Association mapping of quantitative traits in molecular cereal breeding (Review Article)

Abdurakhmonov, I. Y. and Abdukarimov, A. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics 2008 (2): 574927.##Abdurakhmonov, I. Y., Kohel, R. J., Yu, J. Z., Pepper, A. E., Abdullaev, A. A., Kushanov, F. N., Salakhutdinov, I. B., Buriev, Z. T., Saha, S., Scheffler, B. E. and Jenkins, J. N. 2008. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92 (6): 478-487.##Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., Yoshida, K., Mitsuoka, C. and Tamiru, M. 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology 30 (2): 174.##Abedi, S., Darvishzadeh, R., Bernousi, I., Abdollahi Mandoulakani, B., Hatami Maleki, H. and Shah D. 2014. Genetic variability of Orobanche aegyptiaca infesting tobacco in Iran by Bayesian analysis. Biologia 69 (12): 1652-1659.##Ahmadpour, S., Sofalian, O., Darvishzadeh, R. and Abbaspour, N. 2018. Preliminary evidence of the associations between DNA markers and morphological characters in sunflower under natural and salt stress conditions. Zemdirbyste-Agriculture 105 (3): 279-286.##Bamshad, M., Wooding, S., Salisbury, B. A. and Stephens, J. C. 2004. Deconstructing the relationship between genetics and race. Nature Reviews Genetics 5 (8): 598.##Basirnia, A., Hatami Maleki, H., Darvishzadeh, R. and Ghavami F. 2014. Mixed linear model association mapping for low chloride accumulation rate in oriental-type tobacco (Nicotiana tabacum L.) germplasm. Journal of Plant Interactions 9 (1): 666-672.##Begum, H., Spindel, J. E., Lalusin, A., Borromeo, T., Gregorio, G., Hernandez, J., Virk, P., Collard, B. and McCouch, S. R. 2015. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa L.). PloS One 10 (3): e0119873.##Bernardo, R. and Yu, J. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Science 47 (3): 1082-1090.##Beyer, S., Daba, S., Tyagi, P., Bockelman, H., Brown-Guedira, G. and Mohammadi, M. 2019. Loci and candidate genes controlling root traits in wheat seedlings-a wheat root GWAS. Functional and Integrative Genomics 19 (1): 91-107.##Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y. and Buckler, E. S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23 (19): 2633-2635.##Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L., D’Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A. and Bolser, D. 2012. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491 (7426): 705.##Camus-Kulandaivelu, L., Veyrieras, J. B., Madur, D., Combes, V., Fourmann, M., Barraud, S., Dubreuil, P., Gouesnard, B., Manicacci, D. and Charcosset, A. 2006. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172 (4): 2449-2463.##Chen, W., Gao, Y., Xie, W., Gong, L., Lu, K., Wang, W., Li, Y., Liu, X., Zhang, H. and Dong, H. 2014. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics 46 (7): 714.##Cui, Y., Zhang, F. and Zhou, Y. 2018. The application of multi-locus GWAS for the detection of salt-tolerance loci in rice. Frontiers in Plant Science 9: 1464. doi:10.3389/fpls.2018.01464.##Dadras, A. R., Sabouri, H., Nejad, G. M., Sabouri, A. and Shoai-Deylami, M. 2014. Association analysis, genetic diversity and structure analysis of tobacco based on AFLP markers. Molecular Biology Reports 41 (5): 3317-3329.##Darvishzadeh, R. 2016a. Population structure, linkage disequilibrium and association mapping for morphological traits in sunflower (Helianthus annuus L.), Biotechnology and Biotechnological Equipment 30 (2): 236-246.##Darvishzadeh, R. 2016b. Detection of ISSR markers linked to seed oil biochemical characteristics in castor (Ricinus communis L.) through association analysis. Genetika 48 (3): 807-817.##Darvishzadeh, R. 2016c. Genetic variability, structure analysis, and association mapping of resistance to broomrape (Orobanche aegyptiaca) in tobacco. Journal of Agricultural Science and Technology 18: 1407-1418.##Darvishzadeh, R., Basirnia A., Hatami Maleki H. and Jafari M. 2014. Association mapping for resistance to powdery mildew in oriental tobacco (Nicotiana tabacum L.) germplasm. Iranian Journal of Genetic and Breeding 3 (1): 21-30.