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pgr 2022, 9(1): 13-26 Back to browse issues page
Genome-Wide Association Study of Seedling Characteristics in Bread Wheat Cultivars Under Normal and Salt Stress Conditions
Razieh Ghorbani , Raheleh Ghasemzadeh * , Hadi Alipour
Abstract:   (536 Views)
In order to identify loci controlling seedling morpho-physiologic characteristics in 88 bread wheat cultivars, a greenhouse experiment based on simple alpha lattice was conducted under both normal and 120 mM (12 ds/m) salt stress condition of the Faculty of Agriculture, Urmia University in 2020-2021 cropping season. Chlorophyll a, b and carotenoid content, proline, plant fresh and dry weight, plant height and leaf relative water content (RWC), Na+, K+ and K+/Na+ concentrations were measured. After genotyping by sequencing with Ion Torrent technology and removal of SNPs with more than 20% of missing data and minor allele frequency less than 5%, a total of 5869 SNP markers were identified. Based on association mapping with the mixed linear model (MLM) method, a total of 25 marker-trait associations were detected under normal conditions. The A and D genomes had the highest and lowest number of significant marker-trait associations (MTAs). Among the studied traits under normal conditions, chlorophyll a had the highest number of MTAs on 1A, 3B, 3D, 5B, 7A chromosomes with eight MTAs. A total of 21 MTAs were identified under salt stress conditions which the genome B and D had the highest and lowest number of MTAs, respectively. Five MTAs were identified for plant fresh weight, which were located on chromosomes 4A and 6B. The results of this study provide valuable information about the loci associated with the studied traits, which can be used in marker assisted selection in wheat breeding programs after confirmation in biparental populations and additional experiments.
Keywords: Bread wheat cultivars, GWAS, Salt stress, SNP markers
Full-Text [PDF 1023 kb]   (85 Downloads)    
Type of Study: Research | Subject: Molecular genetics
Accepted: 2022/09/13
* Corresponding Author Address: Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
1. Akbari Ghogdi, E., Izadi-Darbandi, A., Borzouei, A. and Majdabadi, A. (2011). Evaluation of morphological changes in some wheat genotypes under salt stress. Journal of Soil and Plant Interactions-Isfahan University of Technology, 1(4): 71-83 (In Persian).
2. Akbarpour, O. and Dehghani, H. (2017). Genetic dissection of grain yield and some morphological traits in Iranian bread wheat under field normal and salt stress conditions using Jinks-Hayman approach. Cereal Research, 7(2): 155-169.
3. Akhunov, E.D., Akhunova, A.R., Anderson, O.D., Anderson, J.A., Blake, N., Clegg, M.T., Coleman-Derr, D., Conley, E.J., Crossman, C.C., Deal, K.R. and Dubcovsky, J. (2010). Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics, 11(1): 1-22. [DOI:10.1186/1471-2164-11-702]
4. Alipour, H., (2016). Association mapping of important agronomic traits in bread wheat. Ph.D. Thesis, University of Tehran, Tehran, Iran (In Persian).
5. Barajehfard, M., Siahpoosh, M.R., and Modarresi, M. (2017). QTLs associated with stemlet and rootlet growth in the early stages of germination of wheat. Plant Genetic Researches, 3(2): 59-68 (In Persian). [DOI:10.29252/pgr.3.2.59]
6. Bates, L.S., Waldren, R.P. and Teare, I.D. (1973). Rapid determination of free proline for water-stress studies. Plant and Soil, 39(1): 205-207. [DOI:10.1007/BF00018060]
7. 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. [DOI:10.1093/bioinformatics/btm308]
8. Chao, S., Dubcovsky, J., Dvorak, J., Luo, M.C., Baenziger, S.P., Matnyazov, R., Clark, D.R., Talbert, L.E., Anderson, J.A., Dreisigacker, S. and Glover, K. (2010). Population-and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics, 11(1): 1-17. [DOI:10.1186/1471-2164-11-727]
