Figures (7)  Tables (1)

    • Figure 1. 

      Schematics of tuber and storage root crops. Stem tuber crops, such as potato (Solanum tuberosum), and yam (Dioscorea alata), and five storage root crops like sweetpotato (Ipomoea batatas), cassava (Manihot esculenta), beetroot (Beta vulgaris), carrot (Daucus carota), and radish (Raphanus sativus) are illustrated along with their below ground storage organs. Potato tubers are formed from belowground modified stem, known as stolon, whereas yam tubers are belowground thickened stems. Adventitious roots can thicken and store carbohydrates to develop into storage roots in sweetpotato. Cassava develops tubers from fibrous roots. Beetroot, carrot, and radish have single, enlarged taproots modified to store carbohydrates. Abbreviations: AR, adventitious root; FR, fibrous root; LR, lateral root; PR, pencil root; SR, storage root; St, stolon.

    • Figure 2. 

      Dynamics of phytohormone levels during the developmental stages of potato tubers and sweetpotato storage roots. (a) Schematic of stolon-to-tuber transition stages in potato. (b) Endogenous phytohormone levels during tuber development in potato[101]. Phytohormones were measured from the respective root tissue type-fibrous root or developing storage roots. (c) Schematic of different stages of storage root development in sweetpotato. F, fibrous roots with diameter 1 mm; D1, initiating storage root with diameter 1 cm; D3, storage root with diameter 3 cm; D5, storage root with diameter 5 cm; D10, storage root with diameter 10 cm. Phytohormones were measured from tuberizing stolons/tubers. (d) Endogenous levels of phytohormones during storage root developmental stages in sweetpotato[74].

    • Figure 3. 

      Heat maps showing the expression profiles of key phytohormone-related genes during tuber developmental stages of potato. (a) Schematic of six tuber developmental stages used for transcriptome profiling as a part of NCBI BioProject PRJNA753086. These stages and the samples harvested for RNA sequencing are as follows. HS: hooked stolon, 0.5 cm of tip; SS: Swollen at the base of the tip but no roundness, 2 cm of the tip; TS1: stolon rounded off, harvested tuber part; TS3: round tuber, 5–15 mm; TS4: round tuber, 15–30 mm and TS5: larger and mature tuber, 30 mm plus. Heat maps of genes are categorized based on the type of phytohormones. (b) gibberellin, (c) auxin, (d) ABA, (e) cytokinin, (f) brassinosteroid, (g) salicylic acid, (h) jasmonic acid, (i) strigolactone, and (j) ethylene. The scale bar represents normalized read counts (log2 values). Detailed information of all these and related genes along with their expression values are shown in Supplementary Table S1. Abbreviations used: GA13/20ox: GIBBERELLIN 13/20-OXIDASE; GA2ox: GIBBERELLIN 2-OXIDASE; GA3ox: GIBBERELLIN 3-β-DIOXYGENASE; GID: GIBBERELLIN INSENSITIVE DWARF 1; RGA: REPRESSOR OF GA1-3; TAR1/YUC: TRYPTOPHAN AMINOTRANSFERASE-RELATED PROTEIN1/FLAVIN-CONTAINING MONOOXYGENASE; GH3: GRETCHEN HAGEN3; PIN: PIN-FORMED; TIR1: TRANSPORT INHIBITOR RESPONSE 1; ARF: AUXIN RESPONSE FACTOR; AUX/IAA: AUXIN/INDOLE-3-ACETIC ACID PROTEIN; SAUR: SMALL AUXIN-UP RNA; ETT: ETTIN; MP: MONOPTEROS; NCED: 9-CIS-EPOXYCAROTENOID DIOXYGENASE; AO: ALDEHYDE OXIDASE; ABA'8H: ABSCISIC ACID HYDROXYLASE 8; ABI: ABSCISIC ACID INSENSITIVE; DHPA/PA: DIHYDROPHASEIC ACID/PHASEIC ACID; ABCG; PYR/PYL: PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL); RCAR: REGULATORY COMPONENTS OF ABA RECEPTOR; PP2C: PROTEIN PHOSPHATASE 2C; SnRK: SNF1-RELATED PROTEIN KINASE; DMAPP: DIMETHYLALLYL DIPHOSPHATE; IPT: ISOPENTENYL TRANSFERASE; LOG: LONELY GUY; ZOG: ZEATIN O-GLUCOSYLTRANSFERASE; CKX: CYTOKININ OXIDASE/DEHYDROGENASE; PUP: PURINE PERMEASE; AHK: ARABIDOPSIS HISTIDINE KINASE; AHP: ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN; A/B-RR: Type A/B RESPONSE REGULATOR; CYP707A: CYTOCHROME OXIDASE P450 TYPE A; DWF: DWARF; BRI: BRASSINOSTEROID INSENSITIVE1; BAK: BRI1-ASSOCIATED RECEPTOR KINASE; BIN: BRASSINOSTEROID-INSENSITIVE 2; BAS: BRASSINOSTEROID-DEFICIENT1; ICS: ISOCHORISMATE SYNTHASE; PHB: PROHIBITIN; NPR: NON-EXPRESSOR OF PATHOGENESIS-RELATED 1; AOS: ALLENE OXIDE SYNTHASE; OPR: OXOPHYTODIENOATE REDUCTASE; JAR: JASMONIC ACID-AMIDO SYNTHETASE; JAZ: JASMONATE ZIM-DOMAIN; LOX: LIPOOXYGENASE; CCD: CAROTENOID CLEAVAGE DIOXYGENASE; MAX: MORE AXILLARY GROWTH; LBO: LATERAL BRANCHING OXIDOREDUCTASE; D27/53: DWARF27/53; ACO: 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID OXIDASE; ACS: 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE; ERF: ETHYLENE RESPONSE FACTOR; ETR: ETHYLENE RECEPTOR; EIN: ETHYLENE INSENSITIVE; CTR1: CONSTITUTIVE TRIPLE RESPONSE 1; EIL: ETHYLENE INSENSITIVE3-LIKE; ERP: ETHYLENE RESPONSE PROTEIN.

