Dvorak Jand Akhunov, E. D. Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the aegilops-triticum alliance. Genetics 171, 323–332. https://doi.org/10.1534/genetics.105.041632 (2005).
Google Scholar
Peng, J. H., Sun, D. & Nevo, E. Domestication evolution, genetics and genomics in wheat. Mol. Breed. 28(3), 281 (2011).
Google Scholar
Faris, J. D. Wheat domestication: Key to agricultural revolutions past and future. In Genomics of plant genetic resources (eds Tuberosa, R. & Graner, A.) 439–464 (Springer, 2014).
Li, G. Q. et al. Vernalization requirement duration in winter wheat is controlled by TaVRN-A1 at the protein level. Plant J. 76, 742–753 (2013).
Google Scholar
Yan, L. et al. Genetic Mechanisms of Vernalization Requirement Duration in Winter Wheat Cultivars. In Advances in Wheat Genetics: From Genome to Field (eds Ogihara, Y. et al.) (Springer, 2015).
Armoniene, R., Liatukas, Z. & Brazauskas, G. Evaluation of freezing tolerance of winter wheat (Triticum aestivum L.) under controlled conditions and in the field. Zemdirbyste-Agriculture 100, 417–424 (2013).
Ozturk, A., Caglar, O. & Bulut, S. Growth and yield response of facultative wheat to winter sowing, freezing sowing and spring sowing at different seeding rates. J. Agron. Crop Sci. 192, 10–16 (2006).
FAO. Food and Agriculture Organization of the United Nations. http://www.fao.org/3/ca4526en/ca4526en.pdf (2019)
Braun HJ and Sãulescu, N.N., Breeding winter and facultative wheat. Central Asia 9.6. FAOSTAT, 2020 http://www.faoorg/3/y4011e/y4011e0fhtm (2002)
Barlow, K. M., Christy, B. P., O’leary, G. J., Riffkin, P. A. & Nuttall, J. G. Simulating the impact of extreme heat and frost events on wheat crop production: A review. Field Crops Res. 171, 109–119 (2015).
Trnka, M. et al. Adverse weather conditions for European wheat production will become more frequent with climate change. Nat. Clim. Chang. 4(7), 637–643 (2014).
Google Scholar
Gu, L. et al. The 2007 eastern US spring freeze: Increased cold damage in a warming world?. Bioscience 58(3), 253–262 (2008).
Wu, Y. F. et al. Frost affects grain yield components in winter wheat. N. Z. J. Crop. Hort. Sci. 42, 1–11 (2014).
Google Scholar
Nuttall, J. G. et al. Frost response in wheat and early detection using proximal sensors. J. Agron. Crop Sci. 205(2), 220–234 (2019).
Vagujfalvi, A., Galiba, G., Cattivelli, L. & Dubcovsky, J. The cold-regulated transcriptional activator Cbf3 is linked to the frost-tolerance locus Fr-A2 on wheat chromosome 5A. Mol. Genet. Genomics 269, 60–67 (2003).
Google Scholar
Visioni, A. et al. Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics 14, 13 (2013).
Liu, W. X. et al. Genetic architecture of winter hardiness and frost tolerance in triticale. Plos One 9 (2014)
Kaplan, F. et al. Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J. 50(6), 967–981 (2007).
Google Scholar
Ding, Y. L., Shi, Y. T. & Yang, S. H. Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants. New Phytol. 222, 1690–1704 (2019).
Google Scholar
Todorovska, E. G. et al. The expression of CBF genes at Fr-2 locus is associated with the level of frost tolerance in Bulgarian winter wheat cultivars. Biotechnol. Biotechnol. Equip. 28(3), 392–401 (2014).
Google Scholar
Guo, J., Ren, Y. K., Tang, Z. H., Shi, W. P. & Zhou, M. X. Characterization and expression profiling of the ICE-CBF-COR genes in wheat. PeerJ 7, 19 (2019).