##Darvishzadeh, R., Heidari, A. and Hatami Maleki, H. 2016. Identification of SSR markers associated with resistance to potato virus Y in tobacco germplasm. Genetics in the 3^rd Millennium 14 (2): 4262-4269.##Darvishzadeh, R., Poormohammad Kiani, S., Huguet, T. and Sarrafi, A. 2008. Genetic variation and identification of molecular markers associated with partial resistance to black stem in gamma-irradiation induced mutants in sunflower (Helianthus annuus L.). Canadian Journal of Plant Pathology 30: 106-114.##Davar, R., Darvishzadeh, R., Rezaee Danesh, Y., Kholghi, M., Azizi, M and Shah, D. A. 2012. Single sequence repeat markers associated with partial resistance in sunflower to Phoma macdonaldii. Phytopathologia Mediterrania 51 (3): 541-548.##Devlin, B., Bacanu, S. A. and Roeder, K. 2004. Genomic control to the extreme. Nature Genetics
36 (11): 1129.##Devlin, B. and Risch, N. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29 (2): 311-322.##Devlin, B. and Roeder, K. 1999. Genomic control for association studies. Biometrics 55 (4): 997-1004.##Devlin, B., Roeder, K. and Wasserman, L. 2001. Genomic control, a new approach to genetic-based association studies. Theoretical Population Biology 60 (3): 155-166.##Dingkuhn, M., Pasco, R., Pasuquin, J. M., Damo, J., Soulié, J. C., Raboin, L. M., Dusserre, J., Sow, A., Manneh, B. and Shrestha, S. 2017. Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 1. Phenology. Journal of Experimental Botany 68 (15): 4369-4388.##El Mannai, Y., Shehzad, T. and Okuno, K. 2011. Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis. Genetic Resources and Crop Evolution 58 (7): 983.##Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S. and Mitchell, S. E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6 (5): e19379. doi:10.1371/journal.pone.0019379.##Fusari, C. M., Di Rienzo, J. A., Troglia, C., Nishinakamasu, V., Moreno, M. V., Maringolo, C., Quiroz, F., Álvarez, D., Escande, A. and Hopp, E. 2012. Association mapping in sunflower for sclerotinia head rot resistance. BMC Plant Biology 12 (1): 93.##Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M. and Liu-Cordero, S. N. 2002. The structure of haplotype blocks in the human genome. Science 296 (5576): 2225-2229.##Ghaffari Azar A., Darvishzadeh, R., Hatami Maleki, H., Kahrizi, D., Darvishi, B. and Bernoosi, I. 2018. Identification of inter simple sequence repeat regions associated with agro-morphological traits in maize genome. Cereal Research 8 (1): 97-109. (In Persian with English Abstract).##Goodarzi, F., Hassani, A., Darvishzadeh, R. and Hatami Maleki, H. 2015. Genetic variability and traits association in castor bean (Ricinus communis L.). Genetika 47 (1): 265-274.##Gupta, P. K., Kulwal, P. L. and Jaiswal, V. 2019. Association mapping in plants in the post-GWAS genomics era. Advances in Genetics 104: 75-154.##Gupta, P. K., Rustgi, S. and Kulwal, P. L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology 57 (4): 461-485.##Hao, D., Xue, L., Zhang, Z., Cheng, Y., Chen, G., Zhou, G., Li, P., Yang, Z. and Xu, C. 2019. Combined linkage and association mapping reveal candidate loci for kernel size and weight in maize. Breeding Science: 18185.##Hayes, B. and Goddard, M. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157 (4): 1819-1829.##Hedrick, P. W. 1987. Gametic disequilibrium measures: Proceed with caution. Genetics 117 (2):
331-341.##Hill, W. and Robertson, A. 1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38 (6): 226-231.##Hill, W. and Weir, B. 1994. Maximum-likelihood estimation of gene location by linkage disequilibrium. American Journal of Human Genetics 54 (4): 705.##Hindu, V., Palacios-Rojas, N., Babu, R., Suwarno, W. B., Rashid, Z., Usha, R., Saykhedkar, G. R. and Nair, S. K. 2018. Identification and validation of genomic regions influencing kernel zinc and iron in maize. Theoretical and Applied Genetics 131 (7): 1443-1457.##Holland, J. B. 2007. Genetic architecture of complex traits in plants. Current Opinion in Plant Biology 10 (2): 156-161.