    • Figure 4. 

      Epigenetic regulation of phytohormone genes during tuberization in potato. Four types of epigenetic mechanisms, such as: DNA methylation; histone modifications, especially H3K4me3, H3K27me3 modifications and targets of a histone methyltransferase StE(z)2; microRNA (miRNA); and phased short-interfering RNA (phasiRNA) mediated regulation, are reported in potato that could control the expression of numerous tuberization pathway genes. In this figure, the number of genes from various phytohormone pathways (biosynthesis, catabolism, transport and signalling) that are potentially regulated by these epigenetic mechanisms. are summarized The number of genes represented are from various reports e.g. DNA methylation[50], histone modifications[3,52,53], microRNAs[57,58,66], and siRNAs[3,11,57], and their details are provided in Supplementary Table S2.

    • Figure 5. 

      Heat maps showing differentially expressed phytohormone-related genes during different stages of storage root formation in sweetpotato. (a) Differentially expressed abscisic acid and gibberellic acid related genes. (b) Auxin and cytokinin genes differentially expressed during storage root development. (c) Differentially expressed genes related to brassinosteroid, ethylene, jasmonic acid, salicylic acid, and strigolactone. The expression of genes from various root developmental tissue types, such as F-fibrous root with diameter 1 mm; D1-initiating storage root with diameter 1 cm; D3-storage root with diameter 3 cm; D5-storage root with diameter 5 cm, D10-storage root with diameter 10 cm. The scale bar represents normalized read counts (log2 values). The gene expression values are retrieved from Dong et al.[74] and also provided in Supplementary Table S3. TBtool[102] was used to prepare heat maps. Abbreviations: ABA8'H: ABSCISIC ACID HYDROXYLASE 8; ABI: ABSCISIC ACID INSENSITIVE; ACS: 1-AMINOCYCLOPROPANE-1-CARBOXYLATEOXIDASE, AP2-LIKE: APETALA2-LIKE; APRR: TWO-COMPONENT RESPONSE REGULATOR-LIKE APRR; ARF: AUXIN RESPONSE FACTOR; BBM: BABY BOOM; BIG: AUXIN TRANSPORT PROTEIN BIG; BAK: BRASSINOSTEROID INSENSITIVE RECEPTOR KINASE; CCD: CAROTENOID CLEAVAGE DIOXYGENASE; CKH: CYTOKININ HYDROXYLASE; CKX: CYTOKININ OXIDASE/DEHYDROGENASE; CRF: CYTOKININ RESPONSE FACTOR; CYP84A1: CYTOCHROME P450 CYP85A1; EIN: ETHYLENE INSENSITIVE LIKE; EOL: ETHYLENE-OVERPRODUCTION PROTEIN; ERF: ETHYLENE RESPONSIVE FACTOR; ETR: ETHYLENE RECEPTOR; GAMYB: GA-RESPONSIVE MYB TRANSCRIPTION FACTOR; GA2ox: GIBBERELLIN 2 OXIDASE; GA3ox: GIBBERELLIN 3-β-DIOXYGENASE; GPPS: GERANYL PYROPHOSPHATE SYNTHASE; GRP10_LIKE: GIBBERELLIN REGULATED PROTEIN 10-LIKE; IAA: INDOLE-3-ACETIC ACID INDUCIBLE PROTEIN; IAAO: INDOLE-3-ACETALDEHYDE OXIDASE-LIKE; Ib: Ipomoea batatas; IPT: ISOPENTENYL TRANSFERASE; IRL: IAA-AMINO ACID HYDROLASE; JMT: JASMONATE O-METHYLTRANSFERASE; LAX: LIKE-AUX1; LOG: LONELY GUY; NCED: 9-CIS-EPOXYCAROTENOID DIOXYGENASE; PCNT115: AUXIN-INDUCED PROTEIN PCNT115; PIN: PIN-FORMED; PP2C: PROTEIN PHOSPHATASE 2C; PYL: PYRABACTIN RESISTANCE ABA RECEPTOR; RGL: RGA-LIKE; RAP: RELATED TO APETALA; SA-binding protein: SALICYLIC ACID-BINDING PROTEIN; SAMT: SALICYLATE O-METHYLTRANSFERASE; SAUR: SMALL AUXIN-UP RNA; WAT1: WALLS ARE THIN1; WRI: WRINKLED; ZEP: ZEAXANTHIN EPOXIDASE; ZIM: ZINC-FINGER EXPRESSED IN INFLORESCENCE MERISTEM; ZOG: ZEATIN O-GLUCOSYLTRANSFERASE.

