1001 Genomes Consortium (2016). 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481–491.Adamczyk BJ, Lehti-Shiu MD, Fernandez DE (2007). The MADS domain factors AGL15 and AGL18 act redundantly as repressors of the floral transition in Arabidopsis. Plant J 50, 1007–1019.Angel A, Song J, Dean C, Howard M (2011). A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476, 105–108.Angel A, Song J, Yang H, Questa JI, Dean C, Howard M (2015). Vernalizing cold is registered digitally at FLC. Proc Natl Acad Sci USA 112, 4146–4151.Berry S, Hartley M, Olsson TSG, Dean C, Howard M (2015). Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. eLife 4, e07205.Choi K, Kim J, Hwang HJ, Kim S, Park C, Kim SY, Lee I (2011). The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors. Plant Cell 23, 289–303.Crevillén P, Dean C (2011). Regulation of the floral repressor gene FLC: the complexity of transcription in a chromatin context. Curr Opin Plant Biol 14, 38–44.DeLeo VL, Menge DNL, Hanks EM, Juenger TE, Lasky JR (2020). Effects of two centuries of global environmental variation on phenology and physiology of Arabidopsis thaliana. Glob Change Biol 26, 523–538.Ellis TJ, Postma FM, Oakley CG, ?gren J (2021). Life-history trade-offs and the genetic basis of fitness in Arabidopsis?thaliana. Mol Ecol 30, 2846–2858.He F, Kang D, Ren Y, Qu LJ, Zhen Y, Gu H (2007). Genetic diversity of the natural populations of Arabidopsis thaliana in China. Heredity 99, 423–431.Heo JB, Sung S (2011). Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76–79.Hepworth J, Antoniou-Kourounioti RL, Berggren K, Selga C, Tudor EH, Yates B, Cox D, Collier Harris BR, Irwin JA, Howard M, S?ll T, Holm S, Dean C (2020). Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes. eLife 9, e57671.Jiang D, Gu X, He Y (2009). Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis.?Plant Cell 21, 1733–1746.Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C (2000). Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290, 344–347.Jung JH, Lee HJ, Ryu JY, Park CM (2016). SPL3/4/5 integrate developmental aging and?photoperiodic signals into the FT-FD module in Arabidopsis flowering. Mol Plant 9, 1647–1659.Kim DH, Sung S (2017). Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40, 302–312.Kinoshita A, Richter R (2020). Genetic and molecular basis of floral induction in Arabidopsis thaliana. J Exp Bot 71, 2490–2504.Koornneef M, Hanhart CJ, van der Veen JH (1991). A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229, 57–66.Kr?mer U (2015). Planting molecular functions in an ecological context with Arabidopsis thaliana. eLife 4, e06100.Le Corre V, Roux F, Reboud X (2002). DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol Biol Evol 19, 1261–1271.Lee I, Bleecker A, Amasino R (1993). Analysis of naturally occurring late flowering in Arabidopsis thaliana. Mol Gen Genet 237, 171–176.Li H, Durbin R (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760.Li P, Filiault D, Box MS, Kerdaffrec E, van Oosterhout C, Wilczek AM, Schmitt J, McMullan M, Bergelson J, Nordborg M, Dean C (2014). Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana. Genes Dev 28, 1635–1640.Liu ZW, Zhao N, Su YN, Chen SS, He XJ (2020). Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis. Sci Rep 10, 3094.Mansfeld BN, Grumet R (2018). QTLseqr: an R package for bulk segregant analysis with next-generation sequencing. Plant Genome 11, 180006.Marquardt S, Boss PK, Hadfield J, Dean C (2006). Additional targets of the Arabidopsis autonomous pathway members, FCA and FY. J Exp Bot 57, 3379–3386.Martínez-Berdeja A, Stitzer MC, Taylor MA, Okada M, Ezcurra E, Runcie DE, Schmitt J (2020). Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci USA 117, 2526–2534.McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297–1303.Méndez-Vigo B, Picó FX, Ramiro M, Martínez-Zapater JM, Alonso-Blanco C (2011). Altitudinal and climatic adaptation is mediated by flowering traits and FRI, FLC, and PHYC genes in Arabidopsis.?Plant Physiol 157, 1942–1955.Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C (2016). Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. Plant Cell Environ 39, 282–294.Michaels SD, He Y, Scortecci KC, Amasino RM (2003). Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc Natl Acad Sci USA 100, 10102–10107.Mitchell-Olds T, Schmitt J (2006). Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441, 947–952.Putterill J, Robson F, Lee K, Simon R, Coupland G (1995). The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80, 847–857.Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C (2005). Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiol 138, 1163–1173.Shindo C, Bernasconi G, Hardtke CS (2007). Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology. Ann Bot 99, 1043–1054.Springthorpe V, Penfield S (2015). Flowering time and seed dormancy control use external coincidence to generate life history strategy. eLife 4, e05557.Strange A, Li P, Lister C, Anderson J, Warthmann N, Shindo C, Irwin J, Nordborg M, Dean C (2011). Major-effect alleles at relatively few loci underlie distinct vernalization and flowering variation in Arabidopsis accessions. PLoS One 6, e19949.Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM (2006). Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet 38, 706–710.Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013). QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74, 174–183.Xie Y, Zhou Q, Zhao Y, Li Q, Liu Y, Ma M, Wang B, Shen R, Zheng Z, Wang H (2020). FHY3 and FAR1 integrate light signals with the miR156-SPL module-mediated aging pathway to regulate Arabidopsis flowering. Mol Plant 13, 483–498.Xu X, Xu J, Yuan C, Chen Q, Liu Q, Wang X, Qin C (2022). BBX17 interacts with CO and negatively regulates flowering time in Arabidopsis thaliana. Plant Cell Physiol 63, 401–409.Yin P, Kang J, He F, Qu LJ, Gu H (2010). The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences. BMC Plant Biol 10, 22.Zan Y, Carlborg ? (2019). A polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population. Mol Biol Evol 36, 141–154.Zeng L, Gu Z, Xu M, Zhao N, Zhu W, Yonezawa T, Liu T, Qiong L, Tersing T, Xu L, Zhang Y, Xu R, Sun N, Huang Y, Lei J, Zhang L, Xie F, Zhang F, Gu H, Geng Y, Hasegawa M, Yang Z, Crabbe MJC, Chen F, Zhong Y (2017). Discovery of a high-altitude ecotype and ancient lineage of Arabidopsis thaliana from Tibet. Sci Bull 62, 1628–1630.Zhu P, Lister C, Dean C (2021). Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression. Nature 599, 657–661.Zou YP, Hou XH, Wu Q, Chen JF, Li ZW, Han TS, Niu XM, Yang L, Xu YC, Zhang J, Zhang FM, Tan D, Tian Z, Gu H, Guo YL (2017). Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol 18, 239. |