##Hu, X., Zuo, J., Wang, J., Liu, L., Sun, G., Li, C., Ren, X. and Sun, D. 2018. Multi-locus genome-wide association studies for 14 main agronomic traits in barley. Frontiers in Plant Science 9: 1683.##Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., Guan, J., Fan, D., Weng, Q. and Huang, T. 2009. High-throughput genotyping by whole-genome resequencing. Genome Research 19 (6): 1068-1076.##Huang, X., Yang, S., Gong, J., Zhao, Y., Feng, Q., Gong, H., Li, W., Zhan, Q., Cheng, B. and Xia, J. 2015. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nature Communications 6: 6258.##Jabbari, M., Fakheri, B. A., Aghnoum, R., Mahdi Nezhad, N. and Ataei, R. 2018. GWAS analysis in spring barley (Hordeum vulgare L.) for morphological traits exposed to drought. PLoS One
13 (9): e0204952. doi:10.1371/journal.pone.0204952.##Jain, S. M., Brar, D. S. 2010. Molecular techniques in crop improvement. 2^nd Edition. Springer.##Jia, Z., Liu, Y., Gruber, B. D., Neumann, K., Kilian, B., Graner, A. and von Wiren, N. 2019. Genetic dissection of root system architectural traits in spring barley. Frontiers in Plant Science 10: 400. doi:10.3389/fpls.2019.00400.#3Kaplan, N. and Weir, B. 1992. Expected behavior of conditional linkage disequilibrium. American Journal of Human Genetics 51 (2): 333.##Kordrostami, M., Rabiei, B. and Hassani Kumleh‏, H. 2016. Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to SalTol and morpho-physiological characteristics‏. Plant Systematics and Evolution 302 (7): 871-890‏.##Kumar, J., Saripalli, G., Gahlaut, V., Goel, N., Meher, P. K., Mishra, K. K., Mishra, P. C., Sehgal, D., Vikram, P. and Sansaloni, C. 2018. Genetics of Fe, Zn, β-carotene, GPC and yield traits in bread wheat (Triticum aestivum L.) using multi-locus and multi-traits GWAS. Euphytica
214 (11): 219.##Kumar, V., Singh, A., Mithra, S. A., Krishnamurthy, S., Parida, S. K., Jain, S., Tiwari, K. K., Kumar, P., Rao, A. R. and Sharma, S. 2015. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa L.). DNA Research 22 (2): 133-145.##Lekklar, C., Pongpanich, M., Suriya-Arunroj, D., Chinpongpanich, A., Tsai, H., Comai, L., Chadchawan, S. and Buaboocha, T. 2019. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics 20 (1): 76.##Levin, M. L. and Bertell, S. R. 1978. RE:simple estimation of population attributable risk from case-control studies. American Journal of Epidemiology 108 (1): 78-79.##Lewontin, R. 1964. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49 (1): 49.##Li, G., Xu, X., Tan, C., Carver, B. F., Bai, G., Wang, X., Bonman, J. M., Wu, Y., Hunger, R. and Cowger, C. 2019. Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study (GWAS) and linkage mapping. The Crop Journal 7 (3): 294-306.##Li, H., Peng, Z., Yang, X., Wang, W., Fu, J., Wang, J., Han, Y., Chai, Y., Guo, T. and Yang, N. 2013. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nature Genetics 45 (1): 43.##Li, J., Huang, X., Heinrichs, F., Ganal, M. and Röder, M. 2005. Analysis of QTLs for yield, yield components, and malting quality in a BC 3-DH population of spring barley. Theoretical and Applied Genetics 110 (2): 356-363.##Li, T., Qu, J., Wang, Y., Chang, L., He, K., Guo, D., Zhang, X., Xu, S. and Xue, J. 2018. Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield. BMC Genetics 19 (1): 63. doi:10.1186/s12863-018-0669-9.##Lipka, A. E., Tian, F., Wang, Q., Peiffer, J., Li, M., Bradbury, P. J., Gore, M. A., Buckler, E. S. and Zhang, Z. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics 28 (18): 2397-2399.##Liu, E., Liu, X., Zeng, S., Zhao, K., Zhu, C., Liu, Y., Breria, M. C., Zhang, B. and Hong, D. 2015. Time-course association mapping of the grain-filling rate in rice (Oryza sativa L.). PLoS One
