Genetic Structure and Marker-Trait Associations in Parental Lines of Sunflower (Helianthus annuus L.)

Subject Areas : Genetics

Hossein Zeinalzadeh-Tabrizi ¹ , Arash Hosseinpour ² , Mehdi Ghaffari ³ , Kamil Haliloglu ⁴

1 - Crops and Horticultural Science Research Department, Ardabil Agricultural and Natural Resources Research and Education Center, AREEO, Ardabil, Iran
2 - Crops and Horticultural Science Research Department Ardabil Agricultural and Natural Resources Research and Education Center, AREEO, Ardabil, Iran
3 - Department of Oilseed Crops, Seed and Plant Improvement Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
4 - Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum, Turkey

Received: 2021-06-17 Accepted : 2021-10-16 Published : 2022-01-01

Keywords: Sunflower, SSR, trap, Association analysis, Bayesian clustering,

Abstract :

Association mapping is a reliable tool to detect the association between phenotypic and genotypic data through linkage disequilibrium. In the present study, 21 SSR and 19 TRAP markers were applied to investigate the genetic structure and association analysis in 53 Iranian sunflower parental lines, including 23 restorer and 30 cytoplasmic male sterility lines. In the phenotypic analysis, 18 morpho-physiological traits were measured. The population structure analysis identified two and five actual subpopulations (optimum K) across SSR and TRAP markers, respectively. Using SSR data, population differentiation measurements (FST) between the subpopulations ranged from 0.24 to 0.43 (average 0.32); using TRAP data, FST varied between 0.23 and 0.24 (average 0.24). Association mapping analysis indicated that SSR and TRAP markers were associated with 11 and 17 traits, respectively. SSR loci Ha 494-ar, Ha 806-ar, Ha 991-ar, Ha 1167-ar, Ha 1287-ar, ORS-53, and ORS-54 were associated with seed yield per plant, oil yield per plant, seed yield, and oil yield respectively. On the other hand, several TRAP markers, including K11F05/TRAP03, K11F05/TRAP03, and F15O11F1/TRAP03 were associated with flowering duration, maturity, and 1000-seed weight, respectively. In conclusion, the genetic structure and marker-trait associations reported here can be exploited for marker-assisted selection (MAS) in sunflower breeding programs.

References:

Akbari G., H. Jabbari, J. Daneshian, I. Alahdadi And N. Shahbazian, 2008. 'The effect of limited irrigation on seed physical characteristics in sunflower hybrids'. Journal of Crop Production and Processing. 12(45):513-523 (in Persian).

Al-Chaarani G.R., L. Gentzbittel, X. Huang And A. Sarrafi. 2004. 'Genotypic variation and identification of qtls for agronomic traits, using AFLP and SSR markers in RILs of sunflower (Helianthus annuus L.) '. Theoretical and Applied Genetics. 109(7):1353-1360.

Arias M., M. Hernandez, N. Remondegui, K. Huvenaars, P. Van Dijk and E. Ritter. 2016. 'First genetic linkage map of Taraxacum koksaghyz rodin based on AFLP, SSR, COS and EST-SSR markers'. Scientific Reports. 6:31031.

Bartholomé J., M.C. Bink, J. Van Heerwaarden, E. Chancerel, C. Boury, I. Lesur, F. Isik, L. Bouffier and C. Plomion. 2016. 'Linkage and association mapping for two major traits used in the maritime pine breeding program: Height growth and stem straightness'. PloS one. 11(11): e0165323.

Berrios E.F., L. Gentzbittel, H. Kayyal, G. Alibert and A. Sarrafi. 2000. 'AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.) '. Theoretical and Applied Genetics. 101(8):1299-1306.

Bradbury P.J., Z. Zhang, D.E. Kroon, T.M. Casstevens, Y. Ramdoss and E.S. Buckler. 2007. 'TASSEL: Software for association mapping of complex traits in diverse samples'. Bioinformatics. 23(19):2633-2635.

