Abstract
Caucasian clover is the only perennial herb of the genus Leguminous clover with underground rhizomes. However, we know very little about its development process and mechanism. Transcriptome studies were conducted on the roots of Caucasian clover without a rhizome (NR) at the young seedling stage and the fully developed rhizome, including the root neck (R1), main root (R2), horizontal root (R3), and rhizome bud (R4), of the tissues in the mature phase. Compared with the rhizome in the mature phase, NR had 893 upregulated differentially expressed genes (DEGs), most of which were enriched in ‘phenylpropanoid biosynthesis’, ‘phenylalanine metabolism’, ‘DNA replication’ and ‘biosynthesis of amino acids’. A higher number of transcription factors (AP2/ERF, C2H2 and FAR1) were found in NR. There were highly expressed genes for R4, such as auxin response factor SAUR, galacturonosyltransferase (GAUT), and sucrose synthase (SUS). Phenylpropanoids are very important for the entire process of rhizome development. We drew a cluster heat map of genes related to the phenylpropanoid biosynthesis pathway, in which the largest number of genes belonged to COMT, and most of them were upregulated in R4.
Highlights
Caucasian clover (Trifolium ambiguum Bieb.), known as Kura clover) is the only longlived leguminous clover with developed underground rhizomes and strong clonal reproduction ability
We identified differentially expressed genes (DEGs) in rhizome development, which served as the foundation for further exploration of the developmental mechanism of Caucasian clover and related gene function research
The length distribution of the unigenes is shown in S1 Fig. The clean data of each sample were aligned with the assembled transcript or unigene library, and the results of the comparison are shown in S2 Table
Summary
Caucasian clover (Trifolium ambiguum Bieb.), known as Kura clover) is the only longlived leguminous clover with developed underground rhizomes and strong clonal reproduction ability. Its rhizome characteristics have been confirmed to be closely related to plant cold resistance [1], drought resistance [2] and grazing resistance [3]. Due to the lack of genomic information, the molecular mechanism of rhizome formation in Caucasian clover is still poorly understood. An increasing number of genes related to rhizome formation and development have been discovered and identified in different plants. Some genes are highly abundant in or specific to plant rhizomes, including energy and metabolism-related genes, such as monosaccharide
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