Identification of SSR loci related to some important agromorphological traits in different sunflower (Helianthus annus L.) lines using association mapping

Sahranavard Azartamar, Fatemeh; Darvishzadeh, Reza; Ghadimzadeh, Mortaza; Azizi, Heydar; Aboulghasemi, Zahra

Identification of SSR loci related to some important agromorphological traits in different sunflower (Helianthus annus L.) lines using association mapping

Document Type : Research Paper

Authors

¹ M.Sc. in Plant Breeding, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran.

² Associate Professor, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran.

³ Ph.D. student in Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

⁴ M.Sc. in Plant Breeding, Department of Agronomy and Plant Breeding, Islamic Azad University, Tabriz Branch

Abstract

Since the economic value of cultivar depends on different characteristics, thus detailed knowledge on genetic behavior and identification of genomic loci linked to these traits will help to improve plant cultivars. In this investigation, relation and linkage between of 30 microsatellite markers with some of important agromorphological traits in 106 different sunflower lines was evaluated through GLM and MLM association models in Structure and TASSEL software. Based on the 30 microsatellite markers used in this study, population genetic structure subdivided into five subpopulations (K=5) that barplat results also confirmed it. In association analysis based on GLM and MLM models, 9 and 16 loci showed significant relation with assessed traits, respectively, and explained considerable variations of this studied traits. In this study, some co-localized QTLs were identified for studied traits. Common markers between of traits can be due to pleiotropic effects or linkage between of genomic regions involved in these traits. Results of the current study presented useful information about the genetic basis of the studied traits and can be used in different sunflower breeding programs including marker aided selection. In future studies, coding genes of important agronomical traits could be identified by sequencing of loci with highest R2 (ORS1209, ORS822 and ORS649). Markers with highest association to traits can be used for saturating linkage maps.

Keywords

20.1001.1.22520783.1394.5.10.6.5

Main Subjects

Molecular Plant Breeding

References

Abdi N, Darvishzadeh R, Jafari M, Pirzad A, Haddadi P (2012) Genetic analysis and QTL mapping of agro-morphological traits in sunflower (Helianthus annuus L.) under two contrasting water treatment conditions. Plant Omics. 5(2): 149-158.

Allinne C, Maury P, Sarrafi A, Grieu P (2009) Genetic control of physiological traits associated to low temperature growth in sunflower under early sowing conditions. Plant Sci. 177: 349-359.

Al-Maskri AH, Sajjad M, Khan SH (2012) Association mapping: a step forward to discovering new alleles for crop improvement. Int. J. Agric. Biol. 14: 153-160.

Andersen JR, Zein I, Wenzel G, Krützfeldt B, Eder J, Ouzunova M, Lübberstedt T (2007) High levels of linkage disequi-librium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor. Appl. Genet. 114: 307-319.

Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome. 36: 181-186.

Anonymus (2014) Custom statistics of Islamic Republic of Iran. Ministry of Economic and Wealth affairs.

Berrios EF, Gentzbittel L, Kayyal H, Alibert G, Sarrafi A (2000) AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.). Theor. Appl. Genet. 101(8): 1299-1306.

Bert PF, Jouan I, Labrouhe TD, Serre F, Nicolas P, Vear F (2002) Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). QTL involved in resistance to Sclerotinia sclerotiorum and Diaporthe helianthi. Theor. Appl. Genet. 105: 985-993.

Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics. 172: 1165-1177.

Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics. 3:19.

Darvishzadeh R, Azizi M, Hatami-Maleki H, Bernousi I, Abdollahi Mandoulakani B, Jafari M (2010) Molecular characterization and similarity relationships among sunflower (Helianthus annuus L.) inbred lines using some mapped simple sequence repeats. Afric. J. Biotech. 9(43): 7280-7288.

Darvishzadeh R, Poormohammad Kiani S, Dechamp-Guillaume G, Gentzbittel L, Sarrafi A (2007). Quantitative trait loci associated with isolate specific and isolate nonspecific partial resistance to Phoma macdonaldii in sunflower. Plant Pathol. 56: 855-861.

Davar R, Darvishzadeh R, Majd A, Ghosta Y, Sarrafi A (2010) QTL mapping of partial resistance to basal stem rot in sunflower using recombinant inbred lines. Phytopathol. Mediterr. 49: 330-341.

Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1(4): 19-21.

DeWan A, Liu M, Hartman S, Zhang SS, Liu DTL (2006) HTRA1 promoter polymorphism in wet age-related macular degeneration. Science. 314: 989-992.

Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat. Genet. 3(1): 43-52.

Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620.

FAO (Food and Agriculture Organization) Rome (2013) http://faostat.fao.org/.

