Rodriguez-Zaccaro F Daniela, Lieberman Meric, Groover Andrew
USDA Forest Service, Pacific Southwest Research Station, Davis, CA, United States.
University of California Davis, Genome Center, Davis, CA, United States.
Front Plant Sci. 2024 May 29;15:1375506. doi: 10.3389/fpls.2024.1375506. eCollection 2024.
Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.
木材是树木茎干中的水分传导组织。与大多数被子植物树木一样，杨树木材含有水分传导的导管分子，其功能特性会影响水分运输和生长速率，以及在水分胁迫和干旱期间发生栓塞和水力失效的易感性。在此，我们利用一个独特的杂交杨谱系，该谱系带有经基因组特征分析的染色体插入和缺失，对导管性状进行系统基因组学分析。我们检测了来自基因型克隆复制品的木材形成组织中的基因表达，这些基因型涵盖具有插入和缺失的剂量数量性状位点、具有极端导管性状表型的基因型以及对照基因型。通过基因共表达分析将基因分配到模块中，然后在综合分析中使用这些模块来识别与性状相关的模块，识别与每个模块相关的假定分子和细胞过程，最后使用包括剂量反应性在内的多个标准来识别候选基因。这些分析确定了与导管性状相关的已知过程，包括应激反应、脱落酸和细胞壁生物合成，此外还确定了以前未探索的过程，包括细胞周期和蛋白质泛素化。我们讨论了我们的发现与导致导管性状变异的组成过程的关系，包括信号传导、细胞周期、细胞扩张和细胞分化。
