Genome Wide Association Study of Yield and Yield-Related Traits in Elite Spring Bread Wheat Genotypes Grown under High Temperature Environment in Sudan
Genetic improvement of wheat for heat tolerance is the main breeding
objective in Sudan as it is the principal limiting factor for wheat production.
To this end, the availability of wheat genetic diversity is key for success.
Genetic diversities and genome-wide association studies were conducted to parse
the complex genetic composition of yield-related traits of 250 bread wheat
genotypes which were selected from ICARDA’s advanced materials. The genotypes
were evaluated under heat stress environment for two seasons (2016/17 and 2017/18)
in two sowing dates (optimum and late) at the Gezira Research Farm (GRF), of the Agricultural Research
Corporation (ARC), Wad Medani, Sudan. Yield levels ranged from 4016 - 5120
kg/ha for optimum and late sowing dates respectively in the first season and
from 5386 - 3926 kg/ha for optimum and late sowing dates respectively in the second
season. The top 20 genotypes were better than the best check in the two seasons
except, Imam which ranked number 18 in the second season. Two genotypes,
genotypes 27 and 37, produced high grain yield in both seasons. Wide ranges of
variations among genotypes were found for yield and yield-related traits,
including days to heading and maturity,
plant height, number of seeds/spike, 1000 seed weight, biomass and harvest index.
Genome wide association analyses were performed using 15 kSNPmarkers and the phenotypic data. A total of
282, 355 and 475 significant (P < 0.05) markers associated with grain yield
were observed in the first season, second
season and across seasons, respectively. Markers (6B/Kukri_ c27662, 6B/.BobWhite_c23771_525, 6B/Excalibur_c32219_491,
6B/RAC875_c31299_13021302, 6B/BS00046264_51,6A/wsnp_Ex_rep_c69373_68312188, 6A/Tdurum contig12123_1650, 6BKukri_c27662_675 and 6A/BobWhite_c15802_72) on chromosomes 6B and 6A for
grain yield were highly significantly associated and stable in every season and across seasons. Highly significant
Marker-traits associations (MTAs) were observed for many traits
including days to heading and maturity, plant height, number of seeds/spike,
1000 seed weight, biomass and harvest index. The currently identified MTAs
should be further validated using other elite sets of genotypes so that they
can be used for MAS in the breeding program. The high yielding and heat tolerant
genotypes identified in this study will be evaluated across key locations in
Sudan for potential release in Sudan. Furthermore, they will be used as parents
in the breeding program for heat tolerance.
References
[1]
Battisti, D.S. and Naylor, R.L. (2010) Historical Warnings of Future Food Insecurity with Unprecedented Seasonal Heat. Science, 323, 240-244.
https://doi.org/10.1126/science.1164363
[2]
Hansen, J., Sato, M., Ruedy, R., Lo, K., Lea, D.L. and Medina-Elizade, M. (2006) Global Temperature Change. Proceedings of the National Academy of Sciences of the United States of America, 103, 14288-14293.
https://doi.org/10.1073/pnas.0606291103
[3]
Tadesse, W., Morgounov, A.I., Braun, H.J., Akin, B., Keser, M., et al. (2013) Breeding Progress for Yield in Winter Wheat Genotypes Targeted to Irrigated Environments of the CWANA Region. Euphytica, 194, 177-185.
https://doi.org/10.1007/s10681-013-0903-5
[4]
Wahid, A., Gelani, S., Ashraf, M. and Foolad, M.R. (2007) Heat Tolerance in Plants: An Overview. Environmental and Experimental Botany, 61, 199-223.
https://doi.org/10.1016/j.envexpbot.2007.05.011
[5]
Tadesse, W., Suleiman, S., Tahir, I., Sanchez-Garcia, M., Jighly, A., Hagras, A., Thabet, S. and Baum, M. (2019) Heat-Tolerant QTLs Associated with Grain Yield and Its Components in Spring Bread Wheat under Heat-Stressed Environments of Sudan and Egypt. Crop Science, 59, 199-211. https://doi.org/10.2135/cropsci2018.06.0389
[6]
Hamblin, M.T., Buckler, E.S. and Jannink, J.-L. (2011) Population Genetics of Genomics-Based Crop Improvement Methods. Trends in Genetics, 7, 98-106.