Cadic E., M. Coque, F. Vear, B. Grezes-Besset, J. Pauquet, J. Piquemal, Y. Lippi, P. Blanchard, M. Romestant and N. Pouilly. 2013. 'Combined linkage and association mapping of flowering time in sunflower (Helianthus annuus L.) '. Theoretical and Applied Genetics. 126(5):1337-1356.

Darvishzadeh R. 2012. 'Association of SSR markers with partial resistance to Sclerotinia sclerotiorum isolates in sunflower (Helianthus annuus L.) '. Australian Journal of Crop Science. 6(2):276.

Davar R., A. Majd, R. Darvishzadeh and A. Sarrafi. 2011. 'Mapping quantitative trait loci for seedling vigour and development in sunflower (Helianthus annuus L.) using recombinant inbred line population'. Plant Omics. 4:418-427.

Dehmer K. and W. Friedt. 1998. 'Evaluation of different microsatellite motifs for analysing genetic relationships in cultivated sunflower (Helianthus annuus L.) '. Plant Breeding. 117(1):45-48.

Dice L.R. 1945. 'Measures of the amount of ecologic association between species'. Ecology. 26(3):297-302.

Ebrahimi A., P. Maury, M. Berger, S. Poormohammad Kiani, A. Nabipour, F. Shariati, P. Grieu and A. Sarrafi. 2008.  'QTL mapping of seed-quality traits in sunflower recombinant inbred lines under different water regimes'. Genome. 51(8):599-615.

Evanno G., S. Regnaut and J. Goudet. 2005. 'Detecting the number of clusters of individuals using the software structure: A simulation study'. Molecular Ecology. 14(8):2611-2620.

Eyvaznejad N. And R. Darvishzadeh. 2014. 'Identification of QTLs for grain yield and some agro-morphological traits in sunflower (Helianthus annuus L.) using SSR and SNP markers'. Journal of Plant Molecular Breeding. 2(2):68-87.

Fernández-Martínez J., B. Pérez-Vich and L. Velasco. 2009. Sunflower. In ‘oil crops’. (eds j vollmann, i rajcan) pp. 155–232. Springer: New York.

Filippi C.V., N. Aguirre, J.G. Rivas, J. Zubrzycki, A. Puebla, D. Cordes, M.V. Moreno, C.M. Fusari, D. Alvarez and R.A. Heinz. 2015. 'Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers'. BMC Plant Biology. 15(1):52.

Fusari C.M., J.A. Di Rienzo, C. Troglia, V. Nishinakamasu, M.V. Moreno, C. Maringolo, F. Quiroz, D. Álvarez, A. Escande and E. Hopp. 2012. 'Association mapping in sunflower for sclerotinia head rot resistance'. BMC Plant Biology. 12(1):93.

Fusari C.M., V.V. Lia, H.E. Hopp, R.A. Heinz and N.B. Paniego. 2008. 'Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach'. BMC Plant Biology. 8(1):7.

Haddadi P., B. Yazdi-Samadi, M. Naghavi, A. Kalantari, P. Maury and A. Sarrafi. 2011. 'QTL analysis of agronomic traits in recombinant inbred lines of sunflower under partial irrigation'. Plant Biotechnology Reports. 5(2):135-146.

Hall D., C. Tegström and P.K. Ingvarsson. 2010. 'Using association mapping to dissect the genetic basis of complex traits in plants'. Briefings in Functional Genomics. 9(2):157-165.

Holland J.B. 2007. 'Genetic architecture of complex traits in plants'. Current Opinion in Plant Biology. 10(2):156-161.

Hu J. And B.A. Vick. 2003. 'Target region amplification polymorphism: A novel marker technique for plant genotyping'. Plant Molecular Biology Reporter. 21(3):289-294.

Ingvarsson P.K. and N.R. Street. 2011. 'Association genetics of complex traits in plants'. New Phytologist. 189(4):909-922.

