Molecular Characterization and Target Prediction of Candidate miRNAs Related to Abiotic Stress Responses and/or Storage Root Development in Sweet Potato

Sweet potato is a tuberous root crop with strong environmental stress resistance. It is beneficial to study its storage root formation and stress responses to identify sweet potato stress- and storage-root-thickening-related regulators. Here, six conserved miRNAs (miR156g, miR157d, miR158a-3p, miR161.1, miR167d and miR397a) and six novel miRNAs (novel 104, novel 120, novel 140, novel 214, novel 359 and novel 522) were isolated and characterized in sweet potato. Tissue-specific expression patterns suggested that miR156g, miR157d, miR158a-3p, miR167d, novel 359 and novel 522 exhibited high expression in fibrous roots or storage roots and were all upregulated in response to storage-root-related hormones (indole acetic acid, IAA; zeaxanthin, ZT; abscisic acid, ABA; and gibberellin, GAs). The expression of miR156g, miR158a-3p, miR167d, novel 120 and novel 214 was induced or reduced dramatically by salt, dehydration and cold or heat stresses. Moreover, these miRNAs were all upregulated by ABA, a crucial hormone modulator in regulating abiotic stresses. Additionally, the potential targets of the twelve miRNAs were predicted and analyzed. Above all, these results indicated that these miRNAs might play roles in storage root development and/or stress responses in sweet potato as well as provided valuable information for the further investigation of the roles of miRNA in storage root development and stress responses.

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Comparative analysis of the SPL genes among four Ipomoea species and the evidence for a role of some IbSPLs in storage root development in sweet potato (Ipomoea batatas)

10.21203/rs.3.rs-654042/v1 ◽

2021 ◽

Author(s):

Haoyun Sun ◽

Jingzhao Mei ◽

Wenqian Hou ◽

Yang Zhang ◽

Tao Xu ◽

...

Keyword(s):

Root Development ◽

Ipomoea Batatas ◽

Target Genes ◽

Functional Divergence ◽

Expression Patterns ◽

Evolutionary Analysis ◽

Storage Root ◽

Storage Roots ◽

Spl Genes ◽

Storage Root Development

Abstract Background As a major family of plant-specific transcription factors, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes play crucial regulatory roles in plant growth, development, and stress tolerance. SPL transcription factor family has been widely studied in various plant species, however, there are no systematic studies on SPL genes in genus Ipomoea. Results In this study, a total of 29, 27, 26, 23 SPL genes were identified in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Phylogenetic analysis indicated that Ipomoea SPL genes could be clustered into eight clades. SPL members within the same clade showed similar gene structures, domain organizations, and cis-acting element compositions, suggesting similarity of biological function potentially. Evolutionary analysis revealed that segmental duplication events played a major role in the Ipomoea genus-specific expansion of SPL genes. Of these Ipomoea SPL genes, 69 were predicted as the target genes of miR156, and 7 IbSPL genes were further confirmed by degradome data. Additionally, IbSPL genes showed diverse expression patterns in various tissues, implying their functional conservation and divergence. Finally, by combining the information from expression patterns and regulatory sub-networks, we found that four IbSPL genes (IbSPL16/IbSPL17/IbSPL21/IbSPL28) may be involved in the formation and development of storage roots. Conclusions This study not only provides novel insights into the evolutionary and functional divergence of the SPL genes in all available sequenced species in genus Ipomoea, but also lays a foundation for further elucidation of the potential functional roles of IbSPL genes during storage root development.

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A low-cost aeroponic phenotyping system for storage root development: unravelling the below-ground secrets of cassava (Manihot esculenta)

Plant Methods ◽

10.1186/s13007-019-0517-6 ◽

2019 ◽

Vol 15 (1) ◽

Cited By ~ 4

Author(s):

Michael Gomez Selvaraj ◽

Maria Elker Montoya-P ◽

John Atanbori ◽

Andrew P. French ◽

Tony Pridmore

Keyword(s):

Root Growth ◽

Root Development ◽

Low Cost ◽

Root Traits ◽

Suitable Model ◽

Root Initiation ◽

Storage Root ◽

Economic Traits ◽

Storage Roots ◽

Storage Root Development

Abstract Background Root and tuber crops are becoming more important for their high source of carbohydrates, next to cereals. Despite their commercial impact, there are significant knowledge gaps about the environmental and inherent regulation of storage root (SR) differentiation, due in part to the innate problems of studying storage roots and the lack of a suitable model system for monitoring storage root growth. The research presented here aimed to develop a reliable, low-cost effective system that enables the study of the factors influencing cassava storage root initiation and development. Results We explored simple, low-cost systems for the study of storage root biology. An aeroponics system described here is ideal for real-time monitoring of storage root development (SRD), and this was further validated using hormone studies. Our aeroponics-based auxin studies revealed that storage root initiation and development are adaptive responses, which are significantly enhanced by the exogenous auxin supply. Field and histological experiments were also conducted to confirm the auxin effect found in the aeroponics system. We also developed a simple digital imaging platform to quantify storage root growth and development traits. Correlation analysis confirmed that image-based estimation can be a surrogate for manual root phenotyping for several key traits. Conclusions The aeroponic system developed from this study is an effective tool for examining the root architecture of cassava during early SRD. The aeroponic system also provided novel insights into storage root formation by activating the auxin-dependent proliferation of secondary xylem parenchyma cells to induce the initial root thickening and bulking. The developed system can be of direct benefit to molecular biologists, breeders, and physiologists, allowing them to screen germplasm for root traits that correlate with improved economic traits.

