Acevedo M, Zurn J, Molero G, Kumar Singh P, He X, Aoun M, Juliana P, Bockleman H, Bonman M, El-Sohl M, Amri A, Coffman R, McCandles L. 2018. The role of wheat in global food security. In: Agricultural Development and Sustainable Intensification. Routledge, London. 30.

Barrett J C, Fry B, Maller J B, Daly M J. 2004. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.

Bäurle I, Dean C. 2006. The timing of developmental transitions in plants. Cell, 125, 655–664.

Benaouda S, Dadshani S, Koua P, Léon J, Ballvora A. 2022. Identification of QTLs for wheat heading time across multiple-environments. Theoretical and Applied Genetics, 135, 2833–2848.

Boden S A, Cavanagh C, Cullis B R, Ramm K, Greenwood J, Jean Finnegan E, Trevaskis B, Swain S M. 2015. Ppd-1 is a key regulator of inflorescence architecture and paired spikelet development in wheat. Nature Plants, 1, 14016.

Chen A, Li C, Hu W, Lau M Y, Lin H, Rockwell N C, Martin S S, Jernstedt J A, Lagarias J C, Dubcovsky J. 2014. Phytochrome C plays a major role in the acceleration of wheat flowering under long-day photoperiod. Proceedings of the National Academy of Sciences of the United States of America, 111, 10037–10044.

Chen F, Zhang F, Cheng X, Morris C, Xu H, Dong Z, Zhan K, Cui D. 2010. Association of Puroindoline b-B2 variants with grain traits, yield components and flag leaf size in bread wheat (Triticum aestivum L.) varieties of the Yellow and Huai Valleys of China. Journal of Cereal Science, 52, 247–253.

Chen J, Zhang F, Zhao C, Lv G, Sun C, Pan Y, Guo X, Chen F. 2019. Genome-wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat. Plant Biotechnology Journal, 17, 2106–2122. 

Chen W, Gao Y, Xie W, Gong L, Lu K, Wang W, Li Y, Liu X, Zhang H, Dong H, Zhang W, Zhang L, Yu S, Wang G, Lian X, Luo J. 2014. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics, 46, 714–721.

Csizmok V, Forman-Kay J D. 2018. Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. Current Opinion in Structural Biology, 48, 58–67.

Dixon A L, Liang L, Moffatt M F, Chen W, Heath S, Wong K C C, Taylor J, Burnett E, Gut I, Farrall M, Lathrop G M, Abecasis G R, Cookson W O C. 2007. A genome-wide association study of global gene expression. Nature Genetics, 39, 1202–1207.

Du Z Z, He J B, Jiao W B. 2024. SynDiv: An efficient tool for chromosome collinearity-based population genomics analyses. Plant Communications, 5, 101071.

Ergoren M, Neumann R, Berg I, Jeffreys A. 2017. Cis-and trans-regulation controls of human meiotic recombination at a hotspot. The EuroBiotech Journal, 1, 319–331.

Fourquet L, Barber T, Campos-Mantello C, Howell P, Orman-Ligeza B, Percival-Alwyn L, Rose G A, Sheehan H, Wright T I C, Longin F, Würschum T, Novoselovic D, Greenland A J, Mackay I, Cockram J, Bentley A R. 2024. An eight-founder wheat MAGIC population allows fine-mapping of flowering time loci and provides novel insights into the genetic control of flowering time. Theoretical and Applied Genetics, 137, 277.

Gao F, Wen W, Liu J, Rasheed A, Yin G, Xia X, Wu X, He Z. 2015. Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the chinese wheat cross Zhou 8425B/Chinese Spring. Frontiers in Plant Science, 6, 1099.

Gardiner L J, Wingen L U, Bailey P, Joynson R, Brabbs T, Wright J, Higgins J D, Hall N, Griffiths S, Clavijo B J, Hall A. 2019. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biology, 20, 69.

Henderson I R, Bomblies K. 2021. Evolution and plasticity of genome-wide meiotic recombination rates. Annual Review of Genetics, 55, 23–43.

