Genetic structure of population and association analysis of some morpho-physiological traits of bread wheat under salinity stress using Simple Sequence Repeats (SSR)
Subject Areas : Genetic
Sasan Farhangian Kashani
1
,
Amin Azadi
2
,
shahab Khaghani
3
,
Mehdi Changizi
4
,
Masood Gomarian
5
1 - Department of Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
2 - Department of Plant Breeding, Yadgar Imam Khomeini (RA) Shahri Unit, Islamic Azad University, Tehran, Iran
3 - Department of Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
4 - Department of Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
5 - Department of Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
Keywords: Bread Wheat, population structure, Association analysis, Salinity and Simple Sequence Repeats,
Abstract :
Association analysis of 105 bread wheat (Triticum aestivum L.) genotypes was carried out using 12 SSR markers. For this purpose, wheat seeds were planted in pots in a randomized complete block design with three replications under normal (10 mM NaCl) and saline (120 mM NaCl) conditions and the activity of catalase (CAT), ascorbate peroxidase (APX), and total protein contents were measured. The results of combined analysis of variance showed that the activity of catalase, ascorbate peroxidase, and total protein contents were significantly different in the bread wheat cultivars under study. The results of multiple regression analysis showed that gwm67b and gwm282d markers under salinity conditions were more correlated with catalase activity in the studied species. Also, gwm291a, wmc73a, and barc124a markers were the most effective markers in association with APX enzyme. Analysis of the population structure and the resulting plot showed that the K Index and the Average Likelihood Logarithm had the highest value at K =2 (57.38), thus the population under study has most probably 2 subpopulations. Tassel analysis of SSR markers under normal irrigation and salinity irrigation conditions obtained 54 loci related to the traits under study in control condition and 61 loci in salinity condition based on the general linear model (GLM) and also 35 related loci in control condition and 20 loci in salinity condition based on the mixed linear model (MLM)
Acosta-Motos, J.R., Ortuño, M.F., Bernal-Vicente, A., Diaz-Vivancos, P., Sanchez-Blanco, M.J. and Hernandez, J.A. (2017). Plant Responses to Salt Stress: Adaptive Mechanisms. Agronomy, 7, 18.
Aebi, H. (1983). In "Methods of Enzymatic Analysis" (H.U. Bergmeyer, ed.), 3rd Ed. Verlag Chemic, Weinheim, F. R. G., in preparation.
Ahmad, M., Shahzad, A., Iqbal, M., Asif, M. and Hirani, A.H. (2013). Morphological and molecular genetic variation in wheat for salinity tolerance at germination and early seedling stage. Aust J Crop Sci. 7(1): 66–74.
Al-Ashkar, I., Alderfasi, A., Ben Romdhane, W., Seleiman, M.F., El-Said, R.A. and Al-Doss, A. (2020). "Morphological and Genetic Diversity within Salt Tolerance Detection in Eighteen Wheat Genotypes" Plants 9, no. 3: 287. https://doi.org/10.3390/plants9030287
Al-jebory, E.I. (2012). Effect of water stress on carbohydrate metabolism during Pisum sativum seedlings growth. Euphrates J. Agric. Sci. 4: 1–12.
Anderson, T.W. and Darling, D.A. (1952). Asymptotic theory of certain goodness of fit criteria based on stochastic processes. Ann. Math. Statist., 23. 193–212.
Anwar, J., Ali, M.A., Hussain, M., Sabir, W., Khan, M.A., Zulkiffal, A. and Abdullah, M. (2009). Assessment of yield criteria in bread wheat through correlation and path analysis ; The Journal of Animal & Plant Sciences. 19(4): 185-188.
Bailly, C. (2004). Active oxygen species and antioxidants in seed biology. Seed Science Research. 14: 93- 107.
Bradbury, P., Zhang, Zh., Kroon, D., Casstevens, T., Ramdoss, Y. and Buckler, E. (2007). TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. Bioinformatics (Oxford, England). 23. 2633-5. 10.1093/bioinformatics/btm308.
Bradford, M.M. (1976). A rapid and sensitive for the quantitation of microgram quantitites of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72: 248-254. 1976.
Byrt, C.S., Platten, J.D., Spielmeyer, W., James, R.A., Lagudah, E.S., Dennis, E.S., Tester, M. and Munns, R. (2007). HKT1; 5-like cation transporters linked to Na+ exclusion loci in wheat, Nax2 and Kna1. Plant Physiol. 143: 1918–1928.
Caldwell, K.S., Russell, J., Langridge, P and Powell, W. (2006). Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics. 172: 557–567.
