Genetic Diversity and Population Structure of Native Bread Wheat Germplasm from Dry Environments
DOI:
https://doi.org/10.19136/era.a13nVI.5140Keywords:
Adaptation, drought, variabilityAbstract
Genetic diversity and population structure of native bread wheat (Triticum aestivum L.) materials were evaluated to identify patterns of variation associated with climatic origin and potential adaptation to drought stress. From an initial collection of 990 accessions from the CIMMYT germplasm bank, 45 materials originating from arid and semi-arid regions were selected based on geographic, climatic (aridity index ≥ 30), and genetic criteria. Analyses were performed using 10 811 high-quality genomic SNP markers. Intrapopulation genetic diversity was estimated using the Shannon entropy index, while genetic structure was assessed through UPGMA clustering, principal component analysis (PCA), and Bayesian ancestry inference. The results revealed intermediate genetic diversity (H = 0.46) and weak to moderate population structure, characterized by high intragroup variation and partial clustering trends associated with climatic origin. Ancestry analysis identified five genetic groups with varying degrees of admixture. Overall, the results indicate incipient genetic structuring influenced by environmental conditions and significant historical gene flow, highlighting the value of these materials for conservation and wheat breeding programs.
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Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai G, 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
Babalola KO, Monacelli N, Gozzi M, Ceccarelli S, Folloni S, Galaverna G (2025) Genetic diversity and climate change adaptation in wheat: a systematic review of landraces, composite cross populations, and evolutionary populations. Frontiers in Sustainable Food Systems 9: 1504922. https://doi.org/10.3389/fsufs.2025.1504922
Balfourier F, Bouchet S, Robert S, De Oliveira R, Rimbert H, Kitt J, Choulet F, International Wheat Genome Sequencing Consortium, BreedWheat Consortium, Paux E (2019) Worldwide phylogeography and history of wheat genetic diversity. Science Advances 5(5): eaav0536. https://doi.org/10.1126/sciadv.aav0536
Bapela T, Shimelis H, Tsilo TJ, Mathew I (2022) Genetic improvement of wheat for drought tolerance: Progress, challenges and opportunities. Plants 11(10): 1331. https://doi.org/10.3390/plants11101331
Barghi N, Hermisson J, Schlötterer C (2020) Polygenic adaptation: a unifying framework to understand positive selection. Nature Reviews Genetics 21(12): 769-781. https://doi.org/10.1038/s41576-020-0250-z
Chao A, Jost L, Hsieh TC, Ma KH, Sherwin WB, Rollins LA (2015) Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model. PLoS ONE 10(6): e0125471. https://doi.org/10.1371/journal.pone.0125471
Cordero S, Carvallo GO, Coronado T, Rosas MR, Romeiro-Brito M, Majure LC, Saldaña A, Villalobos-Barrantes HM and Guerrero PC (2026) Genomic structure and functional trait variation are decoupled across the Atacama-Patagonia arid gradient in the Chilean wineberry. Frontiers in Plant Science 4(16): 1741939. https://doi.org/10.3389/fpls.2025.1741939
Cortés AJ (2013) On the origin of the common bean (Phaseolus vulgaris L.). American Journal of Plant Sciences 4(10): 1998-2000. https://doi.org/10.4236/ajps.2013.410248
Cosgrove DJ (2015) Plant expansins: diversity and interactions with plant cell walls. Current Opinion in Plant Biology 25: 162-172. https://doi.org/10.1016/j.pbi.2015.05.014
Curtis T, Halford NG (2014) Food security: the challenge of increasing wheat yield and the importance of not compromising food safety. Annals of Applied Biology 164(3): 354–372. https://doi.org/10.1111/aab.12108
