Abstract
Key message
A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes.
Abstract
The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.
Similar content being viewed by others
References
Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA, Miedaner T, Würschum T (2011) Detection of segregation distortion loci in triticale (× Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genom 12:380
Bachlava E, Radwan OE, Abratti G, Tang S, Gao W, Heesacker AF, Bazzalo ME, Zambelli A, Leon AJ, Knapp SJ (2011) Downy mildew (Pl 8 and Pl 14 ) and rust (R Adv ) resistance genes reside in close proximity to tandemly duplicated clusters of non-TIR-like NBS-LRR-encoding genes on sunflower chromosomes 1 and 13. Theor Appl Genet 122:1211–1221
Badouin H, Gouzy J, Grassa CJ, Murat F, Evan Staton S, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage M, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB (2017) The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature. https://doi.org/10.1038/nature22380
Berry ST, Leon AJ, Hanfrey CC, Challis P, Burkholz A, Barnes SR, Rufener GK, Lee M, Caligari PD (1995) Molecular marker analysis of Helianthus annuus L. 2. Construction of an RFLP linkage map for cultivated sunflower. Theor Appl Genet 91:195–199
Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. Genes Genomes Genet 2:721–729
Bulos M, Vergani PN, Altieri E (2014) Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower. Breed Sci 64:206–212
de Romano AB, Romano C, Bulos M, Altieri E, Sala C (2010) A new gene for resistance to downy mildew in sunflower. In: Proceedings of int symposium “Sunflower breeding on resistance to diseases”, Krasnodar, Russia, June 23–24
Deschamps S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology 1:460–483
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Faris JD, Laddomada B, Gill BS (1998) Molecular mapping of segregation distortion loci in Aegilops tauschii. Genetics 149:319–327
Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823–835
Franchel J, Bouzidi MF, Bronner G, Vear F, Nicolas P, Mouzeyar S (2013) Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara halstedii race 300. Theor Appl Genet 126:359–367
Friskop AJ, Gulya TJ, Halley SA, Schatz BG, Schaefer JP, Jordahl JG, Meyer SM, Misek KW, Hendrickson P, Markell SG (2015a) Effect of fungicide and timing of application on management of sunflower rust. Plant Dis 99:1210–1215
Friskop AJ, Gulya TJ, Harveson RM, Humann RM, Acevedo M, Markell SG (2015b) Phenotypic diversity of Puccinia helianthi (sunflower rust) in the United States from 2011 to 2012. Plant Dis 99:1604–1609
Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S (2017) Adapting genotyping-by-sequencing for rice F2 populations. Genes Genomes Genet 7:881–893
Gedil MA, Wye C, Berry S, Segers B, Peleman J, Jones R, Leon A, Slabaugh MB, Knapp SJ (2001) An integrated restriction fragment length polymorphism-amplified fragment length polymorphism linkage map for cultivated sunflower. Genome 44:213–221
Gentzbittel L, Vear F, Zhang YX, Berville A, Nicolas P (1995) Development of a consensus linkage RFLP map of cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 90:1079–1086
Gong L, Gulya TJ, Markell SG, Hulke BS, Qi LL (2013a) Genetic mapping of rust resistance genes in confection sunflower line HA-R6 and oilseed line RHA 397. Theor Appl Genet 126:2039–2049
Gong L, Hulke BS, Gulya TJ, Markell SG, Qi LL (2013b) Molecular tagging of a novel rust resistance gene R 12 in sunflower (Helianthus annuus L.). Theor Appl Genet 126:93–99
Goulter KC (1990) Breeding of a rust differential sunflower line. In: Proceedings of the 8th Australian sunflower association workshop. Australian Sunflower association, Toowoomba, pp 120–124
Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barely. Theor Appl Genet 83:250–256
