Despite the importance of secondary dormancy for plant life cycle timing and survival, there is insufficient knowledge about the (epigenetic) regulation of this trait at the molecular level. Our aim was to determine the role of (epi)genetic processes in the regulation of secondary seed dormancy using natural genotypes of the widely distributed Capsella bursa-pastoris. Seeds of nine ecotypes were exposed to control conditions or histone deacetylase inhibitors [trichostatin A (TSA), valproic acid] during imbibition to study the effects of hyper-acetylation on secondary seed dormancy induction and germination. Valproic acid increased secondary dormancy and both compounds caused a delay of t50 for germination (radicle emergence) but not of t50 for testa rupture, demonstrating that they reduced speed of germination. Transcriptome analysis of one accession exposed to valproic acid versus water showed mixed regulation of ABA, negative regulation of GAs, BRs and auxins, as well as up-regulation of SNL genes, which might explain the observed delay in germination and increase in secondary dormancy. In addition, two accessions differing in secondary dormancy depth (deep vs non-deep) were studied using RNA-seq to reveal the potential regulatory processes underlying this trait. Phytohormone synthesis or signalling was generally up-regulated for ABA (e.g. NCED6, NCED2, ABCG40, ABI3) and down-regulated for GAs (GA20ox1, GA20ox2, bHLH93), ethylene (ACO1, ERF4-LIKE, ERF105, ERF109-LIKE), BRs (BIA1, CYP708A2-LIKE, probable WRKY46, BAK1, BEN1, BES1, BRI1) and auxin (GH3.3, GH3.6, ABCB19, TGG4, AUX1, PIN6, WAT1). Epigenetic candidates for variation in secondary dormancy depth include SNL genes, histone deacetylases and associated genes (HDA14, HDA6-LIKE, HDA-LIKE, ING2, JMJ30), as well as sequences linked to histone acetyltransferases (bZIP11, ARID1A-LIKE), or to gene silencing through histone methylation (SUVH7, SUVH9, CLF). Together, these results show that phytohormones and epigenetic regulation play an important role in controlling differences in secondary dormancy depth between accessions.

中文翻译：

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荠菜次级种子休眠深度和萌发的 (Epi) 遗传控制

尽管次级休眠对植物生命周期时间和存活很重要，但对该性状在分子水平上的（表观遗传）调控知之甚少。我们的目的是使用广泛分布的自然基因型来确定 (epi) 遗传过程在调节次生种子休眠中的作用荠菜. 九种生态型的种子在吸胀过程中暴露于对照条件或组蛋白脱乙酰酶抑制剂 [曲古抑菌素 A (TSA)、丙戊酸]，以研究超乙酰化对次级种子休眠诱导和萌发的影响。丙戊酸增加了次级休眠，这两种化合物都会导致发芽延迟 t50（胚根出现），但不会导致种皮破裂延迟 t50，这表明它们降低了发芽速度。暴露于丙戊酸的一个种质的转录组分析相对水表现出对 ABA 的混合调节，对 GAs、BRs 和生长素的负调节，以及对周六夜现场基因，这可能解释了观察到的发芽延迟和次级休眠增加。此外，两个次生休眠深度​​不同的种质（深对比非深度）使用 RNA-seq 进行了研究，以揭示该特征背后的潜在调控过程。植物激素合成或信号传导通常对 ABA 上调（例如NCED6,NCED2,ABCG40,ABI3) 并下调遗传算法 (GA20ox1,GA20ox2,bHLH93）， 乙烯 （ACO1,ERF4-LIKE, ERF105,ERF109类), BR (BIA1,CYP708A2-样, 可能WRKY46,BAK1,本1,BES1,一带一路1) 和生长素 (GH3.3,GH3.6,ABCB19,TGG4,辅助1,PIN6,WAT1). 次生休眠深度​​变化的表观遗传候选者包括周六夜现场基因、组蛋白脱乙酰酶和相关基因（HDA14,HDA6类,类HDA,ING2,JMJ30), 以及与组蛋白乙酰转移酶相关的序列 (bZIP11,类似ARID1A), 或通过组蛋白甲基化使基因沉默 (SUVH7,SUVH9,CLF). 总之，这些结果表明，植物激素和表观遗传调控在控制种质间次生休眠深度​​差异方面起着重要作用。