Study of Genetic Diversity and Population Structure in Barley (Hordeum vulgare L.) Based on SNP Markers

Document Type : Research Paper

Authors

1 Seed and Plant Improvement Institute, Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran

2 Seed and Plant Improvement Institute, Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran

3 Seed and Plant Improvement Institute, Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran.

Abstract

Barley is a major crop and the fourth most important cereal in the world. Genetic diversity is a basic component in breeding programs and is crucial for successful barley improvement. SNPs are a good marker type to study diversity. SNPs represent the most abundant source of genetic variation within the genome and are linked to heritable differences between individuals. in this study we used diverse collection of 100 winter barley (Hordeum vulgare L.) to assess genetic diversity and population structure. Population was genotyped using 3964 SNPs with minor allele frequencies (MAFs) more than 10 percent. PIC was ranged from 0.19 to 0.5 in the whole panel and it was more than 0.25 for 3352 markers. The average of PIC was varied from 0.37 (2H and 5H chromosomes) to 0.42 (3H and 7H chromosomes). strong population structure effect related to ear row number (two-row and six-row) was present in our barley collection. AMOVA analysis and Fst index showed that differentiated regions of genome are correspondence with ear row number loci. In the whole genome, average linkage disequilibrium (LD) was observed to decay at 4cM and in sub populations was more than whole panel. LD decay was more rapid in six-row cultivars compared to two-row. These results indicated considerable genetic variation in winter barley collection and could be used in barley improvement programs.

Keywords

Main Subjects


  1. Barrett, J. C., Fry, B., Maller, J. & Daly, M. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265.
  2. Bolot, S., Abrouk, M., Masood-Quraishi, U., Stein, N., Messing, J., Feuillet, C. & Salse, J. (2009). The ‘inner circle’of the cereal genomes. Current opinion in plant biology, 12(2), 119-125.
  3. Caldwell, K. S., Russell, J., Langridge, P. & Powell, W. (2006). Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics, 172(1), 557-567.
  4. Chen, C., Li, S., Wang, S., Liu, H., Deng, Q., Zheng, A., Zhu, J., Wang, L. & Li, P. (2011). Assessment of the Genetic Diversity and Genetic Structure of Rice Core Parent Guichao 2, its Parents and Derivatives J. Plant Science, 6, 66-76.
  5. Comadran, J., Thomas, W., Van Eeuwijk, F., Ceccarelli, S., Grando, S., Stanca, A., Pecchioni, N., Akar, T., Al-Yassin, A. & Benbelkacem, A. (2009). Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theoretical and Applied Genetics, 119(1), 175-187.
  6. Edwards, K., Mogg, R. & Henry, R. (2001). Plant genotyping by analysis of single nucleotide polymorphisms. In: R. J. Henry (Ed.). Plant genotyping: the DNA fingerprinting of plants (pp. 1-13). UK: CABI.
  7. Evanno, G., Regnaut, S. & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology, 14(8), 2611-2620.
  8. Excoffier, L. & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources, 10(3), 564-567.
  9. Ferreira, J. R., Pereira, J. F., Turchetto, C., Minella, E., Consoli, L. & Delatorre, C. A. (2016). Assessment of genetic diversity in Brazilian barley using SSR markers. Genetics and molecular biology, 39(1), 86-96.

10. Flint-Garcia, S. A., Thornsberry, J. M. & IV, B. (2003). Structure of Linkage Disequilibrium in Plants. Annual Review of Plant Biology, 54(1), 357-374.

11. Flint‐Garcia, S. A., Thuillet, A. C., Yu, J., Pressoir, G., Romero, S. M., Mitchell, S. E., Doebley, J., Kresovich, S., Goodman, M. M. & Buckler, E. S. (2005). Maize association population: a high‐resolution platform for quantitative trait locus dissection. The plant journal, 44(6), 1054-1064.

12. Gupta, P. K. & Varshney, R. K. (2005). Cereal genomics: an overview. Cereal Genomics (pp. 1-18): Springer.

13. Hamblin, M. T., Close, T. J., Bhat, P. R., Chao, S., Kling, J. G., Abraham, K. J., Blake, T., Brooks, W. S., Cooper, B. & Griffey, C. A. (2010). Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Science, 50(2), 556-566.

14. Hammer, Ø., Harper, D. A. T. & Ryan, P. D. (2001). PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica, 4(1), 1-9.

15. Jacoby, W. G. (2000). Loess:: a nonparametric, graphical tool for depicting relationships between variables. Electoral Studies, 19(4), 577-613.

16. Jain, S. M., Brar, D. S. & Ahloowalia, B. S. (2002). Molecular Techniques in Crop Improvement. Kluwer Academic Pub.

17. Kanazin, V., Talbert, H., See, D., DeCamp, P., Nevo, E. & Blake, T. (2002). Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant molecular biology, 48(5-6), 529-537.

18. Kraakman, A. T., Niks, R. E., Van den Berg, P. M., Stam, P. & Van Eeuwijk, F. A. (2004). Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics, 168(1), 435-446.