Jin, Y. N. et al. Identification of genes from the ICE-CBF-COR pathway under cold stress in Aegilops-Triticum composite group and the evolution analysis with those from Triticeae. Physiol. Mol. Biol. Plants 24, 211–229 (2018).
Google Scholar
Shi, Y. T., Ding, Y. L. & Yang, S. H. Cold signal transduction and its interplay with phytohormones during cold acclimation. Plant Cell Physiol. 56, 7–15 (2015).
Google Scholar
Ritonga, F. N. & Chen, S. Physiological and molecular mechanism involved in cold stress tolerance in plants. Plants 9(5), 560 (2020).
Google Scholar
Babben, S. et al. Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes. BMC Genomics 19(1), 1–24 (2018).
Galiba, G., Vágújfalvi, A., Li, C., Soltész, A. & Dubcovsky, J. Regulatory genes involved in the determination of frost tolerance in temperate cereals. Plant Sci. 176(1), 12–19 (2009).
Google Scholar
Dhillon, T. et al. Regulation of freezing tolerance and flowering in temperate cereals: The VRN-1 connection. Plant Physiol 153, 1846–1858. https://doi.org/10.1104/pp.110.159079 (2010).
Google Scholar
Varshney, R.K. et al. Designing future crops: Genomics-assisted breeding comes of age. Trends Plant Sci. (2021)
Li, X. et al. An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops. Mol. Plant 14(6), 874–887 (2021).
Google Scholar
Chen, H. et al. A genome-wide association study identifies genetic variants associated with mathematics ability (vol 7, 2017). Sci. Rep. 7, 1 (2017).
Korte, A. & Farlow, A. The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9, 9 (2013).
Wang, S. C. et al. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol. J. 12, 787–796 (2014).
Google Scholar
Allen, A. M. et al. Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol. J. 15, 390–401 (2017).
Google Scholar
Liu, J. et al. A genome-wide association study of wheat spike related traits in China. Front. Plant Sci. 9 (2018)
Turuspekov, Y. et al. GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum L.) harvested in three regions of Kazakhstan. BMC Plant Biol. 17 (2017)
Valluru, R., Reynolds, M. P., Davies, W. J. & Sukumaran, S. Phenotypic and genome-wide association analysis of spike ethylene in diverse wheat genotypes under heat stress. New Phytol. 214, 271–283 (2017).
Google Scholar
Sukumaran, S., Dreisigacker, S., Lopes, M., Chavez, P. & Reynolds, M. P. Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor. Appl. Genet. 128, 353–363 (2015).
Google Scholar
Zanke, C. et al. Genetic architecture of main effect QTL for heading date in European winter wheat. Front. Plant Sci. 5, 12 (2014).
Arora, et al. Genome-wide association study of grain architecture in wild wheat Aegilops tauschii. Front. Plant Sci. 8 (2017)
Naruoka, Y., Garland-Campbell, K. A. & Carter, A. H. Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.). Theor. Appl. Genet. 128, 1083–1101 (2015).
Google Scholar
Zhao, Y., et al. Genome-wide association study reveals the genetic basis of cold tolerance in wheat. Mol. Breed. 40 (2020)
Båga, M. et al. Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat. Funct. Integr. Genomics 7(1), 53–68 (2007).
Google Scholar
Zhao, Y. et al. Dissecting the genetic architecture of frost tolerance in Central European winter wheat. J. Exp. Bot. 64(14), 4453–4460 (2013).
Google Scholar
Case, A. J., Skinner, D. Z., Garland-Campbell, K. A. & Carter, A. H. Freezing tolerance-associated quantitative trait loci in the brundage x coda wheat recombinant inbred line population. Crop Sci. 54, 982–992 (2014).
Fowler, D. B., N’Diaye, A., Laudencia-Chingcuanco, D., & Pozniak, C. J. Quantitative trait loci associated with phenological development, low-temperature tolerance, grain quality, and agronomic characters in wheat (Triticum aestivum L.). Plos One 11 (2016)
Kruse, E. B. et al. Genomic regions associated with tolerance to freezing stress and snow mold in winter wheat. G3-Genes Genomes Genetics 7, 775–780 (2017).