Hill C B, Li C. 2016. Genetic architecture of flowering phenology in cereals and opportunities for crop improvement. Frontiers in Plant Science, 7, 1906.

Hou W, Lu Q, Ma L, Sun X, Wang L, Nie J, Guo P, Liu T, Li Z, Sun C, Ren Y, Wang X, Yang J, Chen F. 2023. Mapping of quantitative trait loci for leaf rust resistance in the wheat population 'Xinmai 26/Zhoumai 22'. Journal of Experimental Botany, 74, 3019–3032.

Hu J, Wang X, Zhang G, Jiang P, Chen W, Hao Y, Ma X, Xu S, Jia J, Kong L, Wang H. 2020. QTL mapping for yield-related traits in wheat based on four RIL populations. Theoretical and Applied Genetics, 133, 917–933.

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42, 961–967.

Hyles J, Bloomfield M T, Hunt J R, Trethowan R M, Trevaskis B. 2020. Phenology and related traits for wheat adaptation. Heredity, 125, 417–430.

Jaffe A E, Straub R E, Shin J H, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi H S, Quan J, Chen Q, Colantuoni C, Ulrich W S, Maher B J, Deep-Soboslay A, Cross A J, Brandon N J, Leek J T, Hyde T M, Kleinman J E, Weinberger D R, et al. 2018. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nature Neuroscience, 21, 1117–1125.

Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos: An information aesthetic for comparative genomics. Genome Research, 19, 1639–1645.

Kyle I, Rui W, Weidong Z, Justin W, Natalie K, Eduard A, Jianli C. 2021. QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars. Theoretical and Applied Genetics, 134, 2079–2095.

Kyung C J, Hyeonjin P, Gyu J S, Changhyun C, Youngho K, Myeong L S, Yurim K, Jun J B, Hee L J, Wook K S, Jae K W. 2025. Identification and validation of a major quantitative trait locus for precise control of heading date in wheat (Triticum aestivum L.). BMC Plant Biology, 25, 616.

Li C, Distelfeld A, Comis A, Dubcovsky J. 2011. Wheat flowering repressor VRN2 and promoter CO2 compete for interactions with NUCLEAR FACTOR-Y complexes. Plant Journal, 67, 763–773.

Li C, Lin H, Chen A, Lau M, Jernstedt J, Dubcovsky J. 2019. Wheat VRN1, FUL2 and FUL3 play critical and redundant roles in spikelet development and spike determinacy. Development, 146, dev175398.

Li G, Ren Y, Yang Y, Chen S, Zheng J, Zhang X, Li J, Chen M, Sun X, Lv C, Li X, Zhang B, Sun X, Li Y, Zhao M, Dong C, Tang J, Huang Z, Peng Y, Gu D, et al. 2025. Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding. Plant Communications, 6, 101222.

Li H, Ye G, Wang J. 2007. A modified algorithm for the improvement of composite interval mapping. Genetics, 175, 361–374.

Li M, Yeung J M Y, Cherny S S, Sham P C. 2012. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Human Genetics, 131, 747–756.

Li Y, Jin L, Liu X, He C, Bi S, Saeed S, Yan W. 2024a. Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat. Plant Diversity, 46, 386–394.

Li Y, Xiong H, Guo H, Xie Y, Zhao L, Gu J, Li H, Zhao S, Ding Y, Zhou C, Fang Z, Liu L. 2024b. A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat. Plant Biotechnology Journal, 23, 20–35.

Lipka A E, Tian F, Wang Q, Peiffer J, Li M, Bradbury P J, Gore M A, Buckler E S, Zhang Z. 2012. GAPIT: Genome association and prediction integrated tool. Bioinformatics, 28, 2397–2399.

Liu C, Wang J, Sun P, Yu J, Meng F, Zhang Z, Guo H, Wei C, Li X, Shen S, Wang X. 2020. Illegitimate recombination between homeologous genes in wheat genome. Frontiers in Plant Science, 11, 1076.

