Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions
Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
10.22034/pgr.2026.2083043.1029
Abstract
Genomic selection represents one of the most significant advances in the early 21st century plant and animal breeding. To estimate breeding values and identify desirable genotypes, 81 commercial bread wheat cultivars were evaluated during the 2018–2019 growing season under well-watered (normal irrigation) and rainfed conditions. The experiment was conducted using a simple lattice design at the research fields of the Dryland Agricultural Research Institute, Maragheh, Iran. After SNP calling and the removal of markers with more than 10% missing data and a minor allele frequency below 10%, a total of 37,990 SNPs were retained for genomic selection analyses in both environmental conditions. Results indicated that Bayesian methods exhibited higher accuracy and performance. Based on cluster and principal component analyses, under normal irrigation, the cultivars Gahar, Arta, Adl, Pishtaz, Chamran 2, Tajan, and Atrak were identified as desirable in terms of breeding values and grain yield. Under rainfed conditions, the cultivars Maroon, Hamoon, Reyhani, Azadi, Atrak, Inia, Golestan, Naz, and Frontana were selected as superior genotypes. A genome-wide association study (GWAS) using the mixed linear model (MLM) identified 503 and 394 marker–trait associations under normal irrigation and rainfed conditions, respectively. Key markers consistently associated with grain yield and related traits across both conditions included rs63088, rs58821, rs16655, rs20678, rs23370, and rs51942. Gene ontology analysis of significant SNPs identified four key pathways associated with drought adaptation and tolerance in wheat: phenylalanine ammonia-lyase (PAL) on chromosome 2B, arginine and proline metabolism on chromosome 5A, lipid peroxidation such as sphingolipids on chromosome 3D, and lipoic acid metabolism on chromosome 5B.
Abdi, H., Alipour, H., Bernousi, I. and Jafarzadeh, J. (2023). Evaluation of population structure in some bread and durum wheat genotypes using SNP markers and PCA and DAPC methods. Plant Genetic Research, 10(1): 95-110 (In Persian). https://doi.org/10.22034/pgr.10.1.6
Ahmad, P., Jamsheed, S., Hameed, A., Rasool, S., Sharma, I., Azooz, M.M. and Hasanuzzaman, M. (2014). Drought stress induced oxidative damage and antioxidants in plants. In Oxidative damage to plants (pp. 345-367). Academic Press.https://doi.org/10.1016/B978-0-12-799963-0.00011-3
Alemu, A., Åstrand, J., Montesinos-López, O.A., Sánchez, J.I.Y., Fernández-González, J., Tadesse, W., Vetukuri, R.R., Carlsson, A.S., Ceplitis, A., Crossa, J., Ortiz, R. and Chawade, A. (2024). Genomic selection in plant breeding: Key factors shaping two decades of progress. Molecular Plant, 17(4): 552-578. https://doi.org/10.1016/j.molp.2024.03.007
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. https://doi.org/10.3389/fpls.2017.01293
Ed-Daoudy, L., El Gataa, Z., Sbabou, L. and Tadesse, W. (2024). Genome-wide association and genomic prediction study of elite spring bread wheat (Triticum aestivum L.) genotypes under drought conditions across different locations. Plant Gene, 39: 100461. https://doi.org/10.1016/j.plgene.2024.100461
FAO. (2022). Crop prospects and food situation. Quarterly global report. Food and Agriculture Organization of the United Nations. Rome, Italy.