Dagnaw T, Mulugeta B, Haileselassie T, Geleta M, Ortiz R, Tesfaye K (2023) Genetic diversity of durum wheat (Triticum turgidum L. ssp. durum, Desf) germplasm as revealed by morphological and SSR markers. Genes 14(6): 1155. https://doi.org/10.3390/genes14061155
El Gataa Z, Samir K, Tadesse W (2022) Genetic dissection of drought tolerance of elite bread wheat (Triticum aestivum L.) genotypes using genome wide association study in Morocco. Plants 11: 2705. https://doi.org/10.3390/plants11202705
El Gataa Z, El Messoadi K, Ezzahra FR, Imseg I, Ed-Daoudy L, Lahrichi K, Tadesse W (2024) Genetic variability of bread wheat (Triticum aestivum L.) genotypes under drought conditions targeting the CWANA region. Ecological Genetics and Genomics 33: 100307. https://doi.org/10.1016/j.egg.2024.100307
Eltaher S, Sallam A, Belamkar V, Emara HA, Nower AA, Salem KFM, Baenziger SP (2018) Genetic diversity and population structure of F3:6 Nebraska winter wheat genotypes using genotyping-by-sequencing. Frontiers in Genetics 9(76). https://doi.org/10.3389/fgene.2018.00076
Eticha F, Bekele E, Belay G, Börner A (2005) Phenotypic diversity in tetraploid wheats collected from Bale and Wello regions of Ethiopia. Plant Genetic Resources 3(1): 35-43. https://doi.org/10.1079/pgr200457
Farah AA, Mohamed MA, Musse OSH, Bile AN (2025) The multifaceted impact of climate change on agricultural productivity: a systematic literature review of SCOPUS-indexed studies (2015–2024). Discover Sustainability 397(6). https://doi.org/10.1007/s43621-025-01229-2
Frichot E, François O (2015) LEA: An R package for landscape and ecological association studies. Methods in Ecology and Evolution 6(8): 925–929. https://doi.org/10.1111/2041210x.12382
Garcia-Oliveira AL, Ortiz R, Sarsu F, Rasmussen SK, Agre P, Asfaw A, Kante M and Chander S (2025) The importance of genotyping within the climate-smart plant breeding value chain - integrative tools for genetic enhancement programs. Frontiers in Plant Sciences 15: 1518123. https://doi.org/10.3389/fpls.2024.1518123
Gómez-Espejo AL, Sansaloni CP, Burgueño J, Toledo FH, Benavides-Mendoza A, Reyes-Valdés MH (2022) Worldwide selection footprints for drought and heat in bread wheat (Triticum aestivum L.). Plants 11(17): 2289. https://doi.org/10.3390/plants11172289
Guo XJ, Wang JR (2017) Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat. BMC Plant Biology 17(1): 90. https://doi.org/10.1186/S12870-017-1038-Y
Hanif U, Alipour H, Gul A, Jing L, Darvishzadeh R, Amir R, Li H (2021) Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study. Plant Genome 14(3): e20096. https://doi.org/10.1002/tpg2.20096
Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, David J (2007) Grinding up wheat: A massive loss of nucleotide diversity since domestication. Molecular Biology and Evolution 24(7): 1506-1517. https://doi.org/10.1093/molbev/msm077
Hernandez-Ochoa IM, Asseng S, Kassie BT, Xiong W, Robertson R, Luz Pequeno DN, Sonder K, Reynolds M, Babar MA, Molero-Milan A, Hoogenboom G (2018) Climate change impact on Mexico wheat production. Agricultural and Forest Meteorology 263: 373-387. https://doi.org/10.1016/j.agrformet.2018.09.008
Huang QX, Börner A, Röder MS, Ganal MW (2002) Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theoretical and Applied Genetics 105(5): 699-707. https://doi.org/10.1007/s00122-002-0959-4
Khan S, Anwar S, Yu S, Sun M, Yang Z, Gao ZQ (2019) Development of drought-tolerant transgenic wheat: achievements and limitations. International Journal of Molecular Sciences 20(13): 3350. https://doi.org/10.3390/ijms20133350
Kottek M, Grieser J, Beck C, Rudolf B, Rubel F (2006) World map of the Köppen- Geigerclimate classification updated. Meteorologische Zeitschrift 15: 259–263. https://doi.org/10.1127/0941-2948/2006/0130
