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:: Volume 10, Issue 1 (2023) ::
pgr 2023, 10(1): 95-110 Back to browse issues page
Evaluation of Population Structure in Some Bread and Durum Wheat Genotypes Using SNP Markers and PCA and DAPC Methods
Hossein Abdi , Hadi Alipour * , Iraj Bernousi , Jafar Jafarzadeh
Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran , ha.alipour@urmia.ac.ir
Abstract:   (2968 Views)
Evaluating the population structure is essential for understanding diversity patterns, choosing proper parents for crossing, accurate identification of genomic regions controlling traits, and evolutionary and kinship relationship studies. In this research, the genetic structure of a wheat population was studied in a panel consisting of 383 Iranian wheat genotypes of hexaploid (cultivars and landraces) and tetraploid species based on distance-based methods (principal component analysis and discriminant analysis of principal component). For this purpose, 16270 single nucleotide polymorphism (SNP) markers obtained by the GBS technique were used. According to the results, almost a quarter of the total variance was belonged to the diversity between populations, and the Fst coefficient between cultivars and landraces was equal to 0.15. In contrast, the above coefficient between tetraploid samples and hexaploid landraces was high and equal to 0.44. Genome D had the lowest value of Fst index and chromosome 4B showed the highest Fst coefficient, and other genetic diversity indices. Although the PCA biplot distinguished hexaploid wheat cultivars from landraces, it was unable to distinctly separate tetraploid genotypes from other genotypes. Accurate evaluation of the population structure with the DAPC method was able to identify and separate the predetermined successfully groups, suggesting that the DAPC approach maximizes the differentiation between groups and minimizes the changes within the group. Partial admixture between cultivars and landraces of hexaploid wheat can be related to gene exchange between these two groups or perhaps their wrong labeling at the time of collection. In general, the results of this study provided valuable information about the genetic differentiation of Iranian tetraploid and hexaploid wheat, which can be used in future wheat breeding programs. Further, protecting these genotypes in gene banks is necessary for different strategies.
Keywords: Cultivars, Landraces, Fixation index, Tetraploid and hexaploid wheat, SNP markers
Full-Text [PDF 702 kb]   (1288 Downloads)    
Type of Study: Research | Subject: Molecular genetics
References
1. Abdi, H., Alipour, H., Bernousi, I., Jafarzadeh, J. and Rodrigues, P.C. (2023). Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS. Scientific Reports, 13(1): 9927. [DOI:10.1038/s41598-023-36134-z]
2. Alemu, A., Feyissa, T., Letta, T. and Abeyo, B. (2020). Genetic diversity and population structure analysis based on the high-density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum). BMC Genetics, 21(1): 1-12. [DOI:10.1186/s12863-020-0825-x]
3. Alipour, H. (2016). Association mapping of the main agronomic traits in bread wheat. PhD Thesis. University of Tehran, Tehran, Iran (In Persian).
4. Alipour, H., Bai, G., Zhang, G., Bihamta, M.R., Mohammadi, V. and Peyghambari, S.A. (2019). Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references. PLoS One, 14(1): e0208614. [DOI:10.1371/journal.pone.0208614]
5. Alipour, H., Bihamta, M.R., Mohammadi, V., Peyghambari, S.A., Bai, G. and Zhang, G. (2017). Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Frontiers in Plant Science, 8: 1293. [DOI:10.3389/fpls.2017.01293]
6. Ayalew, H., Sorrells, M.E., Carver, B.F., Baenziger, P.S. and Ma, X.F. (2020). Selection signatures across seven decades of hard winter wheat breeding in the Great Plains of the United States. The Plant Genome, 13(3): e20032. [DOI:10.1002/tpg2.20032]
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. Campoy, J.A., Lerigoleur-Balsemin, E., Christmann, H., Beauvieux, R., Girollet, N., Quero-García, J., Dirlewanger, E. and Barreneche, T. (2016). Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC Plant Biology, 16(1): 1-15. [DOI:10.1186/s12870-016-0712-9]
9. Cavanagh, C.R., Chao, S., Wang, S., Huang, B.E., Stephen, S., Kiani, S., Forrest, K., Saintenac, C., Brown-Guedira, G.L., Akhunova, A. and See, D. (2013). Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Sciences, 110(20): 8057-8062. [DOI:10.1073/pnas.1217133110]
10. 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]
11. Deperi, S.I., Tagliotti, M.E., Bedogni, M.C., Manrique-Carpintero, N.C., Coombs, J., Zhang, R., Douches, D. and Huarte, M.A. (2018). Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs. PloS One, 13(3): e0194398. [DOI:10.1371/journal.pone.0194398]
12. Elhaik, E. (2022). Principal component analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Scientific Reports, 12(1): 14683. [DOI:10.1038/s41598-022-14395-4]
13. Fayaz, F., Aghaee Sarbarzeh, M., Talebi, R. and Azadi, A. (2019). Genetic diversity and molecular characterization of Iranian durum wheat landraces (Triticum turgidum durum (Desf.) Husn.) using DArT markers. Biochemical Genetics, 57: 98-116. [DOI:10.1007/s10528-018-9877-2]
14. Fiore, M.C., Blangiforti, S., Preiti, G., Spina, A., Bosi, S., Marotti, I., Mauceri, A., Puccio, G., Sunseri, F. and Mercati, F. (2022). Elucidating the genetic relationships on the original old Sicilian Triticum Spp. collection by SNP genotyping. International Journal of Molecular Sciences, 23(21): 13378. [DOI:10.3390/ijms232113378]
15. Getachew, S.E., Ngalle, H.B., Joseph, M.B. and Wosene, G. (2019). Genotyping by sequencing for plant breeding- A review. Advances in Microbiology and Biotechnology, 14: 555891.
