|
Identification of genomic loci controlling phenologic and morphologic traits in barley (Hordeum vulgare L.) genotypes using association analysis
|
Zahra Koochakpour   , Mahmood Solouki , Barat Ali Fakheri , Reza Aghnoum , Nafiseh Mahdi Nezhad , Mitra Jabbari |
| Professor, University of Zabol, Zabol, Iran |
|
|
Abstract: (1665 Views) |
| Association mapping is a technique with high resolution for QTL mapping based on linkage disequilibrium and has shown more promising for describing genetically complex traits. In addition, it is a powerful tool for describing complex agronomic traits and identifying alleles that can contribute to enhance the desired traits. In this study, whole genome association mapping was used in a set of 148 spring barley cultivars. Phenotypic evaluation was conducted at Zahak Agricultural Research Station, Iran, using alpha-lattice design with two replications, for two croppinhg cycle (2014-2015 and 2015-2016). Traits such as days to anthesis, days to physiological maturity, grain filling period, flag leaf length, flag leaf width, grain number per main spike, thousand grain weight and grain yield were measured. Association analysis between the markers and phenotypic traits was performed with a mixed linear model (MLM with K+Q). In total 28 QTLs were identified which were related to the measured traits. A stable QTL was detected on chromosome 5H (74.76 cM) for days to anthesis. Three QTLs were detected on chromosomes 4H (125.08 cM and 120.64 cM) and 5H (74.76 cM) for grain filling period. One QTL on chromosome 2H (10.87 cM) was associated with days to anthesis, grain filling period and 1000 grain weight. One QTL on chromosome 4H (125.08 cM) was also associated with days to anthesis, grain filling period as well as flag leaf length and 1000 grain weight. Common genetic locations for these traits could be due to pleiotropic effects or genetic linkage. |
|
| Keywords: Association mapping, Barley, Chromosome, Genomic loci and Thousand grain weight. |
|
|
Full-Text [PDF 899 kb]
(775 Downloads)
|
Type of Study: Scientific & Research |
Subject:
Special
Received: 2019/05/5 | Accepted: 2021/01/12 | Published: 2021/02/28
|
|
|
|
|
|
|
| References |
1. Abou-Elwafa, S.F. 2016a. Association mapping for drought tolerance in barley at the reproductive stage. Comptes Rendus Biologies. 339(2): 51-59. [ DOI:10.1016/j.crvi.2015.12.002] 2. Abou-Elwafa, S.F. 2016b. Association mapping for yield and yield-contributing traits in barley under drought conditions with genome-based SSR markers. Comptes Rendus Biologies. 339(5-6): 153-162. [ DOI:10.1016/j.crvi.2016.03.001] 3. Aghnoum, R., T.C. Marcel, A. Johrde, N. Pecchioni, P. Schweizer and R.E. Niks. 2010. Basal host resistance of barley to powdery mildew connecting quantitative trait loci and candidate genes. MPMI. 23(1): 91-102. [ DOI:10.1094/MPMI-23-1-0091] 4. Alqudah, A.M and T. Schnurbusch. 2017. Heading date is not flowering time in spring barley. Front. Plant Sci. 8: 896. DOI: 10.3389/fpls.2017.00896. [ DOI:10.3389/fpls.2017.00896] 5. Bradbury, P.J., Z. Zhang, D.E. Kroon, T.M. Casstevens, Y. Ramdoss and E.S. Buckler. 2007. TASSEL software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19): 2633-2635. [ DOI:10.1093/bioinformatics/btm308] 6. Buckler, E.S. and J.M. Thornsberry. 2002. Plant molecular diversity and applications to genomics. Curr. Opinion Plant Biol. 5(2): 107-111. [ DOI:10.1016/S1369-5266(02)00238-8] 7. Chen, G., T. Krugman, T. Fahima, K. Chen, Y. Hu, M. Roder, E. Nevo and A. Korol. 2010. Chromosomal regions controlling seedling drought resistance in Israeli wild barley, Hordeum spontaneum C. Koch. Genet. Resour. Crop Evol. 57(1): 85-99. [ DOI:10.1007/s10722-009-9453-z] 8. Chen, C.X., S.C. Li, S.Q. Wang, H.N. Liu, Q.M. Deng, A.P. Zheng, J. Zho, L.X. Wang and P. Li. 2011. Assessment of the genetic diversity and genetic structure of rice core parent Guichao2, its parents and derivatives. J. Plant Sci. 6: 66-76. [ DOI:10.3923/jps.2011.66.76] 9. Diab, A.A., B. Teulat, D. This, N.Z. Ozturk, D. Benscher and M.E. Sorrells. 2004. Identification of drought-inducible genes and differentially expressed sequence tags in barley. Theor. Appl. Genet. 109: 1417-1425. [ DOI:10.1007/s00122-004-1755-0] 10. El-Mohsen, A.A.A. 2013. Correlation and regression analysis in barley. World Essays J. 1(3): 88-100. 11. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620. [ DOI:10.1111/j.1365-294X.2005.02553.x] 12. Gordon, D. and S.J. Finch. 