19. Laurentin, H. (2009). Data analysis for molecular characterization of plant genetic resources. Genetic Resources and Crop Evolution, 56(2), 277-292.

20. Malysheva-Otto, L. V., Ganal, M. W. & Röder, M. S. (2006). Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC genetics, 7(1), 6.

21. Mandel, J. R., Nambeesan, S., Bowers, J. E., Marek, L. F., Ebert, D., Rieseberg, L. H., Knapp, S. J. & Burke, J. M. (2013). Association Mapping and the Genomic Consequences of Selection in Sunflower. PLoS genetics, 9(3), e1003378.

22. Mayer, K. F., Taudien, S., Martis, M., Šimková, H., Suchánková, P., Gundlach, H., Wicker, T., Petzold, A., Felder, M. & Steuernagel, B. (2009). Gene content and virtual gene order of barley chromosome 1H. Plant Physiology, 151(2), 496-505.

23. Melchinger, A. E., Graner, A., Singh, M. & Messmer, M. M. (1994). Relationships among European barley germplasm: I. Genetic diversity among winter and spring cultivars revealed by RFLPs. Crop Science, 34(5), 1191-1199.

24. Nasu, S., Suzuki, J., Ohta, R., Hasegawa, K., Yui, R., Kitazawa, N., Monna, L. & Minobe, Y. (2002). Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA research, 9(5), 163-171.

25. Nour-Mohammadi, G., Siadat, A. & Kashani, A. (2004). Cereal Crops (Vol. 1). Iran. Shahid Chamran University.

26. Pasam, R. K., Sharma, R., Malosetti, M., van Eeuwijk, F. A., Haseneyer, G., Kilian, B. & Graner, A. (2012). Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology, 12(1), 16.

27. Pasam, R. K., Sharma, R., Walther, A., Özkan, H., Graner, A. & Kilian, B. (2014). Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates. PLoS One, 9(12), e116164.

28. Paschou, P., Ziv, E., Burchard, E. G., Choudhry, S., Rodriguez-Cintron, W., Mahoney, M. W. & Drineas, P. (2007). PCA-correlated SNPs for structure identification in worldwide human populations. PLoS genetics, 3(9), 1672-1686.

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

30. Ramsay, L., Comadran, J., Druka, A., Marshall, D. F., Thomas, W. T., Macaulay, M., MacKenzie, K., Simpson, C., Fuller, J. & Bonar, N. (2011). INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nature genetics, 43(2), 169-172.

31. Rostoks, N., Ramsay, L., MacKenzie, K., Cardle, L., Bhat, P. R., Roose, M. L., Svensson, J. T., Stein, N., Varshney, R. K. & Marshall, D. F. (2006). Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proceedings of the National Academy of Sciences, 103(49), 18656-18661.

32. Schulte, D., Close, T. J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A. H., Waugh, R. & Wise, R. P. (2009). The international barley sequencing consortium—at the threshold of efficient access to the barley genome. Plant Physiology, 149(1), 142-147.

33. Shahinnia, F., Ebrahim Sayed-Tabatabaei, B., Sato, K., Pourkheirandish, M. & Komatsuda, T. (2009). Mapping of QTL for intermedium spike on barley chromosome 4H using EST-based markers. Breeding science, 59(4), 383-390.

34. Sreenivasulu, N., Graner, A. & Wobus, U. (2008). Barley genomics :an overview. International journal of plant genomics, 2008, 1-13.

35. Stracke, S., Presterl, T., Stein, N., Perovic, D., Ordon, F. & Graner, A. (2007). Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley. Genetics, 175(2), 805-817.

36. Tondelli, A., Xu, X., Moragues, M., Sharma, R., Schnaithmann, F., Ingvardsen, C., Manninen, O., Comadran, J., Russell, J. & Waugh, R. (2013). Structural and temporal variation in genetic diversity of European spring two-row barley cultivars and association mapping of quantitative traits. The plant genome, 6(2), 1-14.

37. Wicker, T., Narechania, A., Sabot, F., Stein, J., Vu, G. T., Graner, A., Ware, D. & Stein, N. (2008). Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC genomics, 9(1), 518.

38. Wicker, T., Schlagenhauf, E., Graner, A., Close, T., Keller, B. & Stein, N. (2006). 454 sequencing put to the test using the complex genome of barley. BMC genomics, 7(1), 275.

39. Yeh, F. C., Yang, R., Boyle, T., Ye, Z. & Mao, J. X. (1999). POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, Canada.

40. Zhang, L. Y., Marchand, S., Tinker, N. A. & Belzile, F. (2009). Population structure and linkage disequilibrium in barley assessed by DArT markers. Theoretical and Applied Genetics, 119(1), 43-52.

 

Volume 49, Issue 2
August 2018
Pages 35-59
  • Receive Date: 15 May 2017
  • Revise Date: 02 September 2017
  • Accept Date: 05 September 2017
  • Publish Date: 23 July 2018