Ficht, A., Konkin, D.J., Cram, D., Sidebottom, C., Tan, Y., Pozniak, C. and Rajcan, I. (2023). Genomic selection for agronomic traits in a winter wheat breeding program. Theoretical and Applied Genetics, 136: 38. https://doi.org/10.1007/s00122-023-04294-1
Fradgley, N., Gardner, K.A., Bentley, A.R., Howell, P., Mackay, I.J., Scott, M.F. and Cockram, J. (2023). Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture for long-term genetic gains in wheat. in silico Plants, 5(1): diad002. https://doi.org/10.1093/insilicoplants/diad002
Funck, D., Stadelhofer, B. and Koch, W. (2008). Ornithine-δ-aminotransfera se is essential for arginine catabolism but not for proline biosynthesis. BMC Plant Biology, 8(1): 40. https://doi.org/10.1186/1471-2229-8-40
Furlan, A.L., Bianucci, E., Giordano, W., Castro, S. and Becker, D.F. (2020). Proline metabolic dynamics and implications in drought tolerance of peanut plants. Plant Physiology and Biochemistry, 151: 566-578.https://doi.org/10.1016/j.plaphy.2020.04.010
Gaber, A., Refat, M.S., Belal, A.A., El-Deen, I.M., Hassan, N., Zakaria, R. and Saied, E.M. (2021). New mononuclear and binuclear Cu (II), Co (II), Ni (II), and Zn (II) thiosemicarbazone complexes with potential biological activity: antimicrobial and molecular docking study. Molecules, 26(8): 2288. https://doi.org/10.3390/molecules26082288
Haghi Asl, N., Darvishzadeh, R., Alipour, H., Fatanatvash, S., & Arzhang, S. (2025). Genomic selection for grain yield in maize (Zea mays L.) under normal and salinity stress conditions. Plant Genetic Research, 12(1):1-20 (In Persian). https://doi.org/10.22034/pgr.2025.2062236.1000
Heffner, E.L., Jannink, J.L., Iwata, H., Souza, E. and Sorrells, M.E. (2011). Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Science, 51(6): 2597-2606. https://doi.org/10.2135/cropsci2011.05.0253
Johansson, E., Lan, Y., Olalekan, O., Kuktaite, R., Chawade, A. and Rahmatov, M. (2024). Alien introgression to wheat for food security: Functional and nutritional quality for novel products under climate change. Frontiers in Nutrition, 11: 1393357. https://doi.org/10.3389/fnut.2024.1393357
Juliana, P., He, X., Marza, F., Islam, R., Anwar, B., Poland, J. and Singh, P.K. (2022). Genomic selection for wheat blast in a diversity panel, breeding panel and full-sibs panel. Frontiers in Plant Science, 12: 745379. https://doi.org/10.3389/fpls.2021.745379
Kakaei, M. and Mirmazloum, S.I. (2024). Evaluation of the genetic diversity and agro-morphophysiological traits of bread wheat varieties under postflowering drought stress using different statistical methods. Journal of Genetic Resources, 10(1): 46-56.
Long, N., Gianola, D., Rosa, G.J. and Weigel, K.A. (2011). Application of support vector regression to genome-assisted prediction of quantitative traits. Theoretical and Applied Genetics, 123: 1065-1074.https://doi.org/10.1007/s00122-011-1648-y
Marcussen, T., Sandve, S.R., Heier, L., Spannagl, M., Pfeifer, M., International Wheat Genome Sequencing Consortium. and Praud, S. (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science, 345(6194): 1250092.
Meuwissen, T.H., Hayes, B.J. and and Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4): 1819-1829. https://doi.org/10.1093/genetics/157.4.1819
Nyaupane, S., Poudel, M.R., Panthi, B., Dhakal, A., Paudel, H. and Bhandari, R. (2024). Drought stress effect, tolerance, and management in wheat - a review. Cogent Food and Agriculture, 10(1): 2296094. https://doi.org/10.1080/23311932.2023.2296094
Olsen, K.M., Lea, U.S., Slimestad, R., Verheul, M. and Lillo, C. (2008). Differential expression of four Arabidopsis PAL genes; PAL1 and PAL2 have functional specialization in abiotic environmental-triggered flavonoid synthesis. Journal of Plant Physiology, 165(14): 1491-1499.https://doi.org/10.1016/j.jplph.2007.11.005
Plavšin, I., Gunjača, J., Šatović, Z., Šarčević, H., Ivić, M., Dvojković, K. and Novoselović, D. (2021). An overview of key factors affecting genomic selection for wheat quality traits. Plants, 10(4): 745. https://doi.org/10.3390/plants10040745