Gulya TJ (1985) Registration of five disease-resistant sunflower germplasms. Crop Sci 25:719–720
Gulya TJ, Markell S (2009) Sunflower rust status-2008 race frequency across the midwest and resistance among commercial hybrids. http://www.sunflowernsa.com/uploads/15/gulya_ruststatus_09.pdf. Accessed 19 Mar 2018
Gulya TJ, Venette R, Venette JR, Lamey HA (1990) Sunflower rust. NDSU Ext Ser Bull, Fargo, p 1557. https://www.ag.ndsu.edu/pubs/plantsci/rowcrops/pp1557.pdf . Accessed 19 Mar 2018
He J, Zhao X, Laroche A, Lu ZX, Liu HK, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484
Hu J, Vick BS (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 21:289–294
Hulke BS, Grassa CJ, Bowers JE, Burke JM, Qi L, Talukder ZI, Rieseberg LH (2015) A unified single nucleotide polymorphism map of sunflower (Helianthus annuus L.) derived from current genomic resources. Crop Sci 55:1696–1702
Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L (2015) Heterozygous mapping strategy (HetMappS) for high resolution genotyping-by-sequencing markers: a case study in grapevine. PLoS One 10:e0134880
Jan CC, Vick BA, Miller JF, Kahler AL, Butler ET III (1998) Construction of an RFLP linkage map for cultivated sunflower. Theor Appl Genet 96:15–22
Jan CC, Quresh Z, Gulya TJ (2004) Registration of seven rust resistance sunflower germplasms. Crop Sci 44:1887–1888
Jupe F, Witek K, Verweij W, Sliwka J, Leighton P, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Milne L, Hein I, Jones JDG (2013) Resistance gene enrichment sequencing (RenSeq) enables re-annotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J 76:530–540
Kong GA, Goulter KC, Kochman JK, Thompson SM (1999) Evolution of pathotypes of Puccinia helianthi on sunflower in Australia. Australas Plant Pathol 28:320–332
Lambrides CJ, Miller JF (1994) Inheritance of rust resistance in a source of MC29 sunflower germplasm. Crop Sci 34:1225–1230
Lawson RR, Goulter KC, Henry RJ, Kong GA, Kochman JK (1998) Marker-assisted selection for two rust resistance genes in sunflower. Mol Breed 4:227–234
Lee J, Izzah NK, Choi BS, Joh HJ, Lee SC, Perumal S, Seo J, Ahn K, Jo EJ, Choi GJ, Nou IS, Yu Y, Yang TJ (2016) Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res 23:29–41
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760
Livaja M, Unterseer S, Erath W, Lehermeier C, Wieseke R, Plieske J, Polley A, Luerßen H, Wieckhorst S, Mascher M, Hahn V, Ouzunova M, Schön C-C, Ganal MW (2016) Diversity analysis and genomic prediction of Sclerotinia resistance in sunflower using a new 25 K SNP genotyping array. Theor Appl Genet 129:317–329
Long YM, Chao WS, Ma GJ, Xu SS, Qi LL (2017) An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theor Appl Genet 130:597–607
Ma GJ, Seiler GJ, Markell SG, Gulya TJ, Qi LL (2015) Registration of two double rust resistant germplasms, HA-R12 and HA-R13 for confection sunflower. J Plant Regist 10:69–74
Ma GJ, Markell SG, Song QJ, Qi LL (2017) Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.). Theor Appl Genet 130:1519–1529
Markell S, Gulya T, McKay K, Hutter M, Hollingsworth C, Ulstad V, Koch R, Knudsvig A (2009) Widespread occurrence of the aecial stage of sunflower rust caused by Puccinia helianthi in North Dakota and Minnesota in 2008. Plant Dis 93:668–669
Miah MAJ, Sackston WE (1970) Genetics of host-pathogen interaction in sunflower. Phytoprotection 51:1–16
Miller JF (1992) Five oilseed sunflower germplasm restorer lines (RHA373-377) and two nuclear male-sterile populations (NMS-274 and 801). Crop Sci 35:1289
Miller JF, Gulya TJ (1988) Registration of six downy mildew resistant sunflower germplasm lines. Crop Sci 28:1040–1041
Miller JF, Gulya TJ (1997) Registration of eight maintainer (HA 393, HA 394 and HA 402 to HA 407) and seven restorer (RHA 395 to RHA 401) sunflower germplasm lines. Crop Sci 37:1988–1989
