In silico genome-wide discovery and characterization of SSRs and SNPs in powdery mildew disease resistant and susceptible cultivated and wild Helianthus species

*Article not assigned to an issue yet

,


Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Website:www.vegetosindia.org
Pub Email: contact@vegetosindia.org
Doi: 10.1007/s42535-022-00418-y
First Page: 0
Last Page: 0
Views: 143


Keywords: Powdery mildew, Sunflower, Genome-wide transcript, SSRs, SNPs, Linkage group


Abstract


In silico approach was applied for the discovery and characterization of SSRs and SNP markers. RNA sequencing was applied to generate large scale genome-wide transcripts associated with powdery mildew disease of sunflower (Helianthus annuus L.). The sunflower materials from which the transcripts were generated comprised one susceptible (PS 2023B), two cultivated resistant accessions (TX16R, ID 25) and three wild species (H. praecox [1823], H. niveus [1452], and H. debilis [DEB-689]). For the susceptible and resistant accessions, control (no infection) and pooled (with infection) samples were created based on which the transcripts were developed. A total of 123,058 SSRs were discovered from the assembled transcriptome of each accession. Out of this total obtained SSRs, 112,326 were classified as perfect and 10,732 as compound SSRs. The percent contribution of compound SSRs in susceptible and in all the tolerant accessions ranged from 8.51 to 9.15%. There was no prominent or significant difference in the number of SSR motifs, comparing the susceptible and resistant accessions tested. A significantly higher CG motif was observed in the susceptible accessions than in the resistant accessions. We, therefore, speculate that the CG motif might play a vital role in the susceptibility of sunflower to powdery mildew disease. Similarly, the percentage of GC motif was found to be significantly higher in the resistant accessions. It is likely that the GC motifs might be involved in the induction of resistance to powdery mildew in sunflower plants. Trinucleotide motif based predictions resulted in significantly higher levels of the following amino acids in the susceptible accession: Ile, Lys, Met, Phe, Pro, Thr and Val. It is presumed that these amino acids might be involved in the vulnerability to the powdery mildew disease in 2023B. In total 35,390 Single Nucleotide Polymorphisms (SNPs) loci were identified that were distributed on all 17 linkage groups with the average resolution of 443.2 Kb/SNP. Linkage group 10 had the highest localized SNPs (3631) with an average of 576 Kb/ SNP and 7 had least (781) with average of 441 Kb/ SNP. Most of the SNPs identified were observed to be transition mutations with mainly A/G type substitutions. The discovered markers will prove useful after wet laboratory studies for screening and marker assisted breeding for powdery mildew resistance in sunflower.


Powdery mildew, Sunflower, Genome-wide transcript, SSRs, SNPs, Linkage group


References


Anonymous (1994) American Phytopathological Society Committee on the standardization of common names for plant diseases: common names for plant diseases. APS Press, St. Paul, pp 147–149


Anonymous (2018) Annual report, sunflower, 2017–18. ICAR-India Institute of Oilseeds Research, Rajendranangar, Hyderabad-500 030


Bachlava E, Taylor CA, Tang S, Bowers JE, Mandel JR, Burke JM, Knapp SJ (2012) SNP discovery and development of a high-density genotyping array for sunflower. PLoS ONE 7:e29814. https://doi.org/10.1371/journal.pone.002981


Bacolla A, Larson E, Collins JR, Li J, Milosavljevic A (2008) Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res 18:1545–1553


Baiswar P, Kumar R, Chandra S, Ngachan SV (2008) First report of powdery mildew on Mexican sunflower in India. New Dis Rep 18:8


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. G2 Genes Genom Genet 2:721–729. https://doi.org/10.1534/g3.112.002659


Braun U (1995) The powdery mildews (Erysiphales) of Europe. G. Fisher Verlag, Jena, pp 1–337


Brunel D (1994) A microsatellite marker in Helianthus annuus L. Plant Mol Biol 24:397–400


Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854


Celik I, Bodur S, Frary A, Doganlar S (2016) Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach. Mol Breed. https://doi.org/10.1007/s11032-016-0558-8


Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM (2008) A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus L.). Plant Cell 20(11):2931–2945


Chen RS, Chu C, Cheng CW, Chen WY, Tsay JG (2008) Differentiation of two powdery mildews of sunflower (Helianthus annuus) by PCR-mediated method based on ITS sequence. Eur J Plant Pathol 121:1–8


Choudhari AK, Ghodke MK, Dudhe MY (2022) Identification of potential parents and hybrids resistant to Plasmopara halstedii race-100 in sunflower for the semi-arid dry land environments of India. Vegetos. https://doi.org/10.1007/s42535-022-00382-7


Chu Y, Corey DR (2012) RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic Acid Ther 22(4):271–274. https://doi.org/10.1089/nat.2012.0367.PMC3426205