Jakobsson M., M.D. Edge and N.A. Rosenberg. 2013. 'The relationship between fst and the frequency of the most frequent allele'. Genetics. 193(2):515-528.

Jannatdoust M., R. Darvishzadeh, H. Azizi, M. Ebrahimi, R. Ziaefard and E. Gholinezhad. 2017. 'Identification of retrotransposon markers associated with agromorphological traits in confectionary sunflower (Helianthus annuus L.) under normal and drought stress conditions'. Journal of Crop Breeding. 8:183-197. (in Persian)

Kolkman J.M., S.T. Berry, A.J. Leon, M.B. Slabaugh, S. Tang, W. Gao, D.K. Shintani, J.M. Burke and S.J. Knapp. 2007. 'Single nucleotide polymorphisms and linkage disequilibrium in sunflower'. Genetics. 177(1):457-468.

Lecomte L., V. Saliba-Colombani, A. Gautier, M. Gomez-Jimenez, P. Duffe, M. Buret and M. Causse. 2004. 'Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato'. Molecular Breeding. 13(1):1-14.

Mackay I. And W. Powell. 2007. 'Methods for linkage disequilibrium mapping in crops'. Trends in Plant Science. 12(2):57-63.

Mandel J.R., S. Nambeesan, J.E. Bowers, L.F. Marek, D. Ebert, L.H. Rieseberg, S.J. Knapp and J.M. Burke. 2013. 'Association mapping and the genomic consequences of selection in sunflower'. PLoS Genetics. 9(3): e1003378.

Mangin B., N. Pouilly, M.-C. Boniface, N.B. Langlade, P. Vincourt, F. Vear and S. Muños. 2017. 'Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits'. Theoretical and Applied Genetics. 130(6):1099-1112.

Mokrani L., L. Gentzbittel, F. Azanza, L. Fitamant, G. Al-Chaarani and A. Sarrafi. 2002. 'Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower (Helianthus annuus L.) '. Theoretical and Applied Genetics. 106(1):149-156.

Moreno, Mv., Cm. Fusari, V. Nishinakamasu, D. Alvarez, Dij. Rienzo, Eh. Heinz, R. Paniego, Vv Lia. 2012. 'Association mapping of drought tolerance in sunflower: phenotypic and genetic characterization of INTA inbred lines'. In 18th International Sunflower Conference. February 2012 (Vol. 27).

Nambeesan S.U., J.R. Mandel, J.E. Bowers, L.F. Marek, D. Ebert, J. Corbi, L.H. Rieseberg, S.J. Knapp and J.M. Burke. 2015. 'Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching'. BMC Plant Biology. 15(1):84.

Nordborg M. and S. Tavaré, 2002. 'Linkage disequilibrium: What history has to tell us'. Trends in Genetics. 18(2):83-90.

Paniego N., M. Echaide, M. Muñoz, L. Fernández, S. Torales, P. Faccio, I. Fuxan, M. Carrera, R. Zandomeni and E.Y. Suárez. 2002. 'Microsatellite isolation and characterization in sunflower (Helianthus annuus L.) '. Genome. 45(1):34-43.

Price A.L., N.J. Patterson, R.M. Plenge, M.E. Weinblatt, N.A. Shadick and D. Reich. 2006. 'Principal components analysis corrects for stratification in genome-wide association studies'. Nature Genetics. 38(8):904-909.

Pritchard J.K., M. Stephens and P. Donnelly. 2000. 'Inference of population structure using multilocus genotype data'. Genetics. 155(2):945-959.

Remington D.L., J.M. Thornsberry, Y. Matsuoka, L.M. Wilson, S.R. Whitt, J. Doebley, S. Kresovich, M.M. Goodman and E.S. Buckler. 2001. 'Structure of linkage disequilibrium and phenotypic associations in the maize genome'. Proceedings of the National Academy of Sciences. 98(20):11479-11484.