Miller JF, Gulya TJ (2001) Registration of three rust resistant sunflower germplasm populations. Crop Sci 41:601
Miller JF, Rodriguez RH, Gulya TJ (1988) Evaluation of genetic materials for inheritance of resistance to Race 4 rust in sunflower. In: Proceedings of the 12th international sunflower conference, Novi Sad, Yugoslavia. International Sunflower Association, Paris, pp 361–365
Moreno PS, de Romano AB, Romamo MC, Verganl P, Sposaro M, Bulos M, Altieri E, Ramos ML, Sala CA (2012) A survey of physiological races of Puccinia helianthi in Argentina. In: Proceedings of the 18th international sunflower conference, Mar del Plata and Balcarce, Argentina, pp 278–281
Mouzeyar S, Roeckel-Drevet P, Gentzbittel L, Philippon J, de Labrouhe DT, Vear F, Nicolas P (1995) RFLP and RAPD mapping of the sunflower Pl 1 locus for resistance to Plasmopara halstedii race 1. Theor Appl Genet 91:733–737
Moyle LC, Graham EB (2006) Genome-wide associations between hybrid sterility QTL and marker transmission ratio distortion. Mol Biol Evol 23:973–980
Myburg AA, Vogl C, Griffen AR, Sederoff RR, Whetten RW (2004) Genetics of postzygotic isolation in Eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus. Genetics 166:1405–1418
Paterson AH, Lander ES, Hewitt J, Peterson S, Lincoln SE (1988) Resolution of quantitative traits into Mendelian factors by using a complete map of restriction fragment length polymorphism. Nature 335:721–726
Pereira MG, Lee M, Bramel-Cox P, Woodman W, Doebley J, Whitkus R (1994) Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 37:236–243
Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92–102
Putt ED, Sackston WE (1963) Studies on sunflower rust. IV. Two genes, R 1 and R 2 for resistance in the host. Can J Plant Sci 43:490–496
Qi LL, Seiler GJ (2013) Registration of a male fertility restorer oilseed sunflower germplasm, HA-R9, resistant to sunflower rust. J Plant Regist 7:353–357
Qi LL, Gulya TJ, Seiler GJ, Hulke BS, Vick BA (2011a) Identification of resistance to new virulent races of rust in sunflowers and validation of DNA markers in the gene pool. Phytopathology 101:241–249
Qi LL, Hulke BS, Vick BA, Gulya TJ (2011b) Molecular mapping of the rust resistance gene R 4 to a large NBS-LRR cluster on linkage group 13 of sunflower. Theor Appl Genet 123:351–358
Qi LL, Gulya TJ, Hulke BS, Vick BA (2012a) Chromosome location, DNA markers and rust resistance of the sunflower gene R 5 . Mol Breed 30:745–756
Qi LL, Seiler GJ, Hulke BS, Vick BA, Gulya TJ (2012b) Genetics and mapping of the R 11 gene conferring resistance to recently emerged rust races, tightly linked to male fertility restoration, in sunflower (Helianthus annuus L.). Theor Appl Genet 125:921–932
Qi LL, Long YM, Jan CC, Ma GJ, Gulya TJ (2015a) Pl 17 is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 128:757–767
Qi LL, Long YM, Ma GJ, Markell SG (2015b) 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 Breed 35:196
Qi LL, Ma GJ, Long YM, Hulke BS, Gong L, Markell SG (2015c) Relocation of a rust resistance gene R 2 and its marker-assisted gene pyramiding in confection sunflower (Helianthus annuus L.). Theor Appl Genet 128:477–488
Radwan O (2010) Isolation and expression of an NBS-LRR protein-encoding resistance gene candidate that segregates with a rust resistance gene in sunflower. J Phytopathol 158:433–443
Radwan O, Bouzidi MF, Vear F, Philipon J, de Labrouhe DT, Nicolas P, Mouzeyar S (2003) Identification of non-TIR-NBS-LRR markers linked to the Pl 5 /Pl 8 locus for resistance to downy mildew in sunflower. Theor Appl Genet 106:1438–1446
Rieseberg LH, Choi HC, Chan R, Spore C (1993) Genomic map of a diploid hybrid species. Heredity 70:285–293