Darvishzadeh, R., Jannatdoust, M. and Azizi, H. (2016). Association Mapping of Quantitative Traits. Urmia university.
Dixit, S. Swamy, B.P.M. Vikram, P. Ahmed, H.U. Sta Cruz, M.T. Amante, M. Atri, D. Leung, H. and Kumar, A. (2012). Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities.Theor Appl Genet, 125. pp: 155-169.
Dresselhaus, T., Hückelhoven, R. (2018). Biotic and Abiotic Stress Responses in Crop Plants. Agronomy. 8:267.
Falush, D., Stephens, M. and Pritchard, J.K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.Genetics. 164: 1567-1587.
Farhangian-kashani, S., Azadi, A., Khaghani, Sh., Changizi, M. and Gomarian, M. (2021). Association analysis and evaluation of genetic diversity in wheat genotypes using SSR markers. Biologia futura, 88:1-12. https://doi.org/10.1007/s42977-021-00088-y.
Ghorbanli, M., Hasheminiya, A. and Peyvandi, M. (2008). The effects of ascorbic acid on salt stress on some physiological responses nigella. Medicinal Plant Research. 26(3): 370-388. (In Persian).
Heidari, M. and Mesri, F. (2010). Studying theeffects of different salinity levels on physiological reactions and sodium and potassium uptake in wheat. Environmental Stresses in Crop Sciences (ESCS) Vol. 3(1): 83-94.
Hittalmani, S., Huang, N., Courtois, B., Venuprasad, R., McLaren, G. and Khush, G. (2003). Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theoretical and Applied Genetics 107: 679-690.
Hoagland, D.R. and Arnon, D.I. (1950). The Water-Culture Method for Growing Plants without Soil. California Agricultural Experiment Station, Circular-347.
Jun, T.H., Van, K., Kim, M.Y., Lee, S.H. and Walker, D.R. (2008). Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica. 62: 179–191.
Kabiri, R. and Nasibi, F. (2014). Farahbakhsh, H. Effect of Exogenous Salicylic Acid on Some Physiological Parametersand Alleviation of Drought Stress in Nigella sativa Plant under Hydroponic Culture.Plant Prot. 50: 43–51. [CrossRef].
Kahrizi, S., Sedghi, M. and Sofalian, O. (2012). Effect of salt stress on proline and activity of antioxidant enzymes in ten durum wheat cultivars. Scholars Research Library. 3 (8): 3870-3874.
Kim, S.Y., Lim, J.H., Park, M.R., Kim, Y.J., Park, T., Seo, Y.W., Choi, K.G. and Yun, S.J. (2005). Enhanced antioxidant enzymes are associated with reduced hydrogen peroxide in barley roots under saline stress.Journal of Biochemistry and Molecular Biology. 38(2): 218-22.
Kolmogorov, A. (1933a). Sulla determinazione empirica di una legge di distribuzionc, 1st. Ital. Attuari. G. 4: 1–11.
Lindsay, M.P., Lagudah, E.S., Hare, R.A., Munns, R. (2004). A locus for sodium exclusion (Nax1), a trait for salt tolerance, mapped in durum wheat. Funct. Plant Biol. 31: 1105–1114.
Mba, C., Afza, R., Jain, S.M., Gregorio, G.B. and Zapata-Arias, F.J. (2007). Induced mutations for enhancing salinity tolerance in rice. In Advances in Molecular Breeding toward Drought and Salt Tolerant Crops, pp. 413–454.
Meng, H.B., Jiang, S.S., Hua, S.J., Lin, X.Y., Li, Y.L., Guo, W.L. and Jiang, L.X. (2011). Comparison Between a Tetraploid Turnip and Its Diploid Progenitor (Brassica rapa L.): The Adaptation to Salinity Stress. Agric. Sci. N.a. 10: 363–375.
Moragues, M., Moralejo, M. A., Sorrells, M. E and Royo, C. (2007). Dispersal of durum wheat landraces across theMediterranean basin assessed by AFLPs and microsatellites. Gen. Res. Crop Evo l. 54:1133–1144.
Nakano, Y. and Asada, K. (1981). Hydrogen peroxide is scavenged by ascorbate-specific peroxidase in spinach chloroplasts. Plant and Cell Physiology. 22: 867–880.
Navabpour, S., Morris, K., Allen, R., Harrison, E., Mackerness, A.H., Buchanan, S. and Wollaston,V. (2004). Molecular andbiochemical analyses of oxidative stress and leaf senescence.Imperial College of Science, Technology and Medicineat Wye University of London. 55-56.