https://doi.org/10.1016/j.tig.2010.12.003
[7]
Risch, N. and Merikangas, K. (1996) The Future of Genetic Studies of Complex Human Diseases. Science, 273, 1516-1517.
https://doi.org/10.1126/science.273.5281.1516
[8]
Rafalski, J.A. (2002) Novel Genetic Mapping Tools in Plants: SNPs and LD-Based Approaches. Plant Science, 162, 329-333.
https://doi.org/10.1016/S0168-9452(01)00587-8
[9]
Breseghello, F. and Sorrells, M.E. (2006) Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars. Genetics, 172, 1165-1177. https://doi.org/10.1534/genetics.105.044586
[10]
Reynolds, M.P., Balota, M., Delgado, M.I.B., Amani, I. and Fischer, R.A. (1994) Physiological and Morphological Traits Associated With Spring Wheat Yield Under Hot, Irrigated Conditions. Australian Journal of Plant Physiology, 21, 717-730.
https://doi.org/10.1071/PP9940717
[11]
Elahmadi, A.B., Ageeb, O.A., Solh, M. and Saxena. (1995) Review of Wheat Production and Improvement in the Sudan. Proceedings of the Research Review Workshop, Wad Medani, 27-30 August 1995.
[12]
Slafer, G.A., Araus, J.L., Royo, C. and Del Moral, L.F.G. (2005) Promising Ecophysiological traits for genetic improvement of cereal yields in Mediterranean environments. Annals of Applied Biology, 146, 61-67.
https://doi.org/10.1111/j.1744-7348.2005.04048.x
[13]
Yu, J. and Buckler, E.S. (2006) Genetic Association Mapping and Genome Organization of Maize. Current Opinion in Biotechnology, 17, 155-160.
https://doi.org/10.1016/j.copbio.2006.02.003
[14]
Pritchard, J.K. and Donnelly, P. (2001) Case-Control Studies of Association in Structured or Admixed Populations. Theoretical Population Biology, 60, 227-237.
https://doi.org/10.1006/tpbi.2001.1543
[15]
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., Glover, K., Chen, J.L., Campbell, K., Bruckner, P.L., Rudd, J.C., Haley, S., Carver, B.F., Perry, S., Sorrells, M.E. and Akhunov, E.D. (2010) Population- and Genome-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Wheat (Triticum aestivum L.). BMC Genomics, 11, Article No. 727. https://doi.org/10.1186/1471-2164-11-727
[16]
Maccaferri, M., Sanguineti, M.C., Corneti, S., Ortega, J.L.A., Ben Salem, M., Bort, J., DeAmbrogio, E., del Moral, L.F.G., Demontis, A., El-Ahmed, A., Maalouf, F., Machlab, H., Martos, V., Moragues, M., Motawaj, J., Nachit, M., Nserallah, N., Ouabbou, H., Royo, C., Slama, A. and Tuberosa, R. (2008) Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum.) Across a Wide Range of Water Availability. Genetics, 178, 489-511.
https://doi.org/10.1534/genetics.107.077297
[17]
Sukumaran, S., Dreisigacker, S., Lopes, M., Chavez, P, and Reynold, M.P. (2014) Genome-Wide Association Study for Grain Yield and Related Traits in an Elite Spring Wheat Population Grown in Temperate Irrigated Environments. Theoretical and Applied Genetics, 128, 353-363. https://doi.org/10.1007/s00122-014-2435-3
[18]
Mwadzingeni, L., Shimelis, H., Rees, D.J.G. and Tsilo, T.J. (2017) Genome-Wide Association Analysis of Agronomic Traits in Wheat under Drought-Stressed and Non-Stressed Conditions. PLOS ONE, 12, e0171692.
https://doi.org/10.1371/journal.pone.0171692
[19]
Yan, L., Loukoianov, A., Tranquilli, G., Helguera, M., Fahima, T. and Dubcovsky, J. (2003) Positional Cloning of the Wheat Vernalization Gene VRN1. Proceedings of the National Academy of Sciences of the United States of America, 100, 6263-6268.
https://doi.org/10.1073/pnas.0937399100
[20]
Tadesse, W., Ogbonnaya, F.C., Jighly, A., Sanchez-Garcia, M., Sohail, Q., Rajaram, S. and Baum, M. (2015) Genome-Wide Association Mapping of Yield and Grain Quality Traits in Winter Wheat Genotypes. PLOS ONE, 10, e0141339.