Liu P, Shi C, Liu S, Lei J, Lu Q, Hu H, Ren Y, Zhang N, Sun C, Chen L, Jiang Y, Feng L, Zhang T, Zhong K, Liu J, Zhang J, Zhang Z, Sun B, Chen J, Tang Y, et al. 2023. A papain-like cysteine protease-released small signal peptide confers wheat resistance to wheat yellow mosaic virus. Nature Communications, 14, 7773.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.

Lv G, Dong Z, Wang Y, Geng J, Li J, Lv X, Sun C, Ren Y, Zhang J, Chen F. 2020. Identification of genetic loci of black point in Chinese common wheat by genome-wide association study and linkage mapping. Plant Disease, 104, 2005–2013.

Lv G, Tian Q, Zhang F, Chen J, Niaz M, Liu C, Hu H, Sun C, Chen F. 2021. Reduced expression of lipoxygenase genes improves flour processing quality in soft wheat. Journal of Experimental Botany, 72, 6247–6259.

Mani P, Yadav V, Das S, Chowdhury S. 2009. Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination. PLoS ONE, 4, e4399.

Mitura K, Cacak-Pietrzak G, Feledyn-Szewczyk B, Szablewski T, Studnicki M. 2023. Yield and grain quality of common wheat (Triticum aestivum L.) depending on the different farming systems (Organic vs. Integrated vs. Conventional). Plants, 12, 1022.

Munch M, Rezette L, Buche P, Chambrey B, Deborde C, Dervaux S, Geoffroy S, Kansou K, Le Gall S, Linossier L, Meleard B, Menut L, Morel M H, Weber M, Saulnier L. 2025. Dataset for common wheat (Triticum aestivum L.) grain and flour characterization using classical and advanced analyses. Data in Brief, 59, 111375.

Naranjo T. 2019. The effect of chromosome structure upon meiotic homologous and homoeologous recombinations in triticeae. Agronomy, 9, 552.

Niaz M, Zhang L, Lv G, Hu H, Yang X, Cheng Y, Zheng Y, Zhang B, Yan X, Htun A, Zhao L, Sun C, Zhang N, Ren Y, Chen F. 2023. Identification of TaGL1-B1 gene controlling grain length through regulation of jasmonic acid in common wheat. Plant Biotechnology Journal, 21, 979–989.

Niu D, He Y. 2024. Molecular epigenetic understanding of seasonal regulation of flowering time in wheat. Biotechnology Bulletin, 40, 30–40.

Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.

Qiao P, Li X, Liu D, Lu S, Zhi L, Rysbekova A, Chen L, Hu Y. 2023. Mining novel genomic regions and candidate genes of heading and flowering dates in bread wheat by SNP-and haplotype-based GWAS. Molecular Breeding, 43, 76.

Ren Y, Yu P B, Wang Y, Hou W X, Yang X, Fan J L, Wu X H, Lv X L, Zhang N, Zhao L, Dong Z D, Chen F. 2020. Development of a rapid approach for detecting sharp eyespot resistance in seedling-stage wheat and its application in Chinese wheat cultivars. Plant Disease, 104, 1662–1667.

Sadeghi-Tehran P, Sabermanesh K, Virlet N, Hawkesford M J. 2017. Automated method to determine two critical growth stages of wheat: Heading and flowering. Frontiers in Plant Science, 8, 252. 

Schadt E E, Monks S A, Drake T A, Lusis A J, Che N, Colinayo V, Ruff T G, Milligan S B, Lamb J R, Cavet G, Linsley P S, Mao M, Stoughton R B, Friend S H. 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297–302.

Shi C, Li P, Jing Z, Yang X, Zhang Q, Niaz M, Sun C, Chen F. 2025. Genome-wide dissection of lesion mimic mutations in wheat: Identification and functional characterization of candidate genes. Theoretical and Applied Genetics, 138, 280.

Shi C, Zhao L, Zhang X, Lv G, Pan Y, Chen F. 2019. Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat. BMC Plant Biology, 19, 6.

Shi C, Zheng Y, Geng J, Liu C, Pei H, Ren Y, Dong Z, Zhao L, Zhang N, Chen F. 2020. Identification of herbicide resistance loci using a genome-wide association study and linkage mapping in Chinese common wheat. The Crop Journal, 8, 666–675.

