 0.05). SNPs in Manhattan plot were placed in kb unit.

Fig 6. The genetic map of the F. virguliforme foliar SDS and root rot resistance SNPL.

Green checked box, foliar SDS SNPL; Pink checked box, root rot SNPL. SNPL are shown with numerical numbers (Tables 1 and 2). Previously identified foliar SDS and root rot resistance QTL are shown with solid green and pink boxes, respectively (S2 Table). The genetic map is generated in centi-Morgan (cM) unit.