The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice

Chromatin modifications affect flowering time in the long-day plant Arabidopsis thaliana, but the role of histone methylation in flowering time regulation of rice (Oryza sativa), a short-day plant, remains to be elucidated. We identified a late-flowering long vegetative phase1 (lvp1) mutant in rice and used map-based cloning to reveal that lvp1 affects the SET domain group protein 724 (SDG724). SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of global histone H3 lysine 36 (H3K36) methylation in vivo. Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod. Chromatin immunoprecipitation assays showed that lvp1 had reduced levels of H3K36me2/3 at MADS50 and RFT1. This suggests that the divergent functions of paralogs RFT1 and Hd3a, and of MADS50 and MADS51, are in part due to differential H3K36me2/3 deposition, which also correlates with higher expression levels of MADS50 and RFT1 in flowering promotion in rice.     

Global analysis of CCT family knockout mutants identifies four genes involved in regulating heading date in rice

Many genes encoding CCT domain‐containing proteins regulate flowering time. In rice (Oryza sativa), 41 such genes have been identified, but only a few have been shown to regulate heading date. Here, to test whether and how additional CCT family genes regulate heading date in rice, we classified these genes into five groups based on their diurnal expression patterns. The expression patterns of genes in the same subfamily or in close phylogenetic clades tended to be similar. We generated knockout mutants of the entire gene family via CRISPR/Cas9. The heading dates of knockout mutants of only 4 of 14 genes previously shown to regulate heading date were altered, pointing to functional redundancy of CCT family genes in regulating this trait. Analysis of mutants of four other genes showed that OsCCT22, OsCCT38, and OsCCT41 suppress heading under long‐day conditions and promote heading under short‐day conditions. OsCCT03 promotes heading under both conditions and upregulates the expression of Hd1 and Ehd1, a phenomenon not previously reported for other such genes. To date, at least 18 CCT domain‐containing genes involved in regulating heading have been identified, providing diverse, flexible gene combinations for generating rice varieties with a given heading date.     

“先驱”转录因子LEC1在早期胚胎重置春化状态的机制

开花是植物由营养生长阶段向生殖生长阶段转变的重要过程, 长时间低温处理即春化对开花起到非常重要的促进作用。春化控制的拟南芥(Arabidopsis thaliana)开花中, 阻抑型转录因子FLC是重要的关节点, 春化记忆依赖于对该基因的控制。何跃辉研究组之前对拟南芥的研究揭示了转录因子VAL1或VAL2可以识别负调控开花的关键基因FLC成核区的顺式DNA元件, 协同PRC2复合体在春化过程中沉默FLC基因的表达, 并在随后的常温下继续维持FLC基因沉默直至受精结束, 使植物产生春化记忆。但在下一代中如何擦除这种记忆功能, 使FLC重新被激活, 以防止植物在过冬前或过冬时开花, 相关机制目前并不清楚。近期, 该研究组揭示了在植物胚胎发育早期一个种子特有的“先驱”转录因子参与擦除春化记忆, 重新激活FLC基因的分子机制, 并解析了胚胎中的基因激活传递到后胚胎发育(营养生长期)的表观遗传机理。该研究是开花领域的重要突破, 为作物开花调控的生产应用提供了新思路。     

Loss of Gn1a/OsCKX2 confers heavy-panicle rice with excellent lodging resistance

Significant achievements have been made in breeding programs for the heavy-panicle-type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1a^R498) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss-of-function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1a^R498 allele with two gain-of-function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor-made crop improvement of both yield and lodging resistance in rice.     

The trxG family histone methyltransferase SET DOMAIN GROUP 26 promotes flowering via a distinctive genetic pathway

Histone methylation is a major component in numerous processes such as determination of flowering time, which is fine‐tuned by multiple genetic pathways that integrate both endogenous and environmental signals. Previous studies identified SET DOMAIN GROUP 26 (SDG26) as a histone methyltransferase involved in the activation of flowering, as loss of function of SDG26 caused a late‐flowering phenotype in Arabidopsis thaliana. However, the SDG26 function and the underlying molecular mechanism remain largely unknown. In this study, we undertook a genetic analysis by combining the sdg26 mutant with mutants of other histone methylation enzymes, including the methyltransferase mutants Arabidopsis trithorax1 (atx1), sdg25 and curly leaf (clf), as well as the demethylase double mutant lsd1‐like1 lsd1‐like2 (ldl1 ldl2). We found that the early‐flowering mutants sdg25, atx1 and clf interact antagonistically with the late‐flowering mutant sdg26, whereas the late‐flowering mutant ldl1 ldl2 interacts synergistically with sdg26. Based on microarray analysis, we observed weak overlaps in the genes that were differentially expressed between sdg26 and the other mutants. Our analyses of the chromatin of flowering genes revealed that the SDG26 protein binds at the key flowering integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1/AGAMOUS‐LIKE 20 (SOC1/AGL20), and is required for histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 36 trimethylation (H3K36me3) at this locus. Together, our results indicate that SDG26 promotes flowering time through a distinctive genetic pathway, and that loss of function of SDG26 causes a decrease in H3K4me3 and H3K36me3 at its target gene SOC1, leading to repression of this gene and the late‐flowering phenotype.     

Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways

Although the molecular basis of flowering time control is well dissected in the long day (LD) plant Arabidopsis, it is still largely unknown in the short day (SD) plant rice. Rice flowering time (heading date) is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) are also epigenetically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.     

水稻抽穗期QTL定位及候选基因分析

水稻(Oryza sativa)抽穗期是决定产量和品质的重要性状, 在育种、制种及引种驯化过程中发挥重要作用。将热研2号(O. sativa subsp. japonica cv. ‘Nekken2’)和华占(O. sativa subsp. indica cv. ‘HZ’)杂交获得F₁代, 经连续多代自交得到120个重组自交系(RILs)群体。在常规水肥管理条件下, 对120个RILs株系的抽穗时间进行统计分析。利用已构建好的高密度遗传图谱, 对水稻抽穗期相关性状进行QTL定位分析, 结果共检测到11个QTLs, 分别位于第1、3、4、5、6、8和12号染色体上, 其中1个LOD值高达5.75。通过分析QTLs区间内的候选基因, 筛选出可能影响两亲本抽穗期的相关基因, 并利用实时定量PCR进行基因表达量分析, 发现LOC_Os03g03070、LOC_Os03g50310、LOC_Os03g55389、LOC_Os04g55510、LOC_Os08g07740和LOC_Os08g01670共6个基因在双亲间的表达量差异显著, 其中LOC_Os03g50310在Nekken2中的表达量比HZ高3.6倍。对双亲间候选基因LOC_Os03g50310进行测序分析, 发现该基因在5′UTR、CDS区及3′UTR存在4处差异, 其中CDS区的单核苷酸多态性(SNP)差异引发单个氨基酸改变。研究通过挖掘水稻抽穗期QTL位点为进一步克隆水稻抽穗期相关基因和品种选育提供了新线索。