Dehemer KJ, Friedt W (1998) Evaluation of different microsatellite motifs for analyzing genetic relationships in cultivated sunflower (Helianthus annuus L.). Plant Breed 1:39–42


DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491–498. https://doi.org/10.1038/ng.806


Dudhe MY, Sujatha M, Meena HP, Alivelu K, Ghodke MK, Shadakshari YG, Tyagi RK, Radhamani K, Ranganatha ARG, Varaprasad KS, Reddy AV (2018) Germplasm catalogue of sunflower (Helianthus annuus L), vol 1. ICAR-Indian Institute of Oilseeds Research, Hyderabad


Fang HC (1973) Powdery mildew of sunflower in Taiwan. Plant Prot Bull (taiwan) 15:5–12


Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652


Gulya TJ, Woods DM, Bell R, Mancl MK (1991) Diseases of sunflower in California. Plant Dis 75:572–574


Gulya T J, Rashid KY, Masirevic SM (1997) Sunflower diseases, Sunflower technology and production. Agron Monogr 35, ASA, CSSA, and SSSA, Madison, WI, pp 21–65


Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512


Haddad LA, Parra C, Pena SD (1998) Characterization and mapping of four novel human expressed polymorphic trinucleotide microsatellites. Genetoics 223:369–374


Heesacker A, Kishore VK, Gao WX, Tang SX, Kolkman JM, Gingle A, Matvienko M, Kozik A, Michelmore RM, Lai Z, Rieseberg LH, Knapp SJ (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 117:1021–1029


Hirata T, Takamatsu S (1996) Nucleotide sequence diversity of rDNA internal transcribed spacers extracted from conidia and cleistothecia of several powdery mildew fungi. Mycoscience 37:283–288


Jacob J, Sujatha M, Varaprasad KS (2016) Screening of cultivated and wild Helianthus species reveals herbicide tolerance in wild sunflowers and allelic variation at Ahasl1 (acetohydroxy acid synthase 1 large subunit) locus. Plant Genet Resour 1:1–9


Jan CC, Chandler JM (1985) Transfer of powdery mildew resistance from Helianthus debilis Nutt. into cultivated sunflower (H. annuus L.). Crop Sci 25:664–666


Jan CC, Chandler JM (1988) Registration of powdery mildew resistant sunflower germplasm pool, PM1. Crop Sci 28:1040


Kiani SP, Grieu P, Maury P, Hewezi T, Gentzbittel L, Sarrafi A (2007) Genetic variability for physiological traits under drought conditions and differential expression of water stress-associated genes in sunflower (Helianthus annuus L.). Theor Appl Genet 114(2):193–207


Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998


Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucl Acids Res 21:1111–1115


Lai Z, Livingstone K, Zou Y, Church SA, Knapp SJ, Andrews J, Rieseberg LH (2005) Identification and mapping of SNPs from ESTs in sunflower. Theor Appl Genet 111:1532–1544. https://doi.org/10.1007/s00122-005-0082-4


Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923


Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21):2987–2993


Lindblad-Toh K, Friedman N, Regev A (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29:644–652


Liu Z, Zhang L, Ma GJ, Seiler GJ, Jan CC, Qi LL (2018) Molecular mapping of the downy mildew and rust resistance genes in a sunflower germplasm line TX16R. Mol Breed 39:19. https://doi.org/10.1007/s11032-018-0921-z


Livaja M, Unterseer S, Erath W, Lehermeier C, Wieseke R, Plieske J, Polley A, Luerßen H, Wieckhorst S, Mascher M, Hahn V, Ouzunova M, SchonGanal CCMW (2016) Diversity analysis and genomic prediction of Sclerotinia resistance in sunflower using a new 25 K SNP genotyping array. Theor Appl Genet 129(2):317–329. https://doi.org/10.1007/s00122-015-2629-3


Madsen BE, Villesen P, Wiuf C (2008) Short tandem repeats in human exons: a target for disease mutations. BMC Genom 9:410


Maher BS, Vladimirov VI, Latendresse SJ, Thiselton DL, McNamee R, Kang M, Bigdeli TB, Chen X, Riley BP, Hettema JM, Chilcoat H, Heidbreder C, Muglia P, Murrelle EL, Dick DM, Aliev F, Agrawal A, Edenberg HJ, Kramer J, Nurnberger J, Tischfield JA, Devlin B, Ferrell RE, Kirillova GP, Tarter RE, Kendler KS, Vanyukov MM (2011) The AVPR1A Gene and substance use disorders: association, replication, and functional evidence. Biol Psychiatry 70:519–527


Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads 17. Bnet Education Minnesota, pp 10–12


Mishra RK, Gangadhar BH, Yu JW, Kim DH, Park SW (2011) Development and characterization of expressed sequence tags based SSR markers in madagascar periwinkle (Catharanthus roseus) and their transferability in other medicinal plants. Plant Omics 4(3):154–162


