Genetics, Molecular Breeding, and Biotechnology for Tuber Crop Improvement

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 16005

Special Issue Editors


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Guest Editor
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Interests: potato; abiotic stress; high temperature; drought stress; salt stress; tuberization process; plant biotechnology (RNAi, gene editing, transgenic); gene family evolution
Special Issues, Collections and Topics in MDPI journals
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Interests: potato; sweet potato; molecular breeding; genetic analysis; GWAS; germplasm resourse; biotic and abotic stress resistance
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun Nandajie, Beijing 100081, China
Interests: potato breeding and genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Tuber crops include potatoes, sweet potatoes, yams, ginger, and others. Their yield potential, production, and quality are the potential objectives for breeders worldwide. However, tuber crop production still faces numerous challenges, including the impacts of biological and abiological factors in addition to the demand for improved yield and nutritional quality. At present, molecular genetics and breeding mainly include biotechnologies such as QTL, GWAS, map-based cloning, omics analysis, and gene or genome editing, which have been widely studied and achieved significant progress in model plants. Therefore, we are developing this Special Issue, which will provide a forum with which to address these problems and present new progress in tuber crop research.

Dr. Hongju Jian
Dr. Kai Zhang
Prof. Dr. Jianfei Xu
Guest Editors

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Keywords

  • potato
  • tuberization process
  • molecular mechanism
  • abiotic stress
  • functional analysis
  • development process
  • sweet potato
  • yam
  • ginger

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Published Papers (8 papers)