Renaut S. 2017. 'Genome sequencing: Illuminating the sunflower genome'. Nature Plants. 3(7):17099.

Ruggieri V., G. Francese, A. Sacco, A. D’alessandro, M.M. Rigano, M. Parisi, M. Milone, T. Cardi, G. Mennella and A. Barone. 2014. 'An association mapping approach to identify favourable alleles for tomato fruit quality breeding'. BMC Plant Biology. 14(1):337.

Sahari K., P. Nicolas, M. Stéphane, B. Aurélie, B.J. Fayçal, V. Patrick and B. Dominique. 2016. 'Genetic diversity and core collection constitution for subsequent creation of new sunflower varieties in tunisia'. Helia. 39(64):123-137.

Soleimani-Gezeljeh A., R. Darvishzadeh, A. Ebrahimi and M.R. Bihamta. 2018. 'Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunflower (Helianthus annuus L.) under natural and water-limited states'. Journal of Genetics. 97(1): 189-203.

Talia P., V. Nishinakamasu, H.E. Hopp, R.A. Heinz and N. Paniego. 2010. 'Genetic mapping of EST-SSR, SSR and INDEL to improve saturation of genomic regions in a previously developed sunflower map'. Electronic Journal of Biotechnology. 13(6):7-8.

Talukder Z.I., B.S. Hulke, L. Qi, B.E. Scheffler, V. Pegadaraju, K. Mcphee and T.J. Gulya. 2014. 'Candidate gene association mapping of sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of coi1 homologs'. Theoretical and Applied Genetics. 127(1):193-209.

Tang S., J.-K. Yu, M. Slabaugh, D. Shintani and S. Knapp. 2002. 'Simple sequence repeat map of the sunflower genome'. Theoretical and Applied Genetics. 105(8):1124-1136.

Thornsberry J.M., M.M. Goodman, J. Doebley, S. Kresovich, D. Nielsen and E.S. Buckler IV. 2001.  'Dwarf8 polymorphisms associate with variation in flowering time'. Nature Genetics. 28(3):286-289.

Wills D.M. and J.M. Burke. 2007. 'Quantitative trait locus analysis of the early domestication of sunflower'. Genetics. 176(4):2589-2599.

Yu J.-K., J. Mangor, L. Thompson, K.J. Edwards, M.B. Slabaugh and S.J. Knapp. 2002. 'Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower. Genome'. 45(4):652-660.

Yu J. And E.S. Buckler. 2006. 'Genetic association mapping and genome organization of maize'. Current Opinion in Biotechnology. 17(2):155-160.

Yue B., X. Cai, B.A. Vick and J. Hu. 2009. 'Genetic diversity and relationships among 177 public sunflower inbred lines assessed by trap markers'. Crop Science. 49(4):1242-1249.

Yue B., S. Radi, B. Vick, X. Cai, S. Tang, S. Knapp, T. Gulya, J. Miller and J. Hu. 2008. 'Identifying quantitative trait loci for resistance to sclerotinia head rot in two USDA sunflower germplasms'. Phytopathology. 98(8):926-931.

Zeinalzadeh-Tabrizi H., K. Haliloglu and A. Razban-Haghighi. 2015. 'Genetic diversity of sunflower genotypes (Helianthus annuus L.) using TRAP markers'. Crop Biotechnology. 12:39-53 (in Persian).

Zeinalzadeh-Tabrizi H., A. Hosseinpour, M. Aydin and K. Haliloglu. 2015. 'A modified genomic DNA extraction method from leaves of sunflower for PCR based analyzes'. J Biol Env Sci. 7:222-225.

Zubrzycki J.E., C.A. Maringolo, C.V. Filippi, F.J. Quiroz, V. Nishinakamasu, A.F. Puebla, J.A. Di Rienzo, A. Escande, V.V. Lia and R.A. Heinz. 2017. 'Main and epistatic QTL analyses for sclerotinia head rot resistance in sunflower'. PloS one. 12(12): e0189859.