2005. Factors affecting statistical power in the detection of genetic association. J. Clin. Invest. 115(6): 1408-1418. [ DOI:10.1172/JCI24756] 13. Jabbari, M., B.A. Fakheri, R. Aghnoum, N. Mahdi Nezhad, and R. Ataei. 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. [ DOI:10.1371/journal.pone.0204952] 14. Kraakman, A.T.W., R.E. Niks, P.M.M.M. Van den Berg, P. Stam and F.A. Van Eeuwijk. 2004. Linkage disequilibrium mapping of yield stability in modern spring barley cultivars. Genetics, 168(1): 435-446. [ DOI:10.1534/genetics.104.026831] 15. Kraakman, A.T.W., F. Martinez, B. Mussiraliev, F.A. Van Eeuwijk and R.E. Niks. 2006. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol. Breed. 17: 41-58. [ DOI:10.1007/s11032-005-1119-8] 16. Kushwaha, U.K.S., V. Mangal, A.K. Bairwa, S. Adhikari, T. Ahmed, P. Bhat, A. Yadav, N. Dhaka, D.R. Prajapati, A. Gaur, R. Tamta, I. Deo and N.K. Singh. 2017. Association mapping, principles and techniques. J. Biol. Environ. Engin. 2(1): 1-9. 17. Locatelli, A., A. Cuesta-Marcos, L. Gutierrez, P.M. Heyes, K.P. Smith and A.J. Castro. 2013. Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay. Mol. Breed. 31(3): 631-654. [ DOI:10.1007/s11032-012-9820-x] 18. Marathi, B., S. Guleria, T. Mohapatra, R. Parsad, N. Mariappan, V.K. Kurungara, S.S. Atwal, K.V. Prabhu, N.K. Singh and A.K. Singh. 2012. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.). BMC Plant Biol. 12: 137. [ DOI:10.1186/1471-2229-12-137] 19. Mueller, J.C. 2004. Linkage disequilibrium for different scales and applications. Brief Bioinform. 5: 355-364. [ DOI:10.1093/bib/5.4.355] 20. Pasam, R.K., R. Sharma, M. Malosetti, F.A. Van Eeuwijk, G. Haseneyer, B. Kilian and A. Graner. 2012. Genome-wide association studies for agronomical traits in a worldwide spring barley collection. BMC Plant Biol, 12: 16. [ DOI:10.1186/1471-2229-12-16] 21. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959. 22. Ramsay L., M. Macaulay, S. Degli-Ivanissevich, K. MacLean, L. Cardle, J. Fuller, K.J. Edwards, S. Tuvesson, M. Morgante, A. Massari, E. Maestri, N. Marmiroli, T. Sjakste, M. Ganal, W. Powell and R. Waugh. 2000. A simple sequence repeats based linkage map of barley. Genetics, 156: 1997-2005. 23. Ramsay, L., J. Comadran, A. Druka, D.F. Marshall, W.T. Thomas, M. Macaulay, K. MacKenzie, K. Simpson, J. Fuller, N. Bonar, P.M. Hayes, U. Lundqvist, J.D. Franckowiak, T.J. Close, G.J. Muhlbauer and R. Waugh. 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Natur. Genet. 43(2): 169-172. [ DOI:10.1038/ng.745] 24. Rustgi, S., M.N. Shafaqat, N. Kumar, P.S. Baenziger, M.L. Ali, I. Dweikat, B.T. Campbell and K.S. Gill. 2013. Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes. PLOS ONE, 8(7): e70526 .doi:10.1371/journal.pone.0070526. [ DOI:10.1371/journal.pone.0070526] 25. Spiertz, J.H.J., B.A. Tenhag and L.J.P. Kupers. 1971. Relation between green area duration and grain yield in some varieties of spring wheat. Neth. J. Agric. Sci. 19: 211-222. [ DOI:10.18174/njas.v19i4.17302] 26. Sun, D., W. Ren, G. Sun and J. Peng. 2011. Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm. Euphytica, 178: 31-43. [ DOI:10.1007/s10681-010-0260-6] 27. Wang, J., G. Sun, X. Ren, C. Li, L. Liu, Q. Wang, B. Du and D. Sun. 2016. QTL underlying some agronomic traits in barley detected by SNP markers. BMC Genet. 17: 103. [ DOI:10.1186/s12863-016-0409-y] 28. Xu, X., R. Sharma, A. Tondelli, J. Russell, J. Comadran, F. Schnaithmann, K. Pillen, B. Kilian, L. Cattivelli, W.T.B. Thomas and A.J. Flavell. 2018. Genome-wide association analysis of grain yield-association traits in a Pan-European barley cultivar collection. Plant Genome, 11(1): 170073. [ DOI:10.3835/plantgenome2017.08.0073] 29. Xue, D.W., M.C. Chen, M.X. Zhou, S. Chen, Y. Mao and G.P. Zhang. 2008. QTL analysis of flag leaf in barley (Hordeum vulgare L.) for morphological traits and chlorophyll content. J. Zhejiang Univ. Sci. B. 9(12): 938-943. [ DOI:10.1631/jzus.B0820105] 30. Yan, J., M. Warburton and J. Crouch. 2011. Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Sci. 51: 433-449. [ DOI:10.2135/cropsci2010.04.0233] |
|
| Send email to the article author |
|
|
|
| Add your comments about this article |
|
|
|
|
Koochakpour Z, Solouki M, Fakheri B A, Aghnoum R, Mahdi Nezhad N, Jabbari M. Identification of genomic loci controlling phenologic and morphologic traits in barley (Hordeum vulgare L.) genotypes using association analysis. علوم زراعی 2021; 22 (4) :291-304 URL: http://agrobreedjournal.ir/article-1-987-en.html
|
