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Map saturation and SNP marker development for the rust resistance genes (R 4 , R 5 , R 13a , and R 13b ) in sunflower (Helianthus annuus L.)

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Abstract

Sunflower rust, which is incited by the fungus Puccinia helianthi Schwein., is the most common disease in Australia, Argentina, South Africa, and North America. Three independent genes, R 5 , R 4 , and R 13 with two alleles R 13a and R 13b , were discovered in sunflower and are promising sources of resistance to rust. R 5 was previously mapped to linkage group (LG) 2, and R 4 and R 13 were mapped to LG13 of the sunflower genome using simple sequence repeat (SSR) markers. The objective of this study was to finely map R 5 , R 4 , R 13a , and R 13b using newly developed single nucleotide polymorphism (SNP) markers in four F2 populations previously used for SSR mapping. Of the 67 LG2 SNP markers screened, two SNPs, SFW03654 and NSA_000267, flanked R 5 at a genetic distance of 0.6 and 1.2 cM, respectively. This flanking narrowed the genetic interval containing R 5 from 5.1 to 1.8 cM in length. A total of 69 LG13 SNP markers were analyzed in the R 4 , R 13a , and R 13b populations. In the R 4 consensus map, the gene R 4 was flanked by seven SNP loci; three co-segregating SNPs are on one side (0.7 cM proximal) and four on the other side (0.6 cM distal). Similarly, SNP markers that are tightly linked to both R 13a and R 13b were identified. R 13a was flanked by SNP markers at genetic distances of 0.4 and 0.2 cM. The SNP SFW00757 co-segregated with R 13b , and another three co-segregating SNPs were 2.4 cM proximal to R 13b . A total of 368 F2 plants from the cross between a resistant BC3F2 plant carrying R 5 with HA-R6 carrying R 13a were first screened by SSR markers to identify “double-resistant” lines. Twelve F2 plants were identified to be homozygous for a combination of R 5 and R 13a , which was further confirmed with additional SNP markers developed in the present study. The double-resistant line developed in this study may provide a source of durable resistance to manage rust in confection sunflower production and will help mitigate selection pressure on each gene by the pathogen.

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Acknowledgments

The authors would like to thank Dr. Loren Rieseberg for providing access to the Sunflower Genome Data Repository. We also thank Drs. Xiwen Cai and Hongxia Wang for critical review of the manuscript, and Angelia Hogness for technical assistance. This project was supported by the USDA-AMS Specialty Crop Block Grant Program 12-25-B-1480, and the USDA-ARS CRIS Project No. 5442-21000-039-00D. Mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

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  1. USDA- Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA

    L. L. Qi

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Y. M. Long

  3. Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA

    G. J. Ma & S. G. Markell

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11032_2015_380_MOESM7_ESM.tif

Supplementary material 7 Fig. S1 PCR amplification of markers SFW03564-R 5 (a) and ZVG61-R 13a (b) in parental lines, HA 89, CONFSCLB1, HA-R2, and HA-R6, and 12 double-resistant F2 plants. The double-resistant F2 plants show HA-R2 (R 5 ) and HA-R6 (R 13a ) alleles in a and b, respectively. (TIFF 382 kb)

11032_2015_380_MOESM8_ESM.tif

Supplementary material 8 Fig. S2 Reliability of selection using single and flanking markers (assuming no crossover interference). The recombination frequency between the target locus and marker A is approximately 5 % (5 cM). Therefore, recombination may occur between the target locus and marker in approximately 5 % of the progeny. The recombination frequency between the target locus and marker B is approximately 4 % (4 cM). The chance of recombination occurring between both marker A and marker B (i.e., double crossover) is much lower than for single markers (approx. 0.4 %). Therefore, the reliability of selection is much greater when flanking markers are used. Adapted from Bertrand et al. (2008). (TIFF 684 kb)

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Qi, L.L., Long, Y.M., Ma, G.J. et al. Map saturation and SNP marker development for the rust resistance genes (R 4 , R 5 , R 13a , and R 13b ) in sunflower (Helianthus annuus L.). Mol Breeding 35, 196 (2015). https://doi.org/10.1007/s11032-015-0380-8

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