16. Ghorbani, R., Chasemzadeh, R. and Alipour, H. (2023). Genome-wide association study of seedling characteristics in bread wheat cultivars under normal and salt stress conditions. Plant Genetic Researches, 9(1): 13-26 (In Persian). [DOI:10.52547/pgr.9.1.2]
17. Hussain, S., Habib, M., Ahmed, Z., Sadia, B., Bernardo, A., Amand, P.S., Bai, G., Ghori, N., Khan, A.I., Awan, F.S. and Maqbool, R. (2022). Genotyping-by-sequencing based molecular genetic diversity of Pakistani bread wheat (Triticum aestivum L.) accessions. Frontiers in Genetics, 13: 772517. [DOI:10.3389/fgene.2022.772517]
18. Janes, J.K., Miller, J.M., Dupuis, J.R., Malenfant, R.M., Gorrell, J.C., Cullingham, C.I. and Andrew, R.L. (2017). The K= 2 conundrum. Molecular Ecology, 26(14): 3594-3602. [DOI:10.1111/mec.14187]
19. Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11): 1403-1405. [DOI:10.1093/bioinformatics/btn129]
20. Jombart, T., Devillard, S. and Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11(1): 1-15. [DOI:10.1186/1471-2156-11-94]
21. Kabbaj, H., Sall, A.T., Al-Abdallat, A., Geleta, M., Amri, A., Filali-Maltouf, A., Belkadi, B., Ortiz, R. and Bassi, F.M. (2017). Genetic diversity within a global panel of durum wheat (Triticum durum) landraces and modern germplasm reveals the history of alleles exchange. Frontiers in Plant Science, 8: 1277. [DOI:10.3389/fpls.2017.01277]
22. Khadka, K., Torkamaneh, D., Kaviani, M., Belzile, F., Raizada, M.N. and Navabi, A. (2020). Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm. BMC Plant Biology, 20(1): 1-12. [DOI:10.1186/s12870-020-02722-8]
23. Liu, L., Zhang, D., Liu, H. and Arendt, C. (2013). Robust methods for population stratification in genome wide association studies. BMC Bioinformatics, 14: 1-12. [DOI:10.1186/1471-2105-14-132]
24. Mahboubi, M., Mehrabi, R., Naji, A.M. and Talebi, R. (2020). Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform. 3 Biotech, 10(2): 48. [DOI:10.1007/s13205-019-2014-z]
25. Miazzi, M.M., Babay, E., De Vita, P., Montemurro, C., Chaabane, R., Taranto, F. and Mangini, G. (2022). Comparative genetic analysis of durum wheat landraces and cultivars widespread in Tunisia. Frontiers in Plant Science, 13: 939609. [DOI:10.3389/fpls.2022.939609]
26. MirMohammadi Maibody, S.A.M. and Golkar, P. (2019). Application of DNA molecular markers in plant breeding. Plant Genetic Researches, 6(1): 1-30 (In Persian). [DOI:10.29252/pgr.6.1.1]
27. Müller, T., Schierscher-Viret, B., Fossati, D., Brabant, C., Schori, A., Keller, B. and Krattinger, S.G. (2018). Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt. Theoretical and Applied Genetics, 131: 407-416. [DOI:10.1007/s00122-017-3010-5]
28. 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): e94000. [DOI:10.1371/journal.pone.0094000]
29. Patterson, N., Price, A.L. and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genetics, 2(12): e190. [DOI:10.1371/journal.pgen.0020190]
30. Peakall, R.O.D. and Smouse, P.E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1): 288-295. [DOI:10.1111/j.1471-8286.2005.01155.x]
31. Peng, J.H., Sun, D. and Nevo, E. (2011). Domestication evolution, genetics and genomics in wheat. Molecular Breeding, 28: 281-301. [DOI:10.1007/s11032-011-9608-4]
32. 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): e32253. [DOI:10.1371/journal.pone.0032253]
33. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38(8): 904-909. [DOI:10.1038/ng1847]
34. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959. [DOI:10.1093/genetics/155.2.945]
35. Pritchard, J.K., Wen, X. and Falush, D. (2010). Documentation for Structure Software. University of Chicago, Chicago, IL, USA.
