Abstract
Raspberries (Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stages by Digital Gene Expression profiling to identify genes that regulate rooting. Sequencing and de novo assembly yielded 26.82 Gb of nucleotides and 59,173 unigenes; 498, 7,346, 4,110, 7,900, 9,397, and 4,776 differently expressed genes were identified in paired comparisons of SAF1 (floricane at developmental stage 1) vs. SAP1 (primocane at developmental stage 1), SAF2 vs. SAP2, SAF3 vs. SAP3, SAP1 vs. SAP2, SAP1 vs. SAP3, and SAP2 vs. SAP3, respectively. SAP1 maintains an extension growth pattern; SAP2 then exhibits growth arrest and vertical (downward) gravitropic deflection; and finally, short roots begin to form on the apex of SAP3. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis of SAP1 vs. SAP2 revealed 12 pathways that were activated in response to shoot growth arrest and root differentiation, including circadian rhythm—plant (ko04712) and plant hormone signal transduction (ko04075). Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus. These findings provide a basis for elucidating the molecular mechanisms of primocane apex rooting in this economically valuable crop.
Highlights
Raspberries (Rubus sp.) are an important economic fruit crop that grows in all temperate regions of the world
Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus
A total of 12 pathways were significantly enriched, with a Q < 0.05 (Table 4). These differentially expressed genes (DEGs) were associated with flavonoid biosynthesis; circadian rhythm—plant; biosynthesis of secondary metabolites; stilbenoid, diarylheptanoid, and gingerol biosynthesis; cyanoamino acid metabolism; sesquiterpenoid and triterpenoid biosynthesis; porphyrin and chlorophyll metabolism; photosynthesis—antenna proteins; limonene and pinene degradation; plant hormone signal transduction; phenylpropanoid biosynthesis; and ascorbate and aldarate metabolism. These results suggest that changes in the expression of genes related to metabolism, environmental adaptation, and signal transduction are involved in the transition from bud development to root formation at the primocane apex of Rubus
Summary
Raspberries (Rubus sp.) are an important economic fruit crop that grows in all temperate regions of the world. The raspberry fruit contains abundant polyphenol antioxidants, including anthocyanin pigments that are important ingredients of health products and can potentially prevent various human diseases (Skrovankova et al, 2015). Raspberries have a unique rooting characteristic, and its biennial shoots can grow several meters and root at the stem apex in autumn (Heslop-Harrison, 1959). In order to prevent excessive vegetative spread via rooting at stem apices, newly planted. After the formation and growth of new root at the stem apex, negatively geotropic shoots form at the rooting boss. Root primordium differentiation and growth arrest and geotropism deflection are involved in formation of adventitious roots (ARs) at the stem apex, in contrast to adventitious roots derived from ordinary shoot cutting
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