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Sweetpotato root development influences susceptibility to black rot caused by the fungal pathogen Ceratocystis fimbriata

Phytopathology ◽

10.1094/phyto-12-20-0541-r ◽

2021 ◽

Author(s):

Camilo Humberto Parada Rojas ◽

Kenneth Pecota ◽

Christie Almeyda ◽

G. Craig Yencho ◽

Lina Quesada-Ocampo

Keyword(s):

Root Development ◽

Disease Incidence ◽

Black Rot ◽

Wild Relative ◽

Storage Root ◽

Storage Roots ◽

Ceratocystis Fimbriata ◽

Breeding Lines ◽

Below Ground ◽

Storage Root Development

Black rot of sweetpotato caused by Ceratocystis fimbriata, is an important reemerging disease threatening sweetpotato production in the United States. This study assessed disease susceptibility of the storage root surface, storage root cambium, and slips (vine cuttings) of 48 sweetpotato cultivars, advanced breeding lines, and wild relative accessions. We also characterized the effect of storage root development on susceptibility to C. fimbriata. None of the cultivars examined at the storage root level were resistant, with most cultivars exhibiting similar levels of susceptibility. In storage roots, Jewel and Covington were the least susceptible and significantly different from White Bonita, the most susceptible cultivar. In the slip, significant differences in disease incidence were observed for above and below ground plant structures among cultivars, advanced breeding lines, and wild relative accessions. Burgundy and Ipomoea littoralis displayed less below ground disease incidence as compared to NASPOT 8, Sunnyside and LSU-417, the most susceptible cultivars. Correlation of black rot susceptibility between storage roots and slips was not significant, suggesting that slip assays are not useful to predict resistance in storage roots. Immature, early developing storage roots were comparatively more susceptible than older, fully developed storage roots. The high significant correlation between storage root cross-section area and cross-sectional lesion ratio suggests the presence of an unfavorable environment for C. fimbriata as the storage root develops. Incorporating applications of effective fungicides at transplanting and during early storage root development when sweetpotato tissues are most susceptible to black rot infection may improve disease management efforts.

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Altered Phenylpropanoid Metabolism in the Maize Lc-Expressed Sweet Potato (Ipomoea batatas) Affects Storage Root Development

Scientific Reports ◽

10.1038/srep18645 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 18

Author(s):

Hongxia Wang ◽

Jun Yang ◽

Min Zhang ◽

Weijuan Fan ◽

Nurit Firon ◽

...

Keyword(s):

Sweet Potato ◽

Root Development ◽

Ipomoea Batatas ◽

Phenylpropanoid Metabolism ◽

Storage Root ◽

Storage Root Development

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Characterization of Adventitious Root Development in Sweetpotato

HortScience ◽

10.21273/hortsci.44.3.651 ◽

2009 ◽

Vol 44 (3) ◽

pp. 651-655 ◽

Cited By ~ 30

Author(s):

Arthur Q. Villordon ◽

Don R. La Bonte ◽

Nurit Firon ◽

Yanir Kfir ◽

Etan Pressman ◽

...

Keyword(s):

Root Development ◽

Adventitious Root ◽

Adventitious Roots ◽

Vascular Cambium ◽

Storage Root ◽

Storage Roots ◽

Adventitious Root Development ◽

Xylem Elements ◽

Storage Root Development

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.

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Comparative Transcriptome Analysis of Storage Root Reveals Regulatory Mechanisms of Lignin Biosynthesis During Root Development in Two Sweetpotato Cultivars

10.21203/rs.3.rs-850254/v1 ◽

2021 ◽

Author(s):

Fuyun Hou ◽

Zhen Qin ◽

Taifeng Du ◽

Yuanyuan Zhou ◽

Aixian Li ◽

...

Keyword(s):

Root Development ◽

Ipomoea Batatas ◽

Molecular Mechanisms ◽

Signal Transduction Pathway ◽

Lignin Biosynthesis ◽

Storage Root ◽

Storage Roots ◽

Homologous Genes ◽

Phenylpropanoid Biosynthesis ◽

Storage Root Development

Abstract BackgroundSweetpotato(Ipomoea batatas (L.) Lam.) is one of the most important crops with high storage roots yield. Lignin affects the storage root formation. However, the molecular mechanisms of lignin biosynthesis in storage roots development have been lacking.ResultsTo reveal the molecular mechanism of lignin biosynthesis and identify new homologous genes in lignin biosynthesis during storage root development, the storage root (SR) at three different stages (D1, D2 and D3) in the two cultivars (Jishu25 and Jishu29) was investigated with full-length and second-generation transcriptome. A total of 52,137 transcripts and 21,148 unigenes were obtained after corrected with Hiseq2500 sequencing. Through the comparative analysis, 9577 unigenes were found to be differently expressed in the different stage in two cultivars. Among of them, 91 unigenes enriched in the phenylpropanoid biosynthesis, and 201 unigenes in hormone signal transduction pathway with KEGG analysis. Weighted gene co-expression network analysis of differentially expressed unigenes showed that lignin biosynthesis genes might be co-expressed with transcription factors such as AP2/ERF and MYB at the transcription level, and regulated by phytohormones auxin and GA3.ConclusionsTaken together, our findings will throw light on molecular regulatory mechanism of lignin biosynthesis involved in storage root development.

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Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

BMC Genomics ◽

10.1186/s12864-019-6316-7 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Yao Chen ◽

Panpan Zhu ◽

Shaoyuan Wu ◽

Yan Lu ◽

Jian Sun ◽

...

Keyword(s):

Sweet Potato ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Raw Material ◽

Functional Study ◽

Ipomoea Trifida ◽

Specific Expression ◽

Adverse Environmental Condition ◽

In The Wild

Abstract Background GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown. Results In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses. Conclusions Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

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