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Research

20 pages, 4795 KiB  
Article
Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE (FRS) Family Members in Potato (Solanum tuberosum)
by Qingshuai Chen, Yang Song, Kui Liu, Chen Su, Ru Yu, Ying Li, Yi Yang, Bailing Zhou, Jihua Wang and Guodong Hu
Plants 2023, 12(13), 2575; https://doi.org/10.3390/plants12132575 - 7 Jul 2023
Cited by 3 | Viewed by 1442
Abstract
FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly [...] Read more.
FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar “Xisen 6”, which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance. Full article
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20 pages, 7281 KiB  
Article
Integrated Characterization of Cassava (Manihot esculenta) Pectin Methylesterase (MePME) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses
by Shijia Wang, Ruimei Li, Yangjiao Zhou, Alisdair R. Fernie, Zhongping Ding, Qin Zhou, Yannian Che, Yuan Yao, Jiao Liu, Yajie Wang, Xinwen Hu and Jianchun Guo
Plants 2023, 12(13), 2529; https://doi.org/10.3390/plants12132529 - 3 Jul 2023
Cited by 2 | Viewed by 1233
Abstract
Plant pectin methylesterases (PMEs) play crucial roles in regulating cell wall modification and response to various stresses. Members of the PME family have been found in several crops, but there is a lack of research into their presence in cassava (Manihot esculent [...] Read more.
Plant pectin methylesterases (PMEs) play crucial roles in regulating cell wall modification and response to various stresses. Members of the PME family have been found in several crops, but there is a lack of research into their presence in cassava (Manihot esculent), which is an important crop for world food security. In this research, 89 MePME genes were identified in cassava that were separated into two types (type-Ⅰ and type-Ⅱ) according to the existence or absence of a pro-region (PMEI domain). The MePME gene members were unevenly located on 17 chromosomes, with 19 gene pairs being identified that most likely arose via duplication events. The MePMEs could be divided into ten sub-groups in type-Ⅰ and five sub-groups in type-Ⅱ. The motif analysis revealed 11 conserved motifs in type-Ⅰ and 8 in type-Ⅱ MePMEs. The number of introns in the CDS region of type-Ⅰ MePMEs ranged between one and two, and the number of introns in type-Ⅱ MePMEs ranged between one and nine. There were 21 type-Ⅰ and 31 type-Ⅱ MePMEs that contained signal peptides. Most of the type-Ⅰ MePMEs had two conserved “RK/RLL” and one “FPSWVS” domain between the pro-region and the PME domain. Multiple stress-, hormone- and tissue-specific-related cis-acting regulatory elements were identified in the promoter regions of MePME genes. A total of five co-expressed genes (MePME1, MePME2, MePME27, MePME65 and MePME82) were filtered from different abiotic stresses via the use of UpSet Venn diagrams. The gene expression pattern analysis revealed that the expression of MePME1 was positively correlated with the degree of cassava postharvest physiological deterioration (PPD). The expression of this gene was also significantly upregulated by 7% PEG and 14 °C low-temperature stress, but slightly downregulated by ABA treatment. The tissue-specific expression analysis revealed that MePME1 and MePME65 generally displayed higher expression levels in most tissues than the other co-expressed genes. In this study, we obtain an in-depth understanding of the cassava PME gene family, suggesting that MePME1 could be a candidate gene associated with multiple abiotic tolerance. Full article
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16 pages, 2072 KiB  
Article
Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato
by Hongju Jian, Shiqi Wen, Rongrong Liu, Wenzhe Zhang, Ziyan Li, Weixi Chen, Yonghong Zhou, Vadim Khassanov, Ahmed M. A. Mahmoud, Jichun Wang and Dianqiu Lyu
Plants 2023, 12(12), 2232; https://doi.org/10.3390/plants12122232 - 6 Jun 2023
Cited by 1 | Viewed by 3332
Abstract
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato’s response to [...] Read more.
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato’s response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress. Full article
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21 pages, 12509 KiB  
Article
Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes
by Maoxing Li, Yuanping Zhou, Kaifeng Li and Huachun Guo
Plants 2023, 12(8), 1731; https://doi.org/10.3390/plants12081731 - 21 Apr 2023
Cited by 1 | Viewed by 1744
Abstract
Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few [...] Read more.
Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species. Full article
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15 pages, 11170 KiB  
Article
Analysis of Potato Physiological and Molecular Adaptation in Response to Different Water and Nitrogen Combined Regimes
by Wenyuan Yan, Junhong Qin, Yinqiao Jian, Jiangang Liu, Chunsong Bian, Liping Jin and Guangcun Li
Plants 2023, 12(8), 1671; https://doi.org/10.3390/plants12081671 - 17 Apr 2023
Cited by 1 | Viewed by 1644
Abstract
Water and nitrogen are essential for potato growth and development. We aim to understand how potato adapts to changes in soil water and nitrogen content. Potato plant adaptations to changes in soil moisture and nitrogen levels were analyzed at the physiological and transcriptomic [...] Read more.
Water and nitrogen are essential for potato growth and development. We aim to understand how potato adapts to changes in soil water and nitrogen content. Potato plant adaptations to changes in soil moisture and nitrogen levels were analyzed at the physiological and transcriptomic levels in four treatment groups: adequate nitrogen under drought, adequate nitrogen under sufficient irrigation, limited nitrogen under drought, and limited nitrogen under sufficient irrigation. Many light-capture pigment complex genes and oxygen release complex genes were differentially expressed in leaves when nitrogen levels were increased under drought conditions, and several genes encoding rate-limiting enzymes in the Calvin–Benson–Bassham cycle were up-regulated; furthermore, leaf stomatal conductance decreased, whereas the saturated vapor pressure difference and relative chlorophyll content in the chloroplasts increased. StSP6A, a key gene in potato tuber formation, was down-regulated in response to increased nitrogen application, and the stolon growth time was prolonged. Genes related to root nitrogen metabolism were highly expressed, and protein content in the tuber increased. Weighted gene co-expression network analysis (WGCNA) revealed 32 gene expression modules that responded to changes in water and nitrogen levels. A total of 34 key candidate genes were identified, and a preliminary molecular model of potato responses to alterations in soil water and nitrogen content was constructed. Full article