Shu F, Xiao H, Li Q, Ren X, Liu Z, Hu B, Wang H, Wang H, Jiang G. 2023. Epigenetic and post-translational modifications in autophagy: Biological functions and therapeutic targets. Signal Transduction and Targeted Therapy, 8, 32.

Song H, Wang Q, Zhang Z, Lin K, Pang E. 2023. Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes. Horticulture Research, 10, uhad038.

Stepanenko I L, Smirnov O G, Titov I I. 2012. A model of the gene network for flowering time regulation in winter wheat and barley. Russian Journal of Genetics (Applied Research), 2, 319–324.

Sun C, Dong Z, Zhao L, Ren Y, Zhang N, Chen F. 2020. The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnology Journal, 18, 1354–1360.

Sun C, Jing Z, Chen X, Chen J, Shang Q, Jin H, Jia J, Ren Y, Zhao L, Gao L, He Z, Chen F. 2025. Reconciliation of wheat 660K and 90K SNP arrays and their utilization in dough rheological properties of bread wheat. Journal of Advanced Research, 77, 1-13.

Sun C, Zhang F, Yan X, Zhang X, Dong Z, Cui D, Chen F. 2017. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. Plant Biotechnology Journal, 15, 953–969.

Swift M L. 1997. GraphPad prism, data analysis, and scientific graphing. Journal of Chemical Information and Computer Sciences, 37, 411–412.

Vos P G, Paulo M J, Voorrips R E, Visser R G F, van Eck H J, van Eeuwijk F A. 2017. Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato. Theoretical and Applied Genetics, 130, 123–135.

Wang S, Wong D, Forrest K, Allen A, Chao S, Huang B E, Maccaferri M, Salvi S, Milner S G, Cattivelli L, Mastrangelo A M, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Consortium I W G S, Lillemo M, Mather D, Appels R, et al. 2014. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal, 12, 787–796.

Wang Y, Tang H, DeBarry J D, Tan X, Li J, Wang X, Lee T, Jin H, Marler B, Guo H, Kissinger J C, Paterson A H. 2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40, e49.

Wittern L, Steed G, Taylor L J, Ramirez D C, Pingarron-Cardenas G, Gardner K, Greenland A, Hannah M A, Webb A A R. 2023. Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations. Plant Physiology, 191, 1383–1403.

Wu L, Xie Z, Li D, Chen Y, Xia C, Kong X, Liu X, Zhang L. 2024. TaMYB72 directly activates the expression of TaFT to promote heading and enhance grain yield traits in wheat (Triticum aestivum L.). Journal of Integrative Plant Biology, 66, 1266–1269.

Würschum T. 2012. Mapping QTL for agronomic traits in breeding populations. Theoretical and Applied Genetics, 125, 201–210.

Xiao J, Xu S, Li C, Xu Y, Xing L, Niu Y, Huan Q, Tang Y, Zhao C, Wagner D, Gao C, Chong K. 2014. O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat. Nature Communications, 5, 4572.

Xu S, Chong K. 2018. Remembering winter through vernalisation. Nature Plants, 4, 997–1009.

Xu S, Dong Q, Deng M, Lin D, Xiao J, Cheng P, Xing L, Niu Y, Gao C, Zhang W, Xu Y, Chong K. 2021. The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat. Molecular Plant, 14, 1525–1538.

Xu X, Liu W, Liu Z, Fan J, Zhou Y. 2020. Mapping powdery mildew resistance gene pmYBL on chromosome 7B of Chinese wheat (Triticum aestivum L.) landrace Youbailan. Plant Disease, 104, 2411–2417.

Yan X, Zhao L, Ren Y, Dong Z, Cui D, Chen F. 2019. Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat. Scientific Reports, 9, 2702.

Yang X, Zhang L, Wei J, Liu L, Liu D, Yan X, Yuan M, Zhang L, Zhang N, Ren Y, Chen F. 2025. A TaSnRK1α-TaCAT2 model mediates resistance to Fusarium crown rot by scavenging ROS in common wheat. Nature Communications, 16, 2549.