    • Figure 6. 

      Differentially expressed miRNAs targeting phytohormone-related genes during storage root developmental stages of sweetpotato. (a) Heat map showing differently expressed miRNAs in storage root developmental tissue types, such as F-fibrous root with diameter 1 mm; D1-initiating storage root with diameter 1 cm; D3-storage root with diameter 3 cm; D5-storage root with diameter 5 cm, D10-storage root with diameter 10 cm. The scale bar represents normalized read counts (log2 values). The expression values of miRNAs are retrieved from the study by Tang et al.[75]. (b) Depiction of selective differently expressed miRNAs targeting phytohormone-related genes. Target prediction analysis was performed using psRNAtarget analysis tool[103], with cleavage efficiency (E) value < 3.0 and sweetpotato cDNA library (http://public-genomes-ngs.molgen.mpg.de/sweetpotato). Detailed information is available in Supplementary Table S4. Abbreviations: ABA8'H: ABSCISIC ACID HYDROXYLASE 8; AIL6: AINTEGUMENTA-LIKE PROTEIN 6; EIN2: ETHYLENE INSENSITIVE 2; AP2-LIKE: APETALA2-LIKE; APRR: TWO-COMPONENT RESPONSE REGULATOR-LIKE APRR; ARF: AUXIN RESPONSE FACTOR; CKX: CYTOKININ OXIDASE/DEHYDROGENASE; ERF: ETHYLENE RESPONSIVE FACTOR; GAMYB: GA-RESPONSIVE MYB TRANSCRIPTION FACTOR; GA2ox: GIBBERELLIN 2 OXIDASE; GRP10_LIKE: GIBBERELLIN REGULATED PROTEIN 10-LIKE; IAA: INDOLE-3-ACETIC ACID INDUCIBLE PROTEIN; IAAO: INDOLE-3-ACETALDEHYDE OXIDASE-LIKE; Iba: Ipomoea batatas; miR: MicroRNA; PCNT115: AUXIN-INDUCED PROTEIN PCNT115; PIN: PIN-FORMED; PP2C: PROTEIN PHOSPHATASE 2C; RAP: RELATED TO APETALA; WAT1: WALLS ARE THIN1; ZEP: ZEAXANTHIN EPOXIDASE.

    • Figure 7. 

      Model for phytohormones' role in tuber and storage root development. The overall phytohormones' role in (a) potato tuber developmental stages, and (b) sweetpotato storage root developmental stages are depicted. Thick line arrow ($\rightarrow $) indicate known positive effect on tuber or storage root development; dotted line arrow ($\dashrightarrow $) indicate proposed positive effect on tuber or storage root development, and symbol (?) indicate phytohormone-related genes not been characterized yet to assign their function.