10 (3): e0119959.##Liu, E., Liu, Y., Wu, G., Zeng, S., Thi, T., Thu, G., Liang, L., Liang, Y., Dong, Z. and She, D. 2016. Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis. Frontiers in Plant Science 7: 596.##Liu, K. and Muse, S. V. 2005. PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21 (9): 2128-2129.##Long, A. D. and Langley, C. H. 1999. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Research 9 (8): 720-731.##Lu, Q., Niu, X., Zhang, M., Wang, C., Xu, Q., Feng, Y., Yang, Y., Wang, S., Yuan, X. and Yu, H. 2018. Genome-wide association study of seed dormancy and the genomic consequences of improvement footprints in rice (Oryza sativa L.). Frontiers in Plant Science 8: 2213.##Lu, Y., Liu, Y., Niu, X., Yang, Q., Hu, X., Zhang, H. Y. and Xia, J. 2015. Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans. Frontiers in Plant Science 6: 1027.##Luo, X., Wang, B., Gao, S., Zhang, F., Terzaghi, W. and Dai, M. 2019. Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings. Journal of Integrative Plant Biology 61 (6): 658-674.##Ma, F., Xu, Y., Ma, Z., Li, L. and An, D. 2018. Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6. Molecular Breeding 38 (7): 91.##Ma, X., Feng, F., Wei, H., Mei, H., Xu, K., Chen, S., Li, T., Liang, X., Liu, H. and Luo, L. 2016. Genome-wide association study for plant height and grain yield in rice under contrasting moisture regimes. Frontiers in Plant Science 7: 1801.##Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J. I., Ebana, K., Yano, M. and Saito, K. 2015. Metabolome‐genome‐wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. The Plant Journal 81 (1): 13-23.##Mayer, K. F., Waugh, R., Brown, J. W., Schulman, A., Langridge, P., Platzer, M., Fincher, G. B., Muehlbauer, G. J., Sato, K., Close, T. J., Wise, R. P. and Stein, N. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature 491 (7426): 711-716.##Melchinger, A. E. and Gumber, R. K. 1998. Overview of heterosis and heterotic groups in agronomic crops. In: Larnkey, K. R. and Staub, J. E. (Eds.). Concepts and breeding of heterosis in crop plants. CSSA Special Publications. pp: 29-44.##Moose, S. P. and Mumm, R. H. 2008. Molecular plant breeding as the foundation for 21^st century crop improvement. Plant Physiology 147 (3): 969-977.##Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E. and Buckler, E. S. 2009. Association mapping: Critical considerations shift from genotyping to experimental design. The Plant Cell 21 (8): 2194-2202.##Najafzadeh, R., Darvishzadeh, R., Musa-Khalifani, Kh., Abrinbana, M. and Alipour, H. 2018. Retrotransposonable regions of sunflower genome having relevance with resistance to Sclerotinia species: S. sclerotiorum and S. minor. Australasian Plant Pathology 47: 511-519.##Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A. and Eichler, E. E. 2009. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461 (7261): 272.##Novakazi, F., Afanasenko, O., Anisimova, A., Platz, G. J., Snowdon, R., Kovaleva, O., Zubkovich, A. and Ordon, F. 2019. Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres). Theoretical and Applied Genetics: 132 (9): 2633-2650.##Oraguzie, N. C., Wilcox, P. L., Rikkerink, E. H. and de Silva, H. N. 2007. Linkage disequilibrium. In: Oraguzie, N. C., Rikkerink, E. H. A., Gardiner, S. E. and De Silva, H. N. (Eds.). Association mapping in plants. Springer, New York. pp: 11-39.##Oyiga, B. C., Sharma, R. C., Baum, M., Ogbonnaya, F. C., Leon, J. and Ballvora, A. 2018. Allelic variations and differential expressions detected at quantitative trait loci for salt stress tolerance in wheat. Plant, Cell and Environment 41 (5): 919-935. doi:10.1111/pce.12898.##Pham, A. T., Maurer, A., Pillen, K., Brien, C., Dowling, K., Berger, B., Eglinton, J. K. and March, T. J. 2019. Genome-wide association of barley plant growth under drought stress using a nested association mapping population. BMC Plant Biology 19 (1): 134. doi:10.1186/s12870-019-1723-0.##Pritchard, J. K. 2001. Deconstructing maize population structure. Nature Genetics 28 (3): 203.##Pritchard, J. K., Stephens, M. and Donnelly, P. 2000a. Inference of population structure using multilocus genotype data. Genetics 155 (2): 945-959.##Pritchard, J. K., Stephens, M., Rosenberg, N. A. and Donnelly, P. 2000b. Association mapping in structured populations. The American Journal of Human Genetics 67 (1): 170-181.