Google Scholar
Würschum, T., Longin, C. F., Hahn, V., Tucker, M. R. & Leiser, W. L. Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat. Plant J. 89(4), 764–773 (2017).
Google Scholar
SASInstitute. SAS Software. Version 9.4. Cary, NC (2019)
IWGSC (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361 (6403)
Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).
Google Scholar
Shin, J. H., Blay, S., McNeney, B. & Graham, J. LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. J. Stat. Softw. 16(3), 1–10 (2006).
Warnes, G., Gorjanc, G., Leisch, F., & Man, M. Genetics: Population genetics. R package version 1.3.8.1. http://CRAN.R-project.org/package=genetics (2013)
Voss-Fels, K. et al. Subgenomic diversity patterns caused by directional selection in bread wheat gene pools. Plant Genome 8 (2015)
Sannemann, W., Huang, B.E., Mathew, B., Leon, J. Multi-parent advanced generation inter-cross in barley: High-resolution quantitative trait locus mapping for flowering time as a proof of concept. Mol. Breed. 35 (2015)
Reif, J. C., Melchinger, A. E. & Frisch, M. Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci. 45(1), 1–7 (2005).
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
Google Scholar
Perrier, X., & Jacquemoud-Collet, J.P. DARwin Software. Dissimilarity Analysis and Represntation for Windows. http://darwin.cirad.fr/ (2006)
Earl, D. A. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).
Bradbury, P. J. et al. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).
Google Scholar
Spataro, G. et al. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theor. Appl. Genet. 122(7), 1281–1291 (2011).
Google Scholar
Sofalian, O., Mohammadi, S. A., Aharizad, S., Moghaddam, M., & Shakiba, M.R. Mapping of QTLs for frost tolerance and heading time using SSR markers in bread wheat. Afr. J. Biotechnol. 8(20) (2009)
Motomura, Y., Kobayashi, F., Iehisa, J. C. & Takumi, S. A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat. Breed. Sci. 63(1), 58–67 (2013).
Google Scholar
Guerra D et al. (2021) Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley. Theoretical and Applied Genetics 1–17
Royo, C., Nazco, R. & Villegas, D. The climate of the zone of origin of Mediterranean durum wheat (Triticum durum Desf.) landraces affects their agronomic performance. Genet. Resour. Crop Evol. 61, 1345–1358 (2014).
Venske, E., Dos Santos, R. S., Busanello, C., Gustafson, P. & de Oliveira, A. C. Bread wheat: A role model for plant domestication and breeding. Hereditas 156(1), 1–11 (2019).
Kajla, M. et al. Increase in wheat production through management of abiotic stresses: a review. J. Appl. Nat. Sci. 7(2), 1070–1080 (2015).
Google Scholar
Muthamilarasan, M. & Prasad, M. An overview of wheat genome sequencing and its implications for crop improvement. J. Genet. 93, 619–622 (2014).
Google Scholar
Li, J., Yang, J., Li, Y. & Ma, L. Current strategies and advances in wheat biology. Crop J. 8(6), 879–891 (2020).
Chen, Y. et al. Application of image-based phenotyping tools to identify QTL for in-field winter survival of winter wheat (Triticum aestivum L.). Theor. Appl. Genetics 132(9), 2591–2604 (2019).
Google Scholar
Sieber, A. N., Longin, C. F., Leiser, W. L. & Würschum, T. Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat. Theor. Appl. Genet. 129(6), 1087–1097 (2016).
Google Scholar
Franklin, K. A. & Whitelam, G. C. Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat. Genet. 39(11), 1410–1413 (2007).
Google Scholar
Wang, F. et al. Crosstalk of PIF4 and DELLA modulates CBF transcript and hormone homeostasis in cold response in tomato. Plant Biotechnol. J. 18(4), 1041–1055 (2020).