Laidò G, Mangini G, Taranto F, Gadaleta A, Blanco A, Cattivelli L, De Vita P (2013) Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) estimated by SSR, DArT and pedigree data. PLoS ONE 8(6): e67280. https://doi.org/10.1371/journal.pone.0067280
Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang L (2021) Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Research 31(4): 592-606. https://doi.org/10.1101/gr.261032.120
Liu H, Xing M, Yang W, Mu X, Wang X, Lu F, Zhang L (2019) Genome-wide identification of and functional insights into the late embryogenesis abundant (LEA) gene family in bread wheat (Triticum aestivum). Scientific Reports 9(1): 13375. https://doi.org/10.1038/s41598-019-49759-w
Liu G, Liu D, Zhang A, Liu H, Sultan MM, Mullan D, Yan G (2023) Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus. Theoretical and Applied Genetics 136(190): 1-13. https://doi.org/10.1007/s00122-023-04438-3
Manjunath KK, Krishna H, Devate NB, Sunilkumar VP, Patil SP, Chauhan D, Singh PK (2023) QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat. Frontiers in Genetics 14: 1282240. https://doi.org/10.3389/fgene.2023.1282240
Morgounov A, Özdemir F, Keser M, Akin B, Dababat AA, Dreisigacker S, Sharma R (2021) Diversity and adaptation of currently grown wheat landraces and modern Germplasm in Afghanistan, Iran, and Turkey. Crops 1(2): 54-67. https://doi.org/10.3390/crops1020007
Nyine M, Davidson D, Adhikari E, Clinesmith M, Wang H, Akhunova A, Fritz A, Akhunov E (2025) Genomic signals of ecogeographic adaptation in a wild relative are associated with improved wheat performance under drought stress. Genome Biology 26(35). https://doi.org/10.1186/s13059-025-03500-1
Omondi EO, Lin CY, Huang SM, Liao CA, Lin YP, Oliva R, van Zonneveld M (2024) Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecology and Evolution 14(7):e11662. https://doi.org/10.1002/ece3.11662
Oliveira HR, Campana MG, Jones H, Hunt HV, Leigh F, Redhouse DI, Jones MK (2012) Tetraploid wheat landraces in the Mediterranean basin: Taxonomy, evolution and genetic diversity. PLoS ONE 7(5): e37063. https://doi.org/10.1371/journal.pone.0037063
R Core Team (2023) R: A Language and Environment for Statistical Computing : R Foundation for Statistical Computing: Vienna, Austria, 2017. https://www.r-project.org/
Reyes-Valdés MH, Williams CG (2005) An entropy-based measure of founder informativeness. Genetical Research 85(1): 81–88. https://doi.org/10.1017/S0016672305007354
Rufo R, Alvaro F, Royo C, Soriano JM (2019) From landraces to improved cultivars: assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS ONE 14(7): e0219867. https://doi.org/10.1371/journal.pone.0219867
Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P (2022) Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. Molecular Breeding 42(1): 1. https://doi.org/10.1007/s11032-021-01272-7
Sansaloni C, Franco J, Santos B, Percival-Alwyn L, Singh S, Petroli C, Pixley K (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nature Communications 11(1): 4572. https://doi.org/10.1038/s41467-020-18404-w
Saroussi S, Redekop P, Karns DAJ, Thomas DC, Wittkopp TM, Posewitz MC, Grossman AR (2023) Restricting electron flow at cytochrome b6f when downstream electron acceptors are severely limited. Plant Physiology 192(2): 789-804. https://doi.org/10.1093/plphys/kiad185
Seyvani-Nezhad S, Alipour H, Darvishzadeh R, Abdi H (2025) A molecular perspective on 268 landraces from Iran of wheat (Triticum aestivum L.) representing five geographical and four climate zones of the country. Genetic Resources and Crop Evolution 73(1): 4. https://doi.org/10.1007/S10722-025-02662-Y
SIAP (2024) Anuario estadístico de la producción agrícola. Secretaría de Agricultura y Desarrollo Rural (SADER). Sistema de Información Agroalimentaria y Pesquera https://www.gob.mx/siap. Fecha de consulta: 15 de diciembre de 2025.