36. Privé, F., Luu, K., Blum, M. G., McGrath, J.J. and Vilhjálmsson, B.J. (2020). Efficient toolkit implementing best practices for principal component analysis of population genetic data. Bioinformatics, 36(16): 4449-4457. [DOI:10.1093/bioinformatics/btaa520]
37. Qin, X., Chiang, C.W. and Gaggiotti, O.E. (2022). KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis. Briefings in Bioinformatics, 23(4): bbac202. [DOI:10.1093/bib/bbac202]
38. Rabieyan, E., Bihamta, M. R., Moghaddam, M.E., Mohammadi, V. and Alipour, H. (2022). Genome-wide association mapping and genomic prediction for pre harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat. BMC Plant Biology, 22(1): 1-23. [DOI:10.1186/s12870-022-03628-3]
39. Rahimi, Y., Bihamta, M.R., Taleei, A., Alipour, H. and Ingvarsson, P.K. (2019). Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC Plant Biology, 19(1): 1-19. [DOI:10.1186/s12870-019-2165-4]
40. Rasheed, A., Xia, X., Mahmood, T., Quraishi, U.M., Aziz, A., Bux, H., Mahmood, Z., Mirza, J.I., Mujeeb‐Kazi, A. and He, Z. (2016). Comparison of economically important loci in landraces and improved wheat cultivars from Pakistan. Crop Science, 56(1): 287-301. [DOI:10.2135/cropsci2015.01.0015]
41. Rimbert, H., Darrier, B., Navarro, J., Kitt, J., Choulet, F., Leveugle, M., Duarte, J., Rivière, N., Eversole, K., International Wheat Genome Sequencing Consortium and Le Gouis, J. (2018). High throughput SNP discovery and genotyping in hexaploid wheat. PloS One, 13(1): e0186329. [DOI:10.1371/journal.pone.0186329]
42. Sansaloni, C., Franco, J., Santos, B., Percival-Alwyn, L., Singh, S., Petroli, C., Campos, J., Dreher, K., Payne, T., Marshall, D. and Kilian, B. (2020). Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nature Communications, 11(1): 4572. [DOI:10.1038/s41467-020-18404-w]
43. Sharifi-Tehrani, M. (2018). A review on the analysis of population genetic structure using dominant molecular markers and introducing the new program STRUCTUREasy. Taxonomy and Biosystematics, 10(36): 35-47 (In Persian).
44. Sthapit, S.R., Ruff, T.M., Hooker, M.A. and See, D.R. (2022). Population structure and genetic diversity of US wheat varieties. The Plant Genome, 15(2): e20196. [DOI:10.1002/tpg2.20196]
45. Tehseen, M.M., Tonk, F.A., Tosun, M., Istipliler, D., Amri, A., Sansaloni, C.P., Kurtulus, E., Mubarik, M.S. and Nazari, K. (2022). Exploring the genetic diversity and population structure of wheat landrace population conserved at ICARDA GenBank. Frontiers in Genetics, 13: 900572. [DOI:10.3389/fgene.2022.900572]
46. Vikram, P., Franco, J., Burgueño, J., Li, H., Sehgal, D., Saint‐Pierre, C., Ortiz, C., Singh, V.K., Sneller, C., Sharma, A. and Tattaris, M. (2021). Strategic use of Iranian bread wheat landrace accessions for genetic improvement: Core set formulation and validation. Plant Breeding, 140(1): 87-99. [DOI:10.1111/pbr.12885]
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Abdi H, Alipour H, Bernousi I, Jafarzadeh J. Evaluation of Population Structure in Some Bread and Durum Wheat Genotypes Using SNP Markers and PCA and DAPC Methods. pgr 2023; 10 (1) :95-110
URL: http://pgr.lu.ac.ir/article-1-280-en.html


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Volume 10, Issue 1 (2023) Back to browse issues page
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