Google Scholar
Novák, A. et al. Light-quality and temperature-dependent CBF14 gene expression modulates freezing tolerance in cereals. J. Exp. Bot. 67(5), 1285–1295 (2016).
Google Scholar
Gierczik, K. et al. Circadian and light regulated expression of CBFs and their upstream signalling genes in barley. Int J Mol Sci 18(8), 1828 (2017).
Google Scholar
Takumi, S. et al. Cold-specific and light-stimulated expression of a wheat (Triticum aestivum L.) Cor gene Wcor15 encoding a chloroplast-targeted protein. J. Exp. Bot. 54, 2265–2274 (2003).
Google Scholar
Limin, A. E. & Fowler, D. B. Low-temperature tolerance and genetic potential in wheat (Triticum aestivum L.): Response to photoperiod, vernalization, and plant development. Planta 224, 360–366. https://doi.org/10.1007/s00425-006-0219-y (2006).
Google Scholar
Huang, X. S., Wang, W., Zhang, Q. & Liu, J. H. A basic helix-loop-helix transcription factor, PtrbHLH, of Poncirus trifoliata confers cold tolerance and modulates peroxidase-mediated scavenging of hydrogen peroxide. Plant Physiol. 162, 1178–1194 (2013).
Google Scholar
Jiang, Y., Yang, B. & Deyholos, M. K. Functional characterization of the Arabidopsis bHLH92 transcriptionfactor in abiotic stress. Mol Genet Genomics 282, 503–516 (2009).
Google Scholar
Kiribuchi, K. et al. Involvement of the basic helix-loop-helix transcription factor RERJ1 in wounding and drought stress responses in rice plants. Biosci. Biotechnol. Biochem. 69(5), 1042–1044 (2005).
Google Scholar
Ogo, Y. et al. Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants. J. Exp. Bot. 57(11), 2867–2878 (2006).
Google Scholar
Wang, Y. J. et al. A rice transcription factor OsbHLH1 is involved in cold stress response. Theor. Appl. Genet. 107(8), 1402–1409 (2003).
Google Scholar
Xu, W. et al. The grapevine basic helix-loop-helix (bHLH) transcription factor positively modulates CBF-pathway and confers tolerance to cold-stress in Arabidopsis. Mol. Biol. Rep. 41(8), 5329–5342 (2014).
Google Scholar
Wang, L., Xiang, L., Hong, J., Xie, Z. & Li, B. Genome-wide analysis of bHLH transcription factor family reveals their involvement in biotic and abiotic stress responses in wheat (Triticum aestivum L.). 3 Biotech. 9(6), 1–12 (2019).
Goossens, J., Mertens, J. & Goossens, A. Role and functioning of bHLH transcription factors in jasmonate signalling. J. Exp. Bot. 68(6), 1333–1347 (2017).
Google Scholar
Sasaki-Sekimoto, Y. et al. Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis. Plant Physiol. 163(1), 291–304 (2013).
Google Scholar
Xiang, L. et al. The cold-induced transcription factor bHLH112 promotes artemisinin biosynthesis indirectly via ERF1 in Artemisia annua. J. Exp. Bot. 70(18), 4835–4848 (2019).
Google Scholar
Jiang, L. et al. The AabHLH35 transcription factor identified from Anthurium andraeanum is involved in cold and drought tolerance. Plants 8(7), 216 (2019).
Google Scholar
Yamasaki, K. et al. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell 16(12), 3448–3459 (2004).
Google Scholar
Chen, L. et al. Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. Sci. Rep. 6(1), 1–4 (2016).
Chen, H. C., Cheng, W. H., Hong, C. Y., Chang, Y. S. & Chang, M. C. The transcription factor OsbHLH035 mediates seed germination and enables seedling recovery from salt stress through ABA-dependent and ABA-independent pathways, respectively. Rice 11(1), 1–7 (2018).
Dong, Y. et al. A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis. Biochem. Biophys. Res. Commun. 450(1), 453–458 (2014).
Google Scholar