Paniego N, Echaide M, Munoz M, Fernandez L, Torales S, Faccio P, Fuxan I, Carrera M, Zandomeni R, Suarez EY, Hopp HE (2002) Microsatellite isolation and characterization in sunflower (Helianthus annuus L.). Genome 45:34–43


Portis E, Portis F, Valente L, Moglia A, Barchi L, Lanteri S, Acquadro A (2016) A Genome-wide survey of the microsatellite content of the globe artichoke genome and the development of a web-based database. PLoS ONE 11:e0162841


Reddy KP, Rao SC, Kirti PB, Sujatha M (2013) Development of a scoring scale for powdery mildew (Golovanomyces cichoracearum (DC.) V.P. Heluta) disease and identification of resistance sources in cultivated and wild sunflowers. Euphytica 190:385–399


Reddy KP, Yadav P, Dandu K, Soni PK, Rao CS, Kirti PB, Sujatha M (2022) Host defense responses during powdery mildew (Golovinomyces latisporus comb. nov.) infection in sunflower (Helianthus annuus L.). Trop Plant Pathol. https://doi.org/10.1007/s40858-022-00501-4


Rojas-Barros P, Jan CC, Gulya TJ (2005) Transferring powdery mildew resistance genes from wild Helianthus into cultivated sunflower. In: Proceedings of the 27th sunflower research workshop, Fargo, ND. http://www.sunflowernsa.com/research/research-workshop/documents/Rojas_PowderyMildew_05.pdf


Saliman M, Yang SM, Wilson L (1982) Reaction of Helianthus species to Erysiphe cichoracearum. Plant Dis 66:572–573


Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14


Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8(1):e54603


SreeLekha D, Sujatha M, Ulaganathan K (2019) Mapping of plastid RNA editing sites of Helianthus and identification of differential editing in fungal infected plants. Curr Plant Biol. https://doi.org/10.1016/j.cpb.2019.100109


Sudhakar C, Thippeswamy M, Sivakumar M, Sudhakarbabu O, Dudhe MY (2019) In silico mining of EST-SSRs from the drought tolerant ESTs in safflower. J Proteom Bioinform 12:8. https://doi.org/10.35248/0974-276X.19.12.506


Sujatha M (2012) Breeding for resistance to various biotic stresses in sunflower through wide hybridization and biotechnological tools. In: 18th ISC, Mar del Plata, Argentina, 2012 vol 1, p 170


Sujatha M, Soni PK, Gonela SK (2016) Morphological and molecular characterization of powdery mildew on sunflower (Helianthus annuus L.), alternate hosts and weeds commonly found in and around sunflower fields in India. Phytoparasitica 44:353–367


Sujatha M, Ulaganathan K, DivyaBhanu B, Soni PK (2018) RNA-Seq data of control and powdery mildew pathogen (Golovinomycesorontii) treated transcriptomes of Helianthus niveus. Data Brief (elsevier) 17:210–217


Takamatsu S, Kano Y (2001) PCR primers useful for nucleotide sequencing of rDNA of the powdery mildew fungi. Mycoscience 42:135–139


Talia P, Nishinakamasu V, Hopp HE, Heinz RA, Paniego N (2010) Genetic mapping of EST-SSRs, SSR and InDels to improve saturation of genomic regions in a previously developed sunflower map. Electron J Biotechnol. https://doi.org/10.2225/vol13-issue6-fulltext-14


Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Lilli Q (2014) A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS ONE 9:e98628. https://doi.org/10.1371/journal.pone.0098628


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


Tsykun T, Rellstab C, Dutech C, Sipos G, Prospero S (2017) Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes. Heredity 119:371–380


Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78. https://doi.org/10.1093/jhered/93.1.77


Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6


Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. https://doi.org/10.1038/nrg2484


Wang J, Pan LQ, Yang Q, Yu S (2010) Development and characterization of EST-SSR markers from NCBI and cDNA library in cultivated peanut (Arachis hypogaea L.). Legume Genom Genet 1(6):30–33


Yang SM, Wei SE, Ge CF, Liang KZ, Wang L (1988) Diseases of cultivated sunflower in Liaoning Province, People’s Republic of China. Plant Dis 72:546


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


Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short- read RNA-Seq data: a comparative study. BMC Bioinform 12(suppl. 14):S2





Pegadaraju V, Nipper R, Hulke B et al (2013) De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genom 14:556. https://doi.org/10.1186/1471-2164-14-556

 


Acknowledgements


The authors thank the Director, ICAR-IIOR, Hyderabad, India for extending all the facilities for carrying out this research work. The financial support of the Department of Science and Technology, Government of India (Project no. SERB/SR/SO/PS/24/2012) to carry out the research is gratefully acknowledged. We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions.


Author Information


Dudhe M. Y.
ICAR-Indian Institute of Oilseeds Research, Hyderabad, India
mangesh.dudhe@icar.gov.in
Mulpuri Sujatha
ICAR-Indian Institute of Oilseeds Research, Hyderabad, India