Rabieyan, E., Bihamta, M.R., Moghaddam, M.E., Alipour, H., Mohammadi, V., Azizyan, K. and Javid, S. (2023). Analysis of genetic diversity and genome-wide association study for drought tolerance related traits in Iranian bread wheat. BMC Plant Biology, 23(1): 431. https://doi.org/10.1186/s12870-023-04416-3
Ray, D.K., Mueller, N.D., West, P.C. and Foley, J.A. (2013). Yield trends are insufficient to double global crop production by 2050. PloS One, 8(6): e66428. https://doi.org/10.1371/journal.pone.0066428
Raza, A., Su, W., Hussain, M.A., Mehmood, S.S., Zhang, X., Cheng, Y. and Lv, Y. (2021). Integrated analysis of metabolome and transcriptome reveals insights for cold tolerance in rapeseed (Brassica napus L.). Frontiers in Plant Science, 12: 721681. https://doi.org/10.3389/fpls.2021.721681
Rezaei, E.E., Webber, H., Asseng, S., Boote, K., Durand, J.L., Ewert, F., Martre, P. and MacCarthy, D.S. (2023). Climate change impacts on crop yields. Nature Reviews Earth and Environment, 4(12): 831-846. https://doi.org/10.1038/s43017-023-00491-0
Tadesse, W., El Gataa, Z., Rachdad, F.E., El-Baouchi, A., Kehel, Z. and Alemu, A. (2023). Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment. Molecular Genetics and Genomics, 298: 1515-1526. https://doi.org/10.1007/s00438-023-02074-6
Tessema, B.B., Liu, H., Sørensen, A.C. andersen, J.R. and Jensen, J. (2020). Strategies using genomic selection to increase genetic gain in breeding programs for wheat. Frontiers in Genetics, 11: 578123. https://doi.org/10.3389/fgene.2020.578123
Wu, P., Guo, Q.Q. and Qin, Z.W. (2016). The fungicide propamocarb increases lignin by activating the phenylpropanoid pathway in Cucumis sativus L. Horticulture, Environment, and Biotechnology, 57: 511-518.https://doi.org/10.1007/s13580-016-0049-1
Yadav, V., Wang, Z., Wei, C., Amo, A., Ahmed, B., Yang, X. and Zhang, X. (2020). Phenylpropanoid pathway engineering: An emerging approach towards plant defense. Pathogens, 9(4): 312.https://doi.org/10.3390/pathogens9040312
Yarnia, M., Arabifard, N., Khoei, F.R. and Zandi, P. (2011). Evaluation of drought tolerance indices among some winter rapeseed cultivars. African Journal of Biotechnology, 10(53): 10914-10922. https://doi.org/10.5897/AJB11.1748
Zamani, P., Soltanloo, H., Ramezanpour, S.S., Bihamta, M.R., Alipour, H. and Poczai, P. (2022). Genome-wide association mapping and genomic prediction of agronomical traits and breeding values in Iranian wheat under rain-fed and well-watered conditions. BMC Genomics, 23: 486. https://doi.org/10.1186/s12864-022-08968-w
Zhao, J., Sun, L., Gao, H., Hu, M., Mu, L., Cheng, X., Wang, J., Zhao, Y., Li, Q., Wang, P., Li, H. and Zhang, Y. (2023). Genome-wide association study of yield-related traits in common wheat (Triticum aestivum L.) under normal and drought treatment conditions. Frontiers in Plant Science, 13: 1098560. https://doi.org/10.3389/fpls.2022.1098560
Azimzadeh,H , Alipour,H , Darvishzadeh,R , Amani,H and Fatanatvash,S . (2026). Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions. Plant Genetic Research, 13(1), 15-42. doi: 10.22034/pgr.2026.2083043.1029
MLA
Azimzadeh,H , , Alipour,H , , Darvishzadeh,R , , Amani,H , and Fatanatvash,S . "Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions", Plant Genetic Research, 13, 1, 2026, 15-42. doi: 10.22034/pgr.2026.2083043.1029
HARVARD
Azimzadeh H, Alipour H, Darvishzadeh R, Amani H, Fatanatvash S. (2026). 'Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions', Plant Genetic Research, 13(1), pp. 15-42. doi: 10.22034/pgr.2026.2083043.1029
CHICAGO
H Azimzadeh, H Alipour, R Darvishzadeh, H Amani and S Fatanatvash, "Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions," Plant Genetic Research, 13 1 (2026): 15-42, doi: 10.22034/pgr.2026.2083043.1029
VANCOUVER
Azimzadeh H, Alipour H, Darvishzadeh R, Amani H, Fatanatvash S. Genome-Wide Association Study and Genomic Estimated Breeding Values of Grain Yield in Bread Wheat Cultivars Under Normal and Rainfed Irrigation Conditions. Plant Genet. Res.. 2026;13(1):15-42 (In Persian). doi: 10.22034/pgr.2026.2083043.1029