##Razi, M., Darvishzadeh R., Amiri, M. E., Doulati-Baneh, H. and Martínez-Gómez P. 2018. Molecular characterization of a diverse Iranian table grapevine germplasm using REMAP markers: Population structure, linkage disequilibrium and association mapping of berry yield and quality traits. Biologia https://doi.org/10.2478/s11756-018-0158-7.##Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P. C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S. F. and Ward, R. 2001. Linkage disequilibrium in the human genome. Nature 411 (6834): 199.Rogers, S. O. and Bendich, A. J. 1987. Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Molecular Biology 9 (5): 509-520.##Roy, J. K., Smith, K. P., Muehlbauer, G. J., Chao, S., Close, T. J. and Steffenson, B. J. 2010. Association mapping of spot blotch resistance in wild barley. Molecular Breeding 26 (2): 243-256.##Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J. and Ackerman, H. C. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419 (6909): 832.##Saeed A. and Darvishzadeh R. 2017. Association analysis of biotic and abiotic stresses resistance in chickpea (Cicer spp.) using AFLP markers. Biotechnology and Biotechnological Equipment https://doi.org/10.1080/13102818.2017.1333455.##Saeed, A., Darvishzadeh, R. and Basirnia, A. 2013. Simple sequence repeat markers associated withagro-morphological traits in chickpea (Cicer arietinum L.). Zemdirbyste-Agriculture 100 (4): 433-440.##Sameri, M., Takeda, K. and Komatsuda, T. 2006. Quantitative trait loci controlling agronomic traits in recombinant inbred lines from a cross of oriental-and occidental-type barley cultivars. Breeding Science 56 (3): 243-252.##Schneeberger, K., Ossowski, S., Lanz, C., Juul, T., Petersen, A. H., Nielsen, K. L., Jørgensen, J. E., Weigel, D. and Andersen, S. U. 2009. SHOREmap: Simultaneous mapping and mutation identification by deep sequencing. Nature Methods 6 (8): 550.##Schulze, T. G. and McMahon, F. J. 2002. Genetic association mapping at the crossroads: which test and why? Overview and practical guidelines. American Journal of Medical Genetics 114 (1):1-11.##Shehzad, T., Iwata, H. and Okuno, K. 2009. Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor L. Moench) by using multiple models. Breeding Science 59 (3): 217-227.##Sheoran, S., Jaiswal, S., Kumar, D., Raghav, N., Sharma, R., Pawar, S., Paul, S., Iquebal, M. A., Jaiswar, A., Sharma, P., Singh, R., Singh, C. P., Gupta, A., Kumar, N., Angadi, U. B., Rai, A., Singh, G. P., Kumar, D. and Tiwari, R. 2019. Uncovering genomic regions associated with 36 agro-morphological traits in indian spring wheat using GWAS. Frontiers in Plant Science 10: 527.##Singh, D., Ziems, L.A., Dracatos, P. M., Pourkheirandish, M., Tshewang, S., Czembor, P., German, S., Fowler, R. A., Snyman, L., Platz, G. J. and Park, R. F. 2018. Genome-wide association studies provide insights on genetic architecture of resistance to leaf rust in a worldwide barley collection. Molecular Breeding 38(4). doi:10.1007/s11032-018-0803-4.##Soleimani Gezeljeh, A., Darvishzadeh, R., Ebrahimi, A. and Bihamta, M. R. 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 https://doi.org/10.1007/s12041-018-0901-4.##Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C.T., Jia, Y., Wu, W., Richmond, T., Kitzman, J. and Rosenbaum, H. 2009. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics 5 (11): e1000734.##Stich, B., Maurer, H. P., Melchinger, A. E., Frisch, M., Heckenberger, M., van der Voort, J. R., Peleman, J., Sørensen, A. P. and Reif, J. C. 2006. Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers. Molecular Breeding 17 (3): 217-226.##Stich, B., Melchinger, A. E., Frisch, M., Maurer, H. P., Heckenberger, M. and Reif, J. C. 2005. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theoretical and Applied Genetics 111 (4): 723-730.##Stich, B., Melchinger, A. E., Piepho, H. P., Hamrit, S., Schipprack, W., Maurer, H. P. and Reif, J. C. 2007. Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations. Theoretical and Applied Genetics 115 (4): 529-536.