    • Gene Function Mutant phenotype
      Potato StCYP707A1 ABA catabolism Overexpression and antisense potato lines showed reduced tuber yield[18].
      StABL1 ABA signalling Overexpression potato lines exhibited an early tuberization phenotype[19];
      AtABF4 Heterologous overexpression in potato positively regulated tuberization[17].
      iaaL Auxin biosynthesis
      		 Overexpression potato lines of Pseudomonas syringae iaaL showed an remarkable increase in tuber numbers; however, average tuber weight was reduced[104];
      StYUCCA-8 Constitutive overexpression displayed increased tuber numbers with reduction in tuber size[13];
      AtYUCCA6 AtYUCCA6 expressing potato lines exhibited lower tuber yield compared to untransformed control plants[105];
      tms1 Overexpression of Agrobacterium tms1 gene enhanced tuber productivity[106].
      StIAA2 Auxin signalling RNAi potato lines displayed no clear difference on stolon length and tuber weight[107].
      StBRI1 BR signalling RNAi potato lines exhibited a reduced tuber yield, whereas overexpression increased tuber yield[22,24];
      StBIN2 Overexpression potato lines exhibited an increase in tuber number and weight[23].
      IPT CK biosynthesis Transgenic potato lines with moderate IPT expression (under native promoter) influenced tuberization, whereas its expression under constitutive promoter prevented tuber formation[108].
      AtIPT and AtCKX CK metabolism AtIPT overexpression potato lines produced few and small tubers, whereas AtCKX overexpression potato lines exhibited small, drop-shaped tubers[14].
      StGA20ox1 GA biosynthesis Overexpression potato lines resulted in delayed tuber formation under short-day conditions[6];
      StGA3ox2 Overexpression potato lines showed delayed tuber formation, whereas RNAi lines produced tubers with smaller average tuber weight[8,9];
      StGA3ox3 Antisense potato lines displayed increased tuber numbers with the total tuber weights remaining unchanged[11].
      StGA2ox1 GA catabolism Overexpression potato lines exhibited an earliness for in vitro tuberization[7].
      AtGA20ox and AtGA2ox GA metabolism Overexpression of AtGA20ox and AtGA2ox in potato resulted in reduced total number of tubers and the overall tuber weight[14].
      StSN2 GA signalling Overexpression potato lines showed increased tuber numbers and size of the tubers[109].
      StCCD8 SL biosynthesis RNAi potato lines showed a reduction in stolon formation[26].
      StJAZ1-like JA signalling Overexpression potato lines attenuated tuber forming potential, leading to reduced stolon numbers and average tuber weights[29].
      Sweetpotato IbCYP714A1 GA catabolism Overexpression sweetpotato lines exhibited inhibition of storage root formation[88].
      IbYUCCA4 Auxin biosynthesis Overexpression sweetpotato lines showed reduced storage root yield[90];
      AtYUCCA6 Overexpression sweetpotato lines showed reduced storage root yield[89].
      IbARF11L Auxin signaling 'IbMYB52/IbARF11L-IbDRM1' module negatively regulates storage root development[91].
      * ABA8'H: ABSCISIC ACID HYDROXYLASE 8; ABF4: ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR; ABL1: ABSCISIC ACID INSENSITIVE 5-LIKE 1; ARF11L: AUXIN RESPONSE FACTOR 11-LIKE; At: ARABIDOPSIS THALIANA; BIN2: BRASSINOSTEROID INSENSITIVE 2; BRI1: BRASSINOSTEROID INSENSITIVE 1; CCD8: CAROTENOID CLEAVAGE DIOXYGENASE 8; CKX: CYTOKININ OXIDASE; CYP714A1: CYTOCHROME P450 encoding a GA deactivation enzyme; GA3ox2: GIBBERELLIN 3-OXIDASE 2; GA3ox3: GIBBERELLIN 3-OXIDASE 3; GA2ox1: GIBBERELLIN 2-OXIDASE 1; GA20ox1: GIBBERELLIN 20-OXIDASE 1; IAA2: INDOLE-3-ACETIC ACID INDUCIBLE 2; iaaL: bacterial auxin biosynthesis gene encoding INDOLEACETAMIDE HYDROLASE; Ib: Ipomoea batatas; IPT: ISOPENTENYL TRANSFERASE; JAZ1-LIKE: JASMONATE ZIM-DOMAIN PROTEIN 1-LIKE; SN2: SNAKIN/GASA family gene encoding SN2 PROTEIN; St: Solanum tuberosum; tms1: bacterial auxin biosynthesis gene encoding TRYPTOPHAN-2-MONOOXYGENASE.

      Table 1. 

      List of phytohormone related genes characterized for their role in tuber development in potato and storage root formation in sweetpotato. The associated phenotypes of gene expression modulation are also described.