Noman, A., Ali, Q., Naseem, J., Javed, M.T., Kanwal, H., Islam, W., Aqeel, M., Khalid, N. and Zafar, S. Tayyeb, M., et al. (2018). Sugar beet extract acts as a natural bio-stimulant for physio-biochemical attributes in water stressedwheat (Triticum aestivum L.). Acta Physiol. Plant. 40, 110. [CrossRef].
Oliveira, A.M., Hemstedt, T.J. and Bading, H. (2012). Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities. Nat Neurosci. 15: 1111–1113.
Oyiga, B.C., Sharma, R.C., Shen, J., Baum, M., Ogbonnaya, F.C., Léon, J. and Ballvora, A. (2016). Identification and Characterization of Salt Tolerance of Wheat Germplasm Using a Multivariable Screening Approach. J.Agron. Sci. 202: 472–485.
Parida, K.P. and Das, A.B. (2005). Salt tolerance and salinity effects on plants: a review. Ecotoxicology and Environmental Safety. 60:324–349.
Prasad, M., Varsheny, R.K., Roy, J.K., Balyan, H.S. and Gupta, P.K. (2009). The use of microsatellite for detection DNA polymorphism, genotype identification and genetic divesity in wheat. Theoretical and Applied Genetics. 100: 584-592.
Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics. 155: 945–959.
Randhawa, H.S., Asif, M., Pozniak, C., Clarke, J.M., Graf, R.J., Fox, S.L., Humphreys, D.G., Knox, R.E., DePauw, R.M., Singh, A.K. and Cuthbert, R.D. (2013). Application of molecular markers to wheat breeding in Canada. Plant Breed. 132:458–71.
Roy, J. K., Bandopadhyay, R., Rustgi, S., Balyan, H. S. and Gupta, P. K. (2006). Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Current Science. 90: 5-10.
Sara, K., Abbaspour, H., Sinaki, J.M. and Makarian, H. (2012). Effects of Water Deficit and Chitosan Spraying on OsmoticAdjustment and Soluble Protein of Cultivars Castor Bean (Ricinus communisL.) .J. Stress Physiol. Biochem. 8: 160–169.
Saeed, M., Wangzhen, G., and Tianzhen, Z. (2014). Association mapping forsalinity tolerance in cotton (‘Gossypium hirsutum’L.) germplasm from US anddiverse regions of China. Australian Journal of Crop Science. 8(3): 338–346.
Szegletes, Z., Erdei, L., Tari, I. and Cseuz, L. (2000). Accumulation of osmoprotectants in wheat cultivars of different drought tolerance. Cereal Research Communications. 28, 403–410. https://doi.org/10.1007/BF03543622
Varshney, R.K., Graner, A. and Sorrells, M.E. (2005). Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23(1):48-55. doi: 10.1016/j.tibtech.2004.11.005
von Mises, R. (1931). Vorlesungen aus dem Gebiete der Angewandten Mathematik; 1. Bd.: Wahrscheinlichkeitsrechnung und ihre Anwendung in der Statistik und theoretischen Physik. Deuticke, Leipzig-Wien.
Yu, L.X., Lorenz, A., Rutkoski, J., Singh, R.P., Bhavani, S., Huerta-Espino, J., Sorrells, M.E.(2011). Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet. 123:1257–1268.
Acosta-Motos, J.R., Ortuño, M.F., Bernal-Vicente, A., Diaz-Vivancos, P., Sanchez-Blanco, M.J. and Hernandez, J.A. (2017). Plant Responses to Salt Stress: Adaptive Mechanisms. Agronomy, 7, 18.
Aebi, H. (1983). In "Methods of Enzymatic Analysis" (H.U. Bergmeyer, ed.), 3rd Ed. Verlag Chemic, Weinheim, F. R. G., in preparation.
Ahmad, M., Shahzad, A., Iqbal, M., Asif, M. and Hirani, A.H. (2013). Morphological and molecular genetic variation in wheat for salinity tolerance at germination and early seedling stage. Aust J Crop Sci. 7(1): 66–74.
Al-Ashkar, I., Alderfasi, A., Ben Romdhane, W., Seleiman, M.F., El-Said, R.A. and Al-Doss, A. (2020). "Morphological and Genetic Diversity within Salt Tolerance Detection in Eighteen Wheat Genotypes" Plants 9, no. 3: 287. https://doi.org/10.3390/plants9030287
Al-jebory, E.I. (2012). Effect of water stress on carbohydrate metabolism during Pisum sativum seedlings growth. Euphrates J. Agric. Sci. 4: 1–12.