##Tabkhkar, N., Rabiei, B., Samizadeh Lahiji, H. and Hosseini Chaleshtori, M. 2020. Identification of a new set of drought-related miRNA-SSR markers and association analysis under drought stress in rice (Oryza sativa L.). Plant Gene 100220‏.##Tessmann, E. and Van Sanford, D. 2018. GWAS for fusarium head blight related traits in winter wheat (Triticum aestivum L.) in an artificially warmed treatment. Agronomy 8 (5): 68.##Thornsberry, J. M., Goodman, M. M., Doebley, J., Kresovich, S., Nielsen, D. and Buckler, E. S. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28 (3): 286.##Ueda, Y., Frimpong, F., Qi, Y., Matthus, E., Wu, L., Höller, S., Kraska, T. and Frei, M. 2014. Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study. Journal of Experimental Botany 66 (1): 293-306.##Varshney, R., Paulo, M., Grando, S., Van Eeuwijk, F., Keizer, L., Guo, P., Ceccarelli, S., Kilian, A., Baum, M. and Graner, A. 2012. Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Research 126: 171-180.##Wang, Y. and Rannala, B. 2005. In silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection. The American Journal of Human Genetics 76 (6): 1066-1073.##Wang, Z., Gerstein, M. and Snyder, M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10 (1): 57.##Wright, S. I. and Gaut, B. S. 2004. Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution 22 (3): 506-519.##Wu, L., Zhang, Y., He, Y., Jiang, P., Zhang, X. and Ma, H. 2019. Genome-wide association mapping of resistance to fusarium head blight spread and deoxynivalenol accumulation in chinese elite wheat germplasm. Phytopathology 109 (7): 1208-1216.##Xu, X., Sharma, R., Tondelli, A., Russell, J., Comadran, J., Schnaithmann, F., Pillen, K., Kilian, B., Cattivelli, L., Thomas, W. T. B. and Flavell, A. J. 2018. Genome-wide association analysis of grain yield-associated traits in a pan-european barley cultivar collection. Plant Genome 11 (1). doi:10.3835/plantgenome2017.##Xu, Y., Li, P., Yang, Z. and Xu, C. 2017. Genetic mapping of quantitative trait loci in crops. The Crop Journal 5 (2):175-184.##Yano, K., Yamamoto, E., Aya, K., Takeuchi, H., Lo, P. C., Hu, L., Yamasaki, M., Yoshida, S., Kitano, H. and Hirano, K. 2016. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nature Genetics 48 (8): 927.##Yu, J. and Buckler, E. S. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17 (2): 155-160.##Yu, J., Pressoir, G., Briggs, W. H., Bi, I. V., Yamasaki, M., Doebley, J.‌ F., McMullen, M. D., Gaut, B. S., Nielsen, D. M. and Holland, J. B. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38 (2): 203.##Zarbafi, S. S., Rabiei, B., Ebadi, A. A. and Ham, J. H. 2020. Association mapping of traits related to leaf blast disease in rice (Oryza sativa L.)‏. Australasian Plant Pathology 49 (1): 31-43‏.##Zhang, M., Lu, Q., Wu, W., Niu, X., Wang, C., Feng, Y., Xu, Q., Wang, S., Yuan, X. and Yu, H. 2017. Association mapping reveals novel genetic loci contributing to flooding tolerance during germination in indica rice. Frontiers in Plant Science 8: 678.##Zhang, Y., Liu, P., Zhang, X., Zheng, Q., Chen, M., Ge, F., Li, Z., Sun, W., Guan, Z. and Liang, T. 2018. Multi-locus genome-wide association study reveals the genetic architecture of stalk lodging resistance-related traits in maize. Frontiers in Plant Science 9: 611.##Zhang, Z., Buckler, E. S., Casstevens, T. M. and Bradbury, P. J. 2009. Software engineering the mixed model for genome-wide association studies on large samples. Briefings in Bioinformatics
10 (6): 664-675.##Zhao, Y., Li, Z., Liu, G., Jiang, Y., Maurer, H.P., Würschum, T., Mock, H.-P., Matros, A., Ebmeyer, E. and Schachschneider, R. 2015. Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding. Proceedings of the National Academy of Sciences 112 (51): 15624-15629.##Zhu, C., Gore, M., Buckler, E. S. and Yu, J. 2008. Status and prospects of association mapping in plants. The Plant Genome 1 (1): 5-20.##Zhu, X., Shao, X., Pei, Y., Guo, X., Li, J., Song, X. and Zhao, M. 2018. Genetic diversity and genome-wide association study of major ear quantitative traits using high-density SNPs in maize. Frontiers in Plant Science 9: 966.##