State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China.
National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
BMC Genom Data. 2024 Apr 30;25(1):38. doi: 10.1186/s12863-024-01219-9.
Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane.
In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage.
The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.
甜根子草（Saccharum spontaneum L.）是甘蔗的近缘种，已成为现代甘蔗品种的重要遗传成分。茎的发育是影响产量的重要因素之一，而甜根子草茎发育的分子机制仍知之甚少。苯丙氨酸解氨酶（PAL）是初生和次生代谢的重要组成部分，对植物的生长、发育和应激防御有重要贡献。然而，目前对甜根子草 PAL 基因的了解仍然有限。因此，通过转录组分析鉴定和表征 PAL 基因将为进一步研究 PAL 基因在甘蔗中的功能提供理论基础。
本研究从甜根子草中鉴定出 42 个 PAL 基因，包括 26 个 SsPAL 基因、8 个来自甘蔗品种 R570 的 ShPAL 基因和 8 个来自高粱的 SbPAL 基因。系统发育分析表明，SsPAL 基因分为三组，可能受到长期自然选择的影响。值得注意的是，20 个 SsPAL 基因存在于第 4 和第 5 条染色体上，表明它们在甜根子草中高度保守。这种保守性可能是由于该基因家族中存在全基因组复制。发现 PAL 基因的上游序列含有保守的顺式作用元件，如 G-盒和 SP1、GT1 基序和 CAT 盒，它们共同调节甜根子草的生长和发育。此外，定量逆转录聚合酶链反应（qRT-PCR）分析表明，茎中的 SsPAL 基因表达显著高于叶片，表明它们可能促进茎的生长和发育，特别是在生长阶段的+6 茎（从上到下的第六节茎）中。
本研究揭示了 SsPAL 基因的分子特征，并表明它们可能在甜根子草茎的生长和发育中发挥重要作用。总之，我们的研究结果将促进对甜根子草茎发育的分子机制的理解，也有助于甘蔗的遗传改良。
