Rice root response atlas

Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource. Overall design: Evaluation of root domains TRAP seq and ATAC-seq profiles in rice roots in different environments and water stresses. Greenhouse pot-based translating ribosome affinity purification and chromatin experiments were conducted in five independent replicates of each line, with T1 or T2 seed stocks and whole root tissue was quickly dissected and frozen in liquid nitrogen. All tissue collection and TRAP and INTACT-ATAC library processing was performed with three biological replicates. Complete root systems were harvested. Nine conditions were assessed. Plate: plants grown from seed on petri dishes with 1X MS, 1 % [w/v] Sucrose, pH 5.8. Plate-based TRAP experiments were conducted with three or four independent replicates. Greenhouse grown plants were cultivated in GreenGrades Profile with seven treatments. (1) Control: controlled well-watered and drained irrigation growth. (2) Water Deficit: 5-6 days of no watering, with a fall to 72% (v/v) relative water content. (3) Waterlogging: 5 days of standing water covering root systems. (4) Submergence: 5 days of complete plant submergence. (5) Water Deficit Recovery: water deficit followed by a 1 day irrigation. (6) Waterlogging Recovery: pots allowed to fully drain for 1 day. (7) Submergence Recovery: plants returned to the bench and pots allowed to drain for 1 day. Field: Seedlings grown in the greenhouse transplanted to a paddy field at age 14 days; tissue collected after 35 days. This was performed with six randomized independent replicates of each line. For greenhouse and field sampling, 3 bioreplicates of up to 2 RNA pools (total mRNA, TRAP-RNA for different root domains) and ATAC-seq.水稻已演化出调控程序与特化细胞类型，使其能够抵御不同环境胁迫。为解析水稻根系如何应对水分胁迫，我们对正常浇水、排水对照（有氧对照）、水分亏缺、涝渍、完全淹水以及恢复处理下的发育特征明确的根系细胞群的翻译组（translatome，核糖体结合mRNA）和染色质开放区域开展了谱型分析。研究发现，涝渍响应仅局限于特定根系区域，而水分亏缺与淹水的基因表达特征谱范围更广，且相较于对照根系，多数特征在恢复处理1天后即可逆转。我们还对稻田栽培水稻的根系进行了评估。特定响应包括：淹水条件下分生组织中细胞周期与DNA合成相关基因的翻译受阻，以及水分亏缺条件下外/内皮层木栓质相关通路的激活增强。通过整合染色质开放区域与翻译组数据，我们构建了随水分可用性动态调控的推断调控网络。本数据集还补充了平板培养幼苗（7日龄）与稻田栽培植株（49日龄）根系的翻译组与染色质开放区域数据。田间栽培植株的8种细胞群翻译组图谱展现了显著的细胞类型特异性表达。综上，这些覆盖多个发育阶段、多种环境（包括2种水分限制胁迫）的特定细胞群数据，将作为公共学术资源供学界使用。 实验总体设计：对不同环境与水分胁迫下的水稻根系开展根系区域翻译核糖体亲和纯化测序（TRAP-seq）与转座酶可及性染色质测序（ATAC-seq）谱型分析。采用基于温室盆栽的翻译核糖体亲和纯化（TRAP）与染色质实验，每个株系设置5次独立重复，使用T1或T2代种子库，完整根系组织快速解离后于液氮中速冻。所有组织收集、TRAP与INTACT-ATAC文库制备均设置3次生物学重复。共收获完整根系，评估了9种处理条件。 平板培养：种子于含1×MS培养基、1%[w/v]蔗糖、pH 5.8的培养皿中萌发生长。平板培养的TRAP实验设置3或4次独立重复。 温室栽培：植株采用GreenGrades Profile基质栽培，设置7种处理：(1) 对照：正常浇水与排水的可控灌溉生长；(2) 水分亏缺：持续5-6天不浇水，植株相对含水量降至72%（v/v）；(3) 涝渍：持续5天保持根系浸没于静水中；(4) 淹水：持续5天完全淹没植株；(5) 水分亏缺恢复：先进行水分亏缺处理，随后灌溉1天；(6) 涝渍恢复：将盆栽完全排水1天；(7) 淹水恢复：将植株放回操作台，盆栽完全排水1天。 田间实验：温室培育的幼苗于14日龄时移栽至稻田，于移栽后35天收集组织。每个株系设置6次随机独立重复。针对温室与田间采样，每个样本设置3次生物学重复，可获得最多2份RNA混合池（总mRNA、对应不同根系区域的TRAP-RNA）以及ATAC-seq数据。