Anderson, T.W. and Darling, D.A. (1952). Asymptotic theory of certain goodness of fit criteria based on stochastic processes. Ann. Math. Statist., 23. 193–212.
Anwar, J., Ali, M.A., Hussain, M., Sabir, W., Khan, M.A., Zulkiffal, A. and Abdullah, M. (2009). Assessment of yield criteria in bread wheat through correlation and path analysis ; The Journal of Animal & Plant Sciences. 19(4): 185-188.
Bailly, C. (2004). Active oxygen species and antioxidants in seed biology. Seed Science Research. 14: 93- 107.
Bradbury, P., Zhang, Zh., Kroon, D., Casstevens, T., Ramdoss, Y. and Buckler, E. (2007). TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. Bioinformatics (Oxford, England). 23. 2633-5. 10.1093/bioinformatics/btm308.
Bradford, M.M. (1976). A rapid and sensitive for the quantitation of microgram quantitites of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72: 248-254. 1976.
Byrt, C.S., Platten, J.D., Spielmeyer, W., James, R.A., Lagudah, E.S., Dennis, E.S., Tester, M. and Munns, R. (2007). HKT1; 5-like cation transporters linked to Na+ exclusion loci in wheat, Nax2 and Kna1. Plant Physiol. 143: 1918–1928.
Caldwell, K.S., Russell, J., Langridge, P and Powell, W. (2006). Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics. 172: 557–567.
Darvishzadeh, R., Jannatdoust, M. and Azizi, H. (2016). Association Mapping of Quantitative Traits. Urmia university.
Dixit, S. Swamy, B.P.M. Vikram, P. Ahmed, H.U. Sta Cruz, M.T. Amante, M. Atri, D. Leung, H. and Kumar, A. (2012). Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities.Theor Appl Genet, 125. pp: 155-169.
Dresselhaus, T., Hückelhoven, R. (2018). Biotic and Abiotic Stress Responses in Crop Plants. Agronomy. 8:267.
Falush, D., Stephens, M. and Pritchard, J.K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.Genetics. 164: 1567-1587.
Farhangian-kashani, S., Azadi, A., Khaghani, Sh., Changizi, M. and Gomarian, M. (2021). Association analysis and evaluation of genetic diversity in wheat genotypes using SSR markers. Biologia futura, 88:1-12. https://doi.org/10.1007/s42977-021-00088-y.
Ghorbanli, M., Hasheminiya, A. and Peyvandi, M. (2008). The effects of ascorbic acid on salt stress on some physiological responses nigella. Medicinal Plant Research. 26(3): 370-388. (In Persian).
Heidari, M. and Mesri, F. (2010). Studying theeffects of different salinity levels on physiological reactions and sodium and potassium uptake in wheat. Environmental Stresses in Crop Sciences (ESCS) Vol. 3(1): 83-94.
Hittalmani, S., Huang, N., Courtois, B., Venuprasad, R., McLaren, G. and Khush, G. (2003). Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theoretical and Applied Genetics 107: 679-690.
Hoagland, D.R. and Arnon, D.I. (1950). The Water-Culture Method for Growing Plants without Soil. California Agricultural Experiment Station, Circular-347.
Jun, T.H., Van, K., Kim, M.Y., Lee, S.H. and Walker, D.R. (2008). Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica. 62: 179–191.
Kabiri, R. and Nasibi, F. (2014). Farahbakhsh, H. Effect of Exogenous Salicylic Acid on Some Physiological Parametersand Alleviation of Drought Stress in Nigella sativa Plant under Hydroponic Culture.Plant Prot. 50: 43–51. [CrossRef].
Kahrizi, S., Sedghi, M. and Sofalian, O. (2012). Effect of salt stress on proline and activity of antioxidant enzymes in ten durum wheat cultivars. Scholars Research Library. 3 (8): 3870-3874.
Kim, S.Y., Lim, J.H., Park, M.R., Kim, Y.J., Park, T., Seo, Y.W., Choi, K.G. and Yun, S.J. (2005). Enhanced antioxidant enzymes are associated with reduced hydrogen peroxide in barley roots under saline stress.Journal of Biochemistry and Molecular Biology. 38(2): 218-22.
Kolmogorov, A. (1933a). Sulla determinazione empirica di una legge di distribuzionc, 1st. Ital. Attuari. G. 4: 1–11.
Lindsay, M.P., Lagudah, E.S., Hare, R.A., Munns, R. (2004). A locus for sodium exclusion (Nax1), a trait for salt tolerance, mapped in durum wheat. Funct. Plant Biol. 31: 1105–1114.