Roeckel-Drevet P, Gagne G, Mouzeyar S, Gentzbittel L, Philippon J, Nicolas P, de Labrouhe DT, Vear F (1996) Colocation of downy mildew (Plasmopara halstedii) resistance genes in sunflower (Helianthus annuus L.). Euphytica 91:225–228
Sendall BC, Kong GA, Goulter KC, Aitken EAB, Thompson SM, Mitchell JHM, Kochman JK, Lawson W, Shatte T, Gulya TJ (2006) Diversity in the sunflower: Puccinia helianthi pathosystem in Australia. Australas Plant Pathol 35:657–670
Slabaugh MB, Yu JK, Tang S, Heesacker A, Hu X, Lu G, Bidney D, Han F, Knapp SJ (2003) Haplotyping and mapping a large cluster of downy mildew resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms. Plant Biotechnol J 1:167–185
Steuernagel B, Periyannan SK, Hernández-Pinzón I, Witek K, Rouse MN, Yu G, Hatta A, Ayliffe M, Bariana H, Jones JDG, Lagudah ES, Wulff BBH (2016) Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat Biotechnol 34:652–655
Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song QJ, Schultz Q, Qi LL (2014) A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R 12 . PLoS One 9:e98628
Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124–1136
Tang S, Kishore VK, Knapp SJ (2003) PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower. Theor Appl Genet 107:6–19
Van Ooijen JW (2006) JoinMap ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen
Vear F, Gentzbittel L, Philippon J, Mouzeyar S, Mestries E, Roeckel-Drevet P, de Labroube DT, Nicolas P (1997) The genetics of resistance to five races of downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.). Theor Appl Genet 95:584–589
Yamagishi M, Takeuchi Y, Tanaka I, Kono I, Murai K, Yano M (2010) Segregation distortion in F2 and doubled haploid populations of temperate japonica rice. J Genet 89:237–241
Yang SM, Antonelli EF, Luciano A, Luciani ND (1986) Reactions of Argentine and Australian sunflower rust differentials to four North American cultures of Puccinia helianthi from North Dakota. Plant Dis 70:883–886
Yang SM, Dowler WM, Luciano A (1989) Gene Pu 6 : a new gene in sunflower for resistance to Puccinia helianthi. Phytopathology 79:474–477
Yu JK, Tang S, Slabaugh MB, Heesacker A, Cole G, Herring M, Soper J, Han F, Chu WC, Webb DM, Thompson L, Edwards KJ, Berry S, Leon AJ, Grondona M, Olungu C, Maes N, Knapp SJ (2003) Towards a saturated molecular genetic linkage map for cultivated sunflower. Crop Sci 43:367–387
Yue B, Vick BA, Cai X, Hu J (2010) Genetic mapping for the Rf 1 (fertility restoration) gene in sunflower (Helianthus annuus L.) by SSR and TRAP markers. Plant Breed 129:24–28
Zamir D, Tadmor Y (1986) Unequal segregation of nuclear genes in plants. Bot Gaz 147:355–358
Zhang M, Liu Z, Jan CC (2016) Molecular mapping of a rust resistance gene R 14 in cultivated sunflower line PH3. Mol Breed 36:32
Zhang ZW, Ma GJ, Zhao J, Markell SG, Qi LL (2017) Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl 19 in confection sunflower (Helianthus annuus L.). Theor Appl Genet 130:29–39
Zhou W, Tang Z, Hou J, Yin T (2015) Genetic map construction and detection of genetic loci underlying segregation distortion in an intraspecific cross of Populus deltoids. PLoS One 10:e0126077
Acknowledgements
We thank Drs. Gerald Seiler and Yueqiang Leng 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 14-SCBGP-ND-0038 and the USDA-ARS CRIS Project No. 3060-21000-039-00D. USDA is an equal opportunity provider and employer.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical standards
The experiments were performed in compliment with the current laws of United States of America.
Additional information
Communicated by Chris Carolin Schön.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ma, G.J., Song, Q.J., Markell, S.G. et al. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.). Theor Appl Genet 131, 1423–1432 (2018). https://doi.org/10.1007/s00122-018-3087-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-018-3087-5