Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)

First author: shumeng Zhang; Affiliations: Northwest A&F University (西北农林科技大学): Yangling, China

Corresponding author: Yajun Xi 

Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.

柳枝稷（Panicum virgatum L.）是多年生禾本科黍属C4草本植物，因其具有丰富的纤维素含量，极好的耐受性，较高的乙醇转化效率等优点，被公认为替代粮食生产燃料乙醇的理想能源作物。然而，柳枝稷存在苗期生长缓慢的现象，导致其在田间与杂草的竞争中处于劣势，规模化种植较为困难。目前对于幼苗生长缓慢的分子原因知之甚少。该研究通过生长指标的测定，对柳枝稷苗期发育过程进行了描述，之后利用转录组测序技术，分析了发育较快的幼苗与发育较慢的幼苗转录组信息的差异，为筛选与幼苗发育速率相关的差异基因提供参考，也解释柳枝稷幼苗发育缓慢的原因提供了新的见解，并有助于柳枝稷的遗传改良工作的进行。对柳枝稷幼苗的株高和鲜重生长指标的监测结果表明，在实验条件下，柳枝稷幼苗的生长发育有一段时间相对停滞。选择快发育苗和慢发育苗生长出现差异的时间段进行转录组测序，得到了678个参与幼苗发育的关键基因。将这些差异基因和玉米叶片发育的基因进行同源性分析，鉴定了128个与幼苗叶片发育相关的关键基因；同时，对柳枝稷不同发育速率的两类幼苗中GA含量的测定结果表明其GA含量存在差异。转录组分析和生理指标表明，柳枝稷幼苗发育速率的差异受参与昼夜节律，硫胺素代谢，能量代谢，GA生物合成、信号转导的基因的差异表达的影响。该研究有助于更好地了解影响幼苗发育和生长速率的原因。鉴定幼苗发育的关键基因对选择更理想的生长特征的柳枝稷品种提供了依据。

通讯：奚亚军  (https://nxy.nwsuaf.edu.cn/szdw/jsyjy/282409.htm)

个人简介：1991年，西北农业大学，学士；1999年，西北农业大学，硕士；2002年，西北农林科技大学，博士。

研究方向：小麦和生物能源作物柳枝稷的遗传改良；小麦和柳枝稷的转基因技术；柳枝稷发育的分子调控。

doi: https://doi.org/10.1186/s13068-019-1534-4

Journal: Biotechnology for Biofuels

Published date: August 05, 2019