The number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) generating a database for the sweetpotato root transcriptome using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous and initiating storage roots; (2) comparing the expression profiles of initiating storage roots and fibrous roots, using the Illumina Genome Analyzer to sequence cDNA libraries of the two root types and map the data onto the root transcriptome database. Use of the 454-Roche platform generated a total of 524,607 reads, 85.6% of which were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database. A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change). The Illumina-based differential expression results were validated for nine putative genes using quantitative real-time PCR. The differential expression profiles indicated down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots, and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, data indicated delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation. This study adds a valuable resource of sweetpotato root transcript sequences to available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel transcripts related to storage root initiation identified in this study provide a starting point for further investigation into the molecular mechanisms underlying this process.

Plants are immobile organisms that require roots to efficiently and cost-effectively exploit their habitat for water and nutrients. Plant root systems are dynamic structures capable of altering root branching, root angle, and root growth rates determining overall architecture. This plasticity involves belowground plant-root mediated synergies coupled through a continuum of environmental interactions and endogenous developmental processes facilitating plants to adapt to favorable or adverse soil conditions. Plant root branching is paramount to ensure adequate access to soil water and nutrients. Although substantial resources have been devoted toward this goal, significant knowledge gaps exist. In well-studied systems such as rice and maize, it has become evident that root branching plays a significant role in the acquisition of nutrients and other soil-based resources. In these crop species, specific root branching traits that confer enhanced nutrient acquisition are well-characterized and are already being incorporated into breeding populations. In contrast, the understanding of root branching in root and tuber crop productivity has lagged behind. In this review article, we highlight what is known about root branching in root and tuber crops (RTCs) and mark new research directions, such as the use novel phenotyping methods, examining the changes in root morphology and anatomy under nutrient stress, and germplasm screening with enhanced root architecture for more efficient nutrient capture. These directions will permit a better understanding of the interaction between root branching and nutrient acquisition in these globally important crop species.

Adventitious roots of ‘Beauregard’ and ‘Georgia Jet’ sweetpotato were observed and anatomically characterized over a period of 60 days of storage root development. The majority of ‘Beauregard’ and ‘Georgia Jet’ adventitious roots sampled at 5 to 7 days after transplanting (DAT) possessed anatomical features (five or more protoxylem elements) associated with storage root development. The majority of ‘Beauregard’ (86%) and ‘Georgia Jet’ (89%) storage roots sampled at 60 to 65 DAT were traced directly to adventitious roots extant at 5 to 7 DAT. The two varieties, however, differed in the timing in which regular and anomalous cambia were formed. Regular vascular cambium development, i.e., initiation and completion, was observed in both varieties at 19 to 21 DAT. Formation of complete regular vascular cambium was negligible for ‘Beauregard’ (4%) in comparison with ‘Georgia Jet’ (32%) at 26 to 28 DAT. However, anomalous cambia development adjacent to xylem elements was greater in ‘Beauregard’ (30%) in comparison with ‘Georgia Jet’ (13%). Nearly 40% to 50% of samples in both varieties showed extensive lignification in the stele region. At 32 to 35 DAT, 62% to 70% of the adventitious roots for both varieties had either been initiated (developed anomalous cambium) or were lignified. The remaining adventitious roots showed intermediate stages of vascular cambium development. The adventitious root count increased up to 19 to 21 DAT and then remained constant up to 32 to 35 DAT. These accumulated results suggest that the initial stages of adventitious root development are critical in determining storage root set in sweetpotato.

This study characterized lateral root (LR) development attributes during the onset of storage root (SR) initiation stage in ‘Beauregard’ sweetpotato. SR initiation has been defined as the appearance of cambia around the protoxylem and secondary xylem elements. Our results showed that 20-day-old adventitious roots (ARs) classified as SRs had 53% and 85% greater mean LR count than pencil roots (PRs) and lignified roots (LGs), respectively. SRs had 53% and 78% greater mean LR density relative to PRs and LGs, respectively. SRs had 66% and 130% greater mean total LR length than PRs and LGs, respectively. SRs had lower mean main root (MR)/LR length ratio compared with PRs (–38%) and LGs (–60%). SRs had 70% and 134% greater mean surface area than PRs and LGs, respectively. SRs had lower mean MR/LR surface area ratio compared with PRs (–42%) and LGs (–62%). The plot of the first and second principal components revealed the presence of a gradient between extreme LG and SR clusters, suggesting a developmental transition between LGs and SRs with PRs representing an intermediate developmental stage. Although AR architecture is not the sole determinant of SR formation, our data help provide a basis for integrating AR architecture attributes with other factors that are known to influence SR initiation. Growth substrate moisture variability influenced LR development during the critical SR initiation period. Relative to the control treatments, water deprivation 10 to 20 days after transplanting (DAT) reduced mean LR count, length, and surface area by 49%, 103%, and 94%, respectively. Saturated conditions 10 to 20 DAT reduced mean LR count, length, and surface area by 75%, 81%, and 77%, respectively. These results represent the first evidence for the association between anatomical cues of SR initiation and root architecture and provide corroborating data that soil moisture variability 10 to 20 DAT directly influences SR yield potential through AR architecture modifications that are associated with diminished SR formation. This information can be used to further optimize SR yield by identifying agroclimatic and management variables that are associated with desirable LR development during the critical SR initiation stage.

This study characterized the influence of nitrogen (N) rates and variation in local availability on root architecture as measured by lateral root (LR) development attributes during the onset of the storage root (SR) initiation stage in ‘Beauregard’ sweetpotato adventitious roots (ARs). In N rate experiments, plants grown without fertilizer N showed significantly lower values for all measured LR attributes compared with fertilized plants. Total first- (1LR) and second-order LR (2LR) length increased by 78% and 2873%, respectively, as N was increased from 0 to 50 kg·ha ⁻¹ . Total 1LR and 2LR number increased by 32% and 1465%, respectively. Increasing the N rates to 100 and 200 kg·ha ⁻¹ did not result in further increases for all LR attributes measured. There were no differences in AR number between untreated controls and plants fertilized with 50 kg N/ha. However, the number of ARs increased by 65% when fertilizer N was increased from 50 to 100 kg·ha ⁻¹ . Increasing the rate to 200 kg·ha ⁻¹ did not result in further increases in AR number. In split-root experiments, roots grown in the compartment with 50 kg N/ha had 135% and 2916% increase in total 1LR and 2LR length, respectively, compared with roots grown in the compartment without fertilizer N. Total 1LR and 2LR number increased by 110% and 2114%, respectively. There were 111% more ARs in the fertilized compartment relative to the unfertilized compartment. There were no differences in LR attributes and AR number between compartments that received similar fertilizer N rates. In fertilizer placement experiments, there were no differences in LR attributes between pre-mixing fertilizer N and placement of fertilizer ≈4 cm below the surface of the growth substrate. There were also no differences between the unfertilized control and placement of fertilizer ≈4 cm from the bottom of the pot. Plants grown in substrate with pre-mixed N showed 38% and 342% increase in 1LR and 2LR length, respectively, relative to the bottom placement of N. Total number of 1LR and 2LR in the growth substrate with pre-mixed N increased by 30% and 312%, respectively, relative to the bottom placement of N. These results represent the first evidence for the association between sweetpotato root architectural attributes and variation in N rate and localized availability. These results are also consistent with findings in model systems in which local N presence is necessary for LR development. This information can be used to further optimize SR yield by helping to ensure the availability of N at the optimum rate across time and space.