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Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing

Abstract

Key message

The Mendelian locus conferring resistance to powdery mildew in soybean was precisely mapped using a combination of phenotypic screening, genetic analyses, and high-throughput genome-wide sequencing.

Abstract

Powdery mildew (PMD), caused by the fungus Microsphaera diffusa Cooke & Peck, leads to considerable yield losses in soybean [Glycine max (L.) Merr.] under favourable environmental conditions and can be controlled by identifying germplasm resources with resistance genes. In this study, resistance to M. diffusa among resistant varieties B3, Fudou234, and B13 is mapped as a single Mendelian locus using three mapping populations derived from crossing susceptible with resistant cultivars. The position of the PMD resistance locus in B3 is located between simple sequence repeat (SSR) markers GMES6959 and Satt_393 on chromosome 16, at genetic distances of 7.1 cM and 4.6 cM, respectively. To more finely map the PMD resistance gene, a high-density genetic map was constructed using 248 F8 recombinant inbred lines derived from a cross of Guizao1 × B13. The final map includes 3748 bins and is 3031.9 cM in length, with an average distance of 0.81 cM between adjacent markers. This genotypic analysis resulted in the precise delineation of the B13 PMD resistance locus to a 188.06-kb genomic region on chromosome 16 that harbours 28 genes, including 17 disease resistance (R)-like genes in the reference Williams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed differences in the expression levels of 9 R-like genes between the resistant and susceptible parents. These results provide useful information for marker-assisted breeding and gene cloning for PMD resistance.

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Abbreviations

BSA:

Bulk segregation analysis

CTAB:

Cetyltrimethylammonium bromide

CIM:

Composite interval mapping method

cv.:

Cultivar

Chr.:

Chromosome

GO:

Gene ontology

LOD:

Log-likelihood

MSG:

Multiplexed shotgun genotyping

M. diffusa :

Microsphaera diffusa

PMD:

Powdery mildew

QTL:

Quantitative trait locus

RIL:

Recombinant inbred line

SLAF-seq:

Specific length amplified fragment sequencing

SNP:

Single nucleotide polymorphism

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Acknowledgements

This work was supported by the National Key R&D Program of China (2017YFD0101500); the Science and Technology Projects of Guangzhou City (201804020015); the China Agricultural Research System (CARS-04-PS09); and the Research Project of the State Key Laboratory of Agricultural and Biological Resources Protection and Utilization in Subtropics (4100-M13024).

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Correspondence to Hai Nian.

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Electronic supplementary material

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Supplementary material 1 (PDF 136 kb)

Supplementary material 2 (PDF 34 kb)

Supplementary Fig. 1: Sequencing data statistics of each individual of RIL population. One single plant taken from every line of the 248 F8 RILs population. Horizontal ordinate shows different lines of RILs population, and vertical coordinate shows total numbers of bases (EPS 33645 kb)

Supplementary Fig. 2: SNP distribution on the 20 soybean chromosomes. The x-axis represents the physical positions (Mb) of the soybean chromosome. The y-axis denotes the soybean chromosome (EPS 9711 kb)

Supplementary Fig. 3: The schematic of bins. The x-axis denotes the positions of 20 soybean chromosomes. The y-axis represents the 248 RILs of the Guizao1 × B13 population. Red is Guizao1 genotype, blue is B13 and pale blue is heterozygote genotype (PDF 51 kb)

Supplementary Fig. 4: Twenty linkage groups of the soybean high-density genetic map. The high-density bin linkage map was constructed covering 3032 cM, with an average distance of 0.81 cM between adjacent bins. The bin markers and their locations are shown on the right and left sides, respectively (PDF 256 kb)

Supplementary Fig. 5: The linear analysis of genetic map and physical map (PDF 42 kb)

Supplementary Fig. 6: Results of Rmd-B13 locus analysis using composite Interval Mapping (CIM) method in the F8-derived RILs from a cross of Guizao1 × B13. a The LOD value distribution on the whole genome of the RIL population. b The LOD value distribution on Chr. 16 of the RIL population. c Rmd_B13 is amplified at the site of bin203 on Chr. 16, which explained 78.4% of the phenotypic variance (EPS 115853 kb)

122_2019_3319_MOESM9_ESM.eps

Supplementary Fig. 7: Distribution of predicted candidate genes for PMD resistance on soybean Chr. 16. Twenty-eight genes are annotated in the region of 37,102,014 bp - 37,290,074 bp in Chr. 16 according to the Williams 82 soybean reference genome (GlymaWm82.a2.v1). Among these genes, 17 are found to contain Toll-interleukin receptor (TIR) -nucleotide-binding site (NBS) -leucine-rich repeat (LRR) domains (accessible at http://soybase.org/) (EPS 6093 kb)

122_2019_3319_MOESM10_ESM.eps

Supplementary Fig. 8: The Gene Ontology (GO) enrichment analysis of the candidate genes. a molecular function; b biological process. The AgriGO toolkit was used to do gene ontology (GO) analysis (http://bioinfo.cau.edu.cn/agriGO/) (EPS 195915 kb)

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Jiang, B., Li, M., Cheng, Y. et al. Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing. Theor Appl Genet 132, 1833–1845 (2019). https://doi.org/10.1007/s00122-019-03319-y

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