Shu K, Yang W (2017) E3 ubiquitin ligases: ubiquitous actors in plant development and abiotic stress responses. Plant and Cell Physiology 58(9): 1461-1476. https://doi.org/10.1093/pcp/pcx071
Tehseen MM, Tonk FA, Tosun M, Istipliler D, Amri A, Sansaloni CP, Nazari K (2022) Exploring the genetic diversity and population structure of wheat landrace population conserved at ICARDA genebank. Frontiers in Genetics 13: 900572. https://doi.org/10.3389/fgene.2022.900572
Ullah G (2025) The impact of climate change on crop yield and agricultural productivity. Journal of Agricultural Science and Botany 9(1): 278. https://doi.org/10.35841/aaascb-9.1.278
Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Saint Pierre C, Ortiz C, Sneller C, Tattaris M, Guzman C, Sansaloni CP, Ellis M, Fuentes-Davila G, Reynolds M, Sonders K, Singh P, Payne T, Wenzl P, Sharma A, Bains NS, Singh GP, Crossa J, Singh S (2016) Unlocking the genetic diversity of Creole wheats. Scientific Reports 6(1): 23092. https://doi.org/10.1038/srep23092
Villa TCC, Maxted N, Scholten M, Ford-Lloyd B (2005) Defining and identifying crop landraces. Plant Genetic Resources 3(3): 373-384. https://doi.org/10.1079/pgr200591
Wang D, Cao Z, Wang W, Zhu W, Hao X, Fang Z, Tang Y (2020) Genome-wide characterization of OFP family genes in wheat (Triticum aestivum L.) reveals that TaOPF29a-A promotes drought tolerance. BioMed Research International 2020(1): 9708324. https://doi.org/10.1155/2020/9708324
Xiong W, Reynolds MP, Crossa J, Schulthess U, Sonder K, Montes C, Addimando N, Singh RP, Ammar K, Gerard B and Payne T (2021) Increased ranking change in wheat breeding under climate change. Nature Plants 7(9): 1207-1212. https://doi.org/10.1038/s41477-021-00988-w
Zan T, Zhang L, Xie T, Li L (2020) Genome-wide identification and analysis of the growth-regulating factor (GRF) gene family and GRF-interacting factor family in Triticum aestivum L. Biochemical Genetics 58(5): 705-724. https://doi.org/10.1007/s10528-020-09969-8
Zomer RJ, Xu J, Trabucco A (2022) Version 3 of the Global aridity index and potential evapotranspiration database. Scientific Data 409. https://doi.org/10.1038/s41597-022-01493-1
Zhou S, Sun X, Yin S, Kong X, Zhou S, Xu Y, Wang W (2014) The role of the F-box gene TaFBA1 from wheat (Triticum aestivum L.) in drought tolerance. Plant Physiology and Biochemistry 84: 213-223. https://doi.org/10.1016/j.plaphy.2014.09.017
Zhou Y, Zhao X, Li Y, Xu J, Bi A, Kang L, Xu D, Chen H, Wang Y, Wang Y, Liu S, Jiao C, Lu H, Wang J, Yin C, Jiao Y and Lu F (2020) Triticum population sequencing provides insights into wheat adaptation. Nature Genetics 52(12): 1412-1422. https://doi.org/10.1038/s41588-020-00722-w
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