https://doi.org/10.1371/journal.pone.0141339
[21]
Wang, R.X., Hai, L., Zhang, X.Y., You, G.X., Yan, C.S. and Xiao, S.H. (2009) QTL Mapping for Grain Filling Rate and Yield-Related Traits in RILs of the Chinese Winter Wheat Population Heshangmai × Yu8679. Theoretical and Applied Genetics, 118, 313-325. https://doi.org/10.1007/s00122-008-0901-5
[22]
Pinto, R.S., Reynolds, M.P., Mathews, K.L., et al. (2010) Heat and Drought Adaptive QTL in a Wheat Population Designed to Minimize Confounding Agronomic Effects. Theoretical and Applied Genetics, 121, 1001-1021.
https://doi.org/10.1007/s00122-010-1351-4
[23]
Chu, C.-G., Xu, S.S., Friesen, T.L. and Faris, J.D. (2008).Whole Genome Mapping in a Wheat Doubled Haploid Population Using SSR sand TRAPs and the Identification of QTL for Agronomic Traits. Molecular Breeding, 22, 251-226.
https://doi.org/10.1007/s11032-008-9171-9
[24]
Qaseem, M.F., Qureshi, R., Shaheen, H. and Shafqat, N. (2019) Genome-Wide Association Analyses for Yield and Yield-Related Traits in Bread Wheat (Triticum aestivum L.) under Pre-Anthesis Combined Heat and Drought Stress in Field Conditions. PLOS ONE, 14, e0213407. https://doi.org/10.1371/journal.pone.0213407
[25]
Ain, Q., Rasheed, A., Anwar, A., Imtiaz, M., Mahmood, T., Xia, X., He, Z. and Quraishi, U.M. (2015) Genome-Wide Association for Grain Yield under Rainfed Conditions in Historical Wheat Cultivars from Pakistan. Frontiers in Plant Science, 6, Article 743. https://doi.org/10.3389/fpls.2015.00743
[26]
Huang, X.Q., Cöster, H., Ganal, M.W. and Röder, M.S. (2003) Advanced Backcross QTL Analysis for the Identification of Quantitative Trait Loci Alleles from Wild Relatives of Wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 106, 1379-1389. https://doi.org/10.1007/s00122-002-1179-7
[27]
Lopes, M.S., Reynolds, M.P., McIntyre, C.L., Mathews, K.L., Jalal Kamali, M.R., Mossad, M., Feltaous, Y., Tahir, I.S.A., Chatrath, R., Ogbonnaya, F. and Baum, M. (2013) QTL for Yield and Associated Traits in the Seri/Babax Population Grown across Several Environments in Mexico, in the West Asia, North Africa, and South Asia Regions. Theoretical and Applied Genetics, 126, 971-984.
https://doi.org/10.1007/s00122-012-2030-4
[28]
Cuthbert, J.L., Somers, D.J., Brûlé-Babel, A.L., Brown, P.D. and Crow, G.H. (2008) Molecular Mapping of Quantitative Trait Loci for Yield and Yield Components in Spring Wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 117, 595-608. https://doi.org/10.1007/s00122-008-0804-5
[29]
Erena Aka, E. (2013) Association Mapping for Yield, Yield Components and Drought Tolerance-Related Traits in Spring Wheat Grown under Rained and Irrigated Condition. Colorado State University, Fort Collins.
[30]
Bennett, D., Izanloo, A., Edwards, J., Kuchel, H., Chalmers, K., Tester, M., Reynolds, M., Schnurbusch, T. and Langridge, P. (2012) Identification of Novel Quantitative Trait Loci for Days to Ear Emergence and Flag Leaf Glaucousness in Bread Wheat (Triticum aestivum L.) Population Adapted to Southern Australian Conditions. Theoretical and Applied Genetics, 124, 697-711.
https://doi.org/10.1007/s00122-011-1740-3
[31]
Reynolds, M. and Tuberosa, R. (2008) Translational Research Impacting on Crop Productivity in Drought-Prone Environments. Current Opinion in Plant Biology, 11, 171-179. https://doi.org/10.1016/j.pbi.2008.02.005
