Pacheco-Escobedo Mario A, Ivanov Victor B, Ransom-Rodríguez Iván, Arriaga-Mejía Germán, Ávila Hibels, Baklanov Ilya A, Pimentel Arturo, Corkidi Gabriel, Doerner Peter, Dubrovsky Joseph G, Álvarez-Buylla Elena R, Garay-Arroyo Adriana
Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico.
Department of Root Physiology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow, 127276 Russia.
Ann Bot. 2016 Oct 1;118(4):763-776. doi: 10.1093/aob/mcw101.
Background and Aims The Arabidopsis thaliana root is a key experimental system in developmental biology. Despite its importance, we are still lacking an objective and broadly applicable approach for identification of number and position of developmental domains or zones along the longitudinal axis of the root apex or boundaries between them, which is essential for understanding the mechanisms underlying cell proliferation, elongation and differentiation dynamics during root development. Methods We used a statistics approach, the multiple structural change algorithm (MSC), for estimating the number and position of developmental transitions in the growing portion of the root apex. Once the positions of the transitions between domains and zones were determined, linear models were used to estimate the critical size of dividing cells (LcritD) and other parameters. Key Results The MSC approach enabled identification of three discrete regions in the growing parts of the root that correspond to the proliferation domain (PD), the transition domain (TD) and the elongation zone (EZ). Simultaneous application of the MSC approach and G2-to-M transition (CycB1;1DB:GFP) and endoreduplication (pCCS52A1:GUS) molecular markers confirmed the presence and position of the TD. We also found that the MADS-box gene XAANTAL1 (XAL1) is required for the wild-type (wt) PD increase in length during the first 2 weeks of growth. Contrary to wt, in the xal1 loss-of-function mutant the increase and acceleration of root growth were not detected. We also found alterations in LcritD in xal1 compared with wt, which was associated with longer cell cycle duration in the mutant. Conclusions The MSC approach is a useful, objective and versatile tool for identification of the PD, TD and EZ and boundaries between them in the root apices and can be used for the phenotyping of different genetic backgrounds, experimental treatments or developmental changes within a genotype. The tool is publicly available at www.ibiologia.com.mx/MSC_analysis.
背景与目的 拟南芥根是发育生物学中的关键实验系统。尽管其很重要，但我们仍缺乏一种客观且广泛适用的方法来确定沿根尖纵轴的发育域或区域的数量和位置，以及它们之间的边界，而这对于理解根发育过程中细胞增殖、伸长和分化动态的潜在机制至关重要。方法 我们使用一种统计方法，即多重结构变化算法（MSC），来估计根尖生长部分发育转变的数量和位置。一旦确定了域和区域之间转变的位置，就使用线性模型来估计分裂细胞的临界大小（LcritD）和其他参数。关键结果 MSC方法能够识别根生长部分的三个离散区域，分别对应增殖域（PD）、过渡域（TD）和伸长区（EZ）。同时应用MSC方法以及G2到M期转变（CycB1;1DB:GFP）和核内复制（pCCS52A1:GUS）分子标记证实了TD的存在和位置。我们还发现，MADS盒基因XAANTAL1（XAL1）是野生型（wt）在生长的前两周PD长度增加所必需的。与wt相反，在xal1功能缺失突变体中未检测到根生长的增加和加速。我们还发现与wt相比，xal1中LcritD发生了改变，这与突变体中较长的细胞周期持续时间有关。结论 MSC方法是一种有用、客观且通用的工具，可用于识别根尖中的PD、TD和EZ以及它们之间的边界，并且可用于对不同遗传背景、实验处理或基因型内的发育变化进行表型分析。该工具可在www.ibiologia.com.mx/MSC_analysis上公开获取。