Fusari CM, Rienzo JAD, Troglia C, Nishinakamasu V, Moreno MV, Maringolo C, Quiroz F, Álvarez D, Escande A, Hopp E, Heinz R, Lia VV, Paniego NB (2012). Association mapping in sunflower for Sclerotinia head rot resistance. BMC Plant Biol. 12(93): 1-13.

Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol. Biol. 57: 461-485.

Jun TH, Van K, Kim MY, Lee SH, Walker DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica. 62: 179-191.

Kholghi M, Darvishzadeh R, Bernousi I, Pirzad A, Hernan L (2012) Assessment of genomic diversity among and within Iranian confectionery sunflower (Helianthus annuus L.) populations by using simple sequence repeat markers. Acta Agric. Scand. Sect. B Soil Plant Sci. 62(6): 488-498.

Leon AJ, Lee M, Andrade FH (2001) Quantitative trait loci for growing degree days to flowering and photoperiod response in sunflower (Helianthus annuus L.). Theor. Appl. Genet. 102: 497-503.

Liu L, Wang L, Yao J, Zheng Y, Zhao C (2010) Association mapping of six agronomic traits on chromosome 4A of Wheat (Triticum aestivum L.). Mol. Breed. 1(5): 1-10.

Maccaferri M, Sanguineti MC, Demontis A, El-Ahmed A, Garcia del Moral L, Maalouf F, Nachit M, Nserallah N, Ouabbou H, Rhouma S, Royo C, Villegas D,Tuberosa R (2011) Association mapping in durum wheat grown across a broad range of water regimes. J. Exp. Bot. 14: 287-293.

Mackay TF, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat. Rev. Genet. 10(8): 565-577.

Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics. 177: 2223-2232.

Mauricio R (2001) Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nat. Genet. 2(5): 370-381.

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

Nooryazdan H, Serieys H, Baciliéri R, David J, Berville A (2010) Structure of wild annual sunflower (Helianthus annuus L.) accessions based on agro-morphological traits. Genet. Resour. Crop Evol. 57(1): 27-39.

Oraguzie NC, Wilcox PL, Rikkerink EHA, de Silva HN (2007) Linkage disequilibrium, Association Mapping in Plants. Springer. New York. NY. pp: 11-39.

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

Pasam RK, Sharma R, Malosetti M, Van Eeuwijk FA, Haseneyer G, Kilian B, Garner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol. 12(1):16.

Pérez-Vich B, Akhtouch B, Knapp SJ, León AJ, Velasco L, Fernández-Martínez JM, Berry ST (2004) Quantitative trait loci for broomrape (Orobanche cumana Wallr.) resistance in sunflower. Theor. Appl. Genet. 109: 92-102.

Poormohammad Kiani S, 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: 193-207.

Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor. Pop. Biol. 60: 227-237.

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

Rachid Al-Chaarani G, Roustaee A, Gentzbittel L, Mokrani L, Barrault G, Dechamp-Guillaume G, Sarrafi A (2002) A QTL analysis of sunflower partial resistance to downy mildew (Plasmopara halstedii) and black stem (Phoma macdonaldii) by the use of recombinant inbred lines (RILs). Theor. Appl. Genet. 104: 490-496.

Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 98: 11479-11484.

Semagn K, Bjørnstad A, Xu Y (2010) The genetic dissection of quantitative traits in crops. Electronic Journal of Biotechnology. 13(5): 1-45.

Shehzad T, Iwata H, Okuno K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breed. Sci. 59: 217-227.

Slatkin M (1994) An exact test for neutrality based on the Ewens snampling distribution. Genetic Research. 64: 71-74.

Spataro G, Tiranti B, Arcaleni P, Bellucci E, Attene G, Papa R, Spagnoletti ZP, Negri V (2011) Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theor. Appl. Genet. 122: 1281-1291.

Tang S, Yu JK, Slabaugh M, Shintani D, Knapp J (2002) Simple sequence repeat map of the sunflower genome. Theor. Appl. Genet. 105(8): 1124-1136.

Tuberosa R, Salvi S, Sanguineti MC, Landi P, Maccaferri M, Conti S (2002) Mapping QTLs regulating morpho-physiological traits and yield in drought-stressed maize: case studies, shortcomings and perspectives. Ann. Bot. 89: 941-963.

Vanitha J, Manivannan N, Chandirakala R (2014) Qualitative trait loci analysis for seed yield and component traits in sunflower. Afric. J. Biotech. 13(6): 754-761.

Wang M, Jiang N, Jia T, Leach L, Cockram J, Comadran J, Shaw P, Waugh R, Luo Z (2012) Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor. Appl. Genet. 124: 233-46.

Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr. Opin Biotechnol. 17(2): 155-160.

Yu JK, Mangor J, Thompson L, Edwards KJ, Slabaugh MB, Knapp SJ (2002) Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower. Genome. 45(4): 652-660.

Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M (2006) A uniﬁed mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203-208.

Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics. 20(2): 176-183.