9. Chartzoulakis, K. and Klapaki, G. (2000). Response of two greenhouse pepper hybrids to NaCl salinity during different growth stages. Scientia Horticulturae, 86(3): 247-260. [DOI:10.1016/S0304-4238(00)00151-5]
10. Chaurasia, S., Singh, A.K., Songachan, L.S., Sharma, A.D., Bhardwaj, R. and Singh, K. (2020). Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.). Genomics, 112(6), 4608-4621. [DOI:10.1016/j.ygeno.2020.08.006]
11. Chen, X., Min, D., Yasir, T.A. and Hu, Y.G. (2012). Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PloS One, 7(9): e44510. [DOI:10.1371/journal.pone.0044510]
12. Edae, E.A., Byrne, P.F., Haley, S.D., Lopes, M.S. and Reynolds, M.P. (2014). Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theoretical and Applied Genetics, 127(4): 791-807. [DOI:10.1007/s00122-013-2257-8]
13. Edae, E.A., Bowden, R.L. and Poland, J. (2015). Application of Population Sequencing (POPSEQ) for ordering and imputing genotyping-by-sequencing markers in hexaploid wheat. G3: Genes, Genomes, Genetics, 5(12): 2547-2553. [DOI:10.1534/g3.115.020362]
14. Ersoz, E.S., Yu, J. and Buckler, E.S. (2009). Applications of Linkage disequilibrium and association mapping in maize. In: Kriz, A.L. and Larkins, B.A., Eds., Molecular Genetic Approaches to Maize Improvement, pp.173-195. Springer, Berlin, Heidelberg. [DOI:10.1007/978-3-540-68922-5_13]
15. Flint‐Garcia, S.A., Thuillet, A.C., Yu, J., Pressoir, G., Romero, S.M., Mitchell, S.E. and Buckler, E.S. (2005). Maize association population: a high‐resolution platform for quantitative trait locus dissection. The Plant Journal, 44(6): 1054-1064. [DOI:10.1111/j.1365-313X.2005.02591.x]
16. Flowers, T.J. (2004). Improving crop salt tolerance. Journal of Experimental Botany, 55(396): 307-319. [DOI:10.1093/jxb/erh003]
17. Gunes, A., Inal, A., Alpuslan, M., Fraslan, F., Guneri, E. and Cicek, N. (2007). Salicylic acid induced changes on some physiological parameters symptomatic for oxidative stress and mineral nutrition in maize grown under salinity. Journal of Plant Physiology, 164: 728-736. [DOI:10.1016/j.jplph.2005.12.009]
18. Hao, C., Wang, L., Ge, H., Dong, Y. and Zhang, X. (2011). Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS One, 6(2): e17279. [DOI:10.1371/journal.pone.0017279]
19. Hu, P., Zheng, Q., Luo, Q., Teng, W., Li, H., Li, B. and Li, Z. (2021). Genome-wide association study of yield and related traits in common wheat under salt-stress conditions. BMC Plant Biology, 21(1): 1-20. [DOI:10.1186/s12870-020-02799-1]
20. Jighly, A., Oyiga, B.C., Makdis, F., Nazari, K., Youssef, O., Tadesse, W. and Ogbonnaya, F.C. (2015). Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm. Theoretical and Applied Genetics, 128(7): 1277-1295. [DOI:10.1007/s00122-015-2504-2]
21. Long, N.V., Dolstra, O., Malosetti, M., Kilian, B., Graner, A., Visser, R.G. and van der Linden, C.G. (2013). Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 126(9): 2335-2351. [DOI:10.1007/s00122-013-2139-0]
22. Lu, F., Lipka, A.E., Glaubitz, J., Elshire, R., Cherney, J.H., Casler, M.D., Buckler, E.S. and Costich, D.E. (2013). Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics, 9(1): e1003215. [DOI:10.1371/journal.pgen.1003215]
23. Ma, Y., Qiu, C.W., Fan, Y., Huang, X., Khan, W., Wu, F., Zhou, M., Wang, Y. and Cao, F. (2022). Genome-wide association and transcriptome analysis reveals candidate genes for potassium transport under salinity stress in wheat. Environmental and Experimental Botany, 202: 105034. [DOI:10.1016/j.envexpbot.2022.105034]
24. Marcussen, T., Sandve, S.R., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K.S., Wulff, B.B., Steuernagel, B., Mayer, K.F., Olsen, O.A. and Rogers, J. (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science, 345(6194): 1250092.