Mba, C., Afza, R., Jain, S.M., Gregorio, G.B. and Zapata-Arias, F.J. (2007). Induced mutations for enhancing salinity tolerance in rice. In Advances in Molecular Breeding toward Drought and Salt Tolerant Crops, pp. 413–454.
Meng, H.B., Jiang, S.S., Hua, S.J., Lin, X.Y., Li, Y.L., Guo, W.L. and Jiang, L.X. (2011). Comparison Between a Tetraploid Turnip and Its Diploid Progenitor (Brassica rapa L.): The Adaptation to Salinity Stress. Agric. Sci. N.a. 10: 363–375.
Moragues, M., Moralejo, M. A., Sorrells, M. E and Royo, C. (2007). Dispersal of durum wheat landraces across theMediterranean basin assessed by AFLPs and microsatellites. Gen. Res. Crop Evo l. 54:1133–1144.
Nakano, Y. and Asada, K. (1981). Hydrogen peroxide is scavenged by ascorbate-specific peroxidase in spinach chloroplasts. Plant and Cell Physiology. 22: 867–880.
Navabpour, S., Morris, K., Allen, R., Harrison, E., Mackerness, A.H., Buchanan, S. and Wollaston,V. (2004). Molecular andbiochemical analyses of oxidative stress and leaf senescence.Imperial College of Science, Technology and Medicineat Wye University of London. 55-56.
Noman, A., Ali, Q., Naseem, J., Javed, M.T., Kanwal, H., Islam, W., Aqeel, M., Khalid, N. and Zafar, S. Tayyeb, M., et al. (2018). Sugar beet extract acts as a natural bio-stimulant for physio-biochemical attributes in water stressedwheat (Triticum aestivum L.). Acta Physiol. Plant. 40, 110. [CrossRef].
Oliveira, A.M., Hemstedt, T.J. and Bading, H. (2012). Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities. Nat Neurosci. 15: 1111–1113.
Oyiga, B.C., Sharma, R.C., Shen, J., Baum, M., Ogbonnaya, F.C., Léon, J. and Ballvora, A. (2016). Identification and Characterization of Salt Tolerance of Wheat Germplasm Using a Multivariable Screening Approach. J.Agron. Sci. 202: 472–485.
Parida, K.P. and Das, A.B. (2005). Salt tolerance and salinity effects on plants: a review. Ecotoxicology and Environmental Safety. 60:324–349.
Prasad, M., Varsheny, R.K., Roy, J.K., Balyan, H.S. and Gupta, P.K. (2009). The use of microsatellite for detection DNA polymorphism, genotype identification and genetic divesity in wheat. Theoretical and Applied Genetics. 100: 584-592.
Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics. 155: 945–959.
Randhawa, H.S., Asif, M., Pozniak, C., Clarke, J.M., Graf, R.J., Fox, S.L., Humphreys, D.G., Knox, R.E., DePauw, R.M., Singh, A.K. and Cuthbert, R.D. (2013). Application of molecular markers to wheat breeding in Canada. Plant Breed. 132:458–71.
Roy, J. K., Bandopadhyay, R., Rustgi, S., Balyan, H. S. and Gupta, P. K. (2006). Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Current Science. 90: 5-10.
Sara, K., Abbaspour, H., Sinaki, J.M. and Makarian, H. (2012). Effects of Water Deficit and Chitosan Spraying on OsmoticAdjustment and Soluble Protein of Cultivars Castor Bean (Ricinus communisL.) .J. Stress Physiol. Biochem. 8: 160–169.
Saeed, M., Wangzhen, G., and Tianzhen, Z. (2014). Association mapping forsalinity tolerance in cotton (‘Gossypium hirsutum’L.) germplasm from US anddiverse regions of China. Australian Journal of Crop Science. 8(3): 338–346.
Szegletes, Z., Erdei, L., Tari, I. and Cseuz, L. (2000). Accumulation of osmoprotectants in wheat cultivars of different drought tolerance. Cereal Research Communications. 28, 403–410. https://doi.org/10.1007/BF03543622
Varshney, R.K., Graner, A. and Sorrells, M.E. (2005). Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23(1):48-55. doi: 10.1016/j.tibtech.2004.11.005
von Mises, R. (1931). Vorlesungen aus dem Gebiete der Angewandten Mathematik; 1. Bd.: Wahrscheinlichkeitsrechnung und ihre Anwendung in der Statistik und theoretischen Physik. Deuticke, Leipzig-Wien.
Yu, L.X., Lorenz, A., Rutkoski, J., Singh, R.P., Bhavani, S., Huerta-Espino, J., Sorrells, M.E.(2011). Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet. 123:1257–1268.