Young N D. 1996. QTL mapping and quantitative disease resistance in plants. Annual Review of Phytopathology, 34, 479–501.

Zhang L, Zhang N, Wang S, Tian H, Liu L, Pei D, Yu X, Zhao L, Chen F. 2023. A TaSnRK1α modulates TaPAP6L-mediated wheat cold tolerance through regulating endogenous jasmonic acid. Advanced Science, 10, e2303478. 

Zhang N, Li S, Sun Z, Dai J, Zhang S, Chen D, Zhao L, Jia A, Chen F. 2025a. A lectin receptor-like kinase TaSRK that is deacetylated by TaHDA9 regulates wheat grain length by mediating the photosystem II protein TaPsbO. Science Bulletin, 70, 3120–3124. 

Zhang N, Tang L, Li S, Liu L, Gao M, Wang S, Chen D, Zhao Y, Zheng R, Soleymaniniya A, Zhang L, Wang W, Yang X, Ren Y, Sun C, Wilhelm M, Wang D, Li M, Chen F. 2025b. Integration of multi-omics data accelerates molecular analysis of common wheat traits. Nature Communications, 16, 2200. 

Zhang N, Wang S, Zhao S, Chen D, Tian H, Li J, Zhang L, Li S, Liu L, Shi C, Yu X, Ren Y, Chen F. 2023. Global crotonylatome and GWAS revealed a TaSRT1-TaPGK model regulating wheat cold tolerance through mediating pyruvate. Science Advances, 9, eadg1012.

Zhang P, Lan C, Asad M A, Gebrewahid T W, Xia X, He Z, Li Z, Liu D. 2019. QTL mapping of adult-plant resistance to leaf rust in the Chinese landraces Pingyuan 50/Mingxian 169 using the wheat 55K SNP array. Molecular Breeding, 39, 98.

Zhang R G, Shang H Y, Milne R I, Almeida-Silva F, Chen H, Zhou M J, Shu H, Jia K H, Van de Peer Y, Ma Y P. 2025. SOI: Robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics. Nucleic Acids Research, 53, gkaf320.

Zhang T, Shi C, Hu H, Zhang Z, Wang Z, Chen Z, Feng H, Liu P, Guo J, Lu Q, Zhong K, Chen Z, Liu J, Yu J, Chen J, Chen F, Yang J. 2022. N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection. Nature Communications, 13, 6576.

Zhang X, Chen J, Yan Y, Yan X, Shi C, Zhao L, Chen F. 2018. Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat. Theoretical and Applied Genetics, 131, 2271–2285.

Zhao H, Huang X, Yang Z, Li F, Ge X. 2023. Synergistic optimization of crops by combining early maturation with other agronomic traits. Trends in Plant Science, 28, 1178–1191. 

Zhao L, Wang C, Wang T, Liu J, Qiao Q, Yang Y, Hu P, Zhang L, Zhao S, Chen D, Ren Y, Zhang N, Dong Z, Chen F. 2023a. Identification of the candidate gene controlling tiller angle in common wheat through genome-wide association study and linkage analysis. The Crop Journal, 11, 870–877.

Zhao L, Zheng Y, Wang Y, Wang S, Wang T, Wang C, Chen Y, Zhang K, Zhang N, Dong Z, Chen F. 2023b. A HST1-like gene controls tiller angle through regulating endogenous auxin in common wheat. Plant Biotechnology Journal, 21, 122–135.

Zhu T, Wang L, Rimbert H, Rodriguez J C, Deal K R, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu Y Q, Mascher M, Dvorak J, Luo M. 2021. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant Journal, 107, 303–314.

Zhu Z, Zhu X, Zhang N, Wang W, Liu J, Zhang F, Ren X, Ding Y, Sun F, He X, Hu S, Li X, Wei S, Guo W, Ni Z, Sun Q, Liu D, Su Z. 2025. Identification and validation of a major QTL, QFhb-6AL, for Fusarium head blight resistance on chromosome 6AL in wheat. Theoretical and Applied Genetics, 138, 74.