25. Munns, R., Rebetzke, G.J., Husain, S., James, R.A. and Hare, R.A. (2003). Genetic control of sodium exclusion in durum wheat. Australian Journal of Agricultural Research, 54(7): 627-635. [DOI:10.1071/AR03027]
26. Naz, A.A., Dadshani, S., Ballvora, A., Pillen, K. and Léon, J. (2019). Genetic analysis and transfer of favorable exotic QTL alleles for grain yield across d genome using two advanced backcross wheat populations. Frontiers in Plant Science, 10: 711. [DOI:10.3389/fpls.2019.00711]
27. Nielsen, N.H., Backes, G., Stougaard, J., Andersen, S.U. and Jahoor, A. (2014). Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PloS One, 9(4): p.e94000. [DOI:10.1371/journal.pone.0094000]
28. Poland, J.A., Brown, P.J., Sorrells, M.E. and Jannink, J.L. (2012). Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS One, 7(2): 1-8. [DOI:10.1371/journal.pone.0032253]
29. Quan, X., Liu, J., Zhang, N., Xie, C., Li, H., Xia, X. and Qin, Y. (2021). Genome-wide association study uncover the genetic architecture of salt tolerance-related traits in common wheat (Triticum aestivum L.). Frontiers in Genetics, 12: 1-11. [DOI:10.3389/fgene.2021.663941]
30. Rahnama Ghahfarokhi, A., Poostini, R., Tavakol Afshar, A., Ahmadi, V. and Alizadeh, H. (2010). Physiological study of sodium excretion in different tissues of susceptible and tolerant cultivars of wheat (Triticum aestivum L.). Iranian Journal of Field Crop Science, 41(1): 79-92 (In Persian).
31. Salami, R., Mohammadi, S.A., Ghafarian, S., and Moghaddam, M. (2016). Expression analysis of Hv TIP2;3 and Hv TIP4;1 in sensitive and tolerant barley genotypes under salinity stress. Plant Genetic Researches, 2(2): 1-14 (In Persian). [DOI:10.29252/pgr.2.2.1]
32. Shahinnia, F., and Sayed Tabatabaei, B.E. (2013). EST-based marker discovery and SNP genotyping in plants genome. Modern Genetics Journal's, 8(2): 117-130 (In Persian).
33. Shavrukov, Y., Suchecki, R., Eliby, S., Abugalieva, A., Kenebayev, S. and Langridge, P. (2014). Application of next-generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan. BMC Plant Biology, 14(1): 1-13. [DOI:10.1186/s12870-014-0258-7]
34. Sun, C., Dong, Z., Zhao, L., Ren, Y., Zhang, N., and Chen, F. (2020). The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat. Plant Biotechnology Journal, 18(6): 1354-1360. [DOI:10.1111/pbi.13361]
35. Turki, N., Shehzad, T., Harrabi, M and Okuno, K. (2015). Detection of QTLs associated with salinity tolerance in durum wheat based on association analysis. Euphytica, 201(1): 29-41. [DOI:10.1007/s10681-014-1164-7]
36. Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B.E., Maccaferri, M., Salvi, S., Milner, S.G., Cattivelli, L. and Mastrangelo, A.M. (2014). Characterization of polyploid wheat genomic diversity using a high‐density 90000 single nucleotide polymorphism array. Plant Biotechnology Journal, 12(6): 787-796. [DOI:10.1111/pbi.12183]
37. Warburton, M.L., Crossa, J., Franco, J., Kazi, M., Trethowan, R., Rajaram, S., Pfeiffer, W., Zhang, P., Dreisigacker, S. and Van Ginkel, M. (2006). Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm. Euphytica, 149(3): 289-301. [DOI:10.1007/s10681-005-9077-0]
38. Würschum, T., Langer, S.M., Longin, C.F.H., Korzun, V., Akhunov, E., Ebmeyer, E., Schachschneider, R., Schacht, J., Kazman, E. and Reif, J.C. (2013). Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theoretical and Applied Genetics, 126(6): 1477-1486. [DOI:10.1007/s00122-013-2065-1]
39. Zeeshan, M., Lu, M., Sehar, S., Holford, P. and Wu, F. (2020). Comparison of biochemical, anatomical, morphological, and physiological responses to salinity stress in wheat and barley genotypes deferring in salinity tolerance. Agronomy, 10(1): 1-15. [DOI:10.3390/agronomy10010127]
40. Zegeye, H., Rasheed, A., Makdis, F., Badebo, A. and Ogbonnaya, F.C. (2014). Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat. PLoS One, 9(8): 1-18. [DOI:10.1371/journal.pone.0105593]
41. Zhang, L., Liu, D., Guo, X., Yang, W., Sun, J., Wang, D., Sourdille, P. and Zhang, A. (2011). Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genetics, 12(1): 1-11. [DOI:10.1186/1471-2156-12-42]
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Ghorbani R, Ghasemzadeh R, Alipour H. Genome-Wide Association Study of Seedling Characteristics in Bread Wheat Cultivars Under Normal and Salt Stress Conditions. pgr 2022; 9 (1) :13-26
URL: http://pgr.lu.ac.ir/article-1-254-en.html

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