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15 pages, 316 KiB  
Article
Evaluation of Yield and Nutraceutical Traits of Orange-Fleshed Sweet Potato Storage Roots in Two Agro-Climatic Zones of Northern Ethiopia
by Gloria Peace Lamaro, Yemane Tsehaye, Atkilt Girma, Andrea Vannini, Riccardo Fedeli and Stefano Loppi
Plants 2023, 12(6), 1319; https://doi.org/10.3390/plants12061319 - 14 Mar 2023
Cited by 5 | Viewed by 1741
Abstract
This study evaluated the genotype by environment interactions in the yield and nutraceutical traits of the orange-fleshed sweet potato (OFSP) storage root in different agro-climatic zones of northern Ethiopia. Five OFSP genotypes were cultivated at three different locations following a randomized complete block [...] Read more.
This study evaluated the genotype by environment interactions in the yield and nutraceutical traits of the orange-fleshed sweet potato (OFSP) storage root in different agro-climatic zones of northern Ethiopia. Five OFSP genotypes were cultivated at three different locations following a randomized complete block design, and the yield, dry matter, beta-carotene, flavonoids, polyphenols, soluble sugars, starch, soluble proteins, and free radical scavenging activity were measured in the storage root. The results showed consistent variations in the nutritional traits of the OFSP storage root depending on both the genotype and the location, as well as on their interaction. Ininda, Gloria, and Amelia were the genotypes that provided the higher yield and dry matter, as well as the higher content of starch and beta-carotene; they also showed a high antioxidant power. These findings suggest that the studied genotypes have the potential to alleviate vitamin A deficiency. This study demonstrated a high possibility of sweet potato production for storage root yield in arid agro-climate regions with limited production inputs. Moreover, the results suggest that it is possible to enhance the yield, dry matter content, beta-carotene, starch, and polyphenols of the OFSP storage root through genotype selection. Full article
15 pages, 1680 KiB  
Article
Application of Grafting Method in Resistance Identification of Sweet Potato Virus Disease and Resistance Evaluation of Elite Sweet Potato [Ipomoea batatas (L.) Lam] Varieties
by Hong Huang, Haohao Han, Yayun Lei, Huanhuan Qiao, Daobin Tang, Yonghui Han, Zhenpeng Deng, Limin Mao, Xuli Wu, Kai Zhang, Jichun Wang and Changwen Lv
Plants 2023, 12(4), 957; https://doi.org/10.3390/plants12040957 - 20 Feb 2023
Cited by 3 | Viewed by 1927
Abstract
Sweet potato virus disease (SPVD) is one of the main virus diseases in sweet potato [Ipomoea batatas (L.) Lam] that seriously affects the yield of sweet potato. Therefore, the establishment of a simple, rapid and effective method to detect SPVD is of [...] Read more.
Sweet potato virus disease (SPVD) is one of the main virus diseases in sweet potato [Ipomoea batatas (L.) Lam] that seriously affects the yield of sweet potato. Therefore, the establishment of a simple, rapid and effective method to detect SPVD is of great significance for the early warning and prevention of this disease. In this study, the experiment was carried out in two years to compare the grafting method and side grafting method for three sweet potato varieties, and the optimal grafting method was selected. After grafting with seedlings infected with SPVD, the symptomatic diagnosis and serological detection were performed in 86 host varieties, and the differences in SPVD resistance were determined by fluorescence quantitative PCR (qRT-PCR) and nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). The results showed that the survival rate of grafting by insertion method was significantly higher than that by side grafting method, and the disease resistance of different varieties to sweet potato virus disease was tested. The detection method established in this study can provide theoretical basis for identification and screening of resistant sweet potato varieties. Full article
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20 pages, 4173 KiB  
Article
Responses of Aerial and Belowground Parts of Different Potato (Solanum tuberosum L.) Cultivars to Heat Stress
by Jinhua Zhou, Kaifeng Li, Youhan Li, Maoxing Li and Huachun Guo
Plants 2023, 12(4), 818; https://doi.org/10.3390/plants12040818 - 12 Feb 2023
Viewed by 1644
Abstract
The mechanism of potato (Solanum tuberosum L.) thermotolerance has been the focus of intensive research for many years because plant growth and tuber yield are highly sensitive to heat stress. However, the linkage between the aerial and belowground parts of potato plants [...] Read more.
The mechanism of potato (Solanum tuberosum L.) thermotolerance has been the focus of intensive research for many years because plant growth and tuber yield are highly sensitive to heat stress. However, the linkage between the aerial and belowground parts of potato plants in response to high temperatures is not clear. To disentangle this issue, the aerial and belowground parts of the heat-resistant cultivar Dian187 (D187) and the heat-sensitive cultivar Qingshu 9 (Qs9) were independently exposed to high-temperature (30 °C) conditions using a special incubator. The results indicated that when the belowground plant parts were maintained at a normal temperature, the growth of the aerial plant parts was maintained even when independently exposed to heat stress. In contrast, the treatment that independently exposed the belowground plant parts to heat stress promoted premature senescence in the plant’s leaves, even when the aerial plant parts were maintained at a normal temperature. When the aerial part of the plant was independently treated with heat stress, tuberization belowground was not delayed, and tuberization suppression was not as severe as when the belowground plant parts independently underwent heat stress. Heat stress on the belowground plant parts alone had virtually no damaging effects on the leaf photosynthetic system but caused distinct tuber deformation, secondary growth, and the loss of tuber skin colour. Transcriptome analysis revealed that the treatment of the belowground plant parts at 30 °C induced 3361 differentially expressed genes in the Qs9 cultivar’s expanding tubers, while the D187 cultivar had only 10,148 differentially expressed genes. Conversely, when only the aerial plant parts were treated at 30 °C, there were just 807 DEGs (differentially expressed genes) in the D187 cultivar’s expanding tubers compared with 6563 DEGs in the Qs9 cultivar, indicating that the two cultivars with different heat sensitivities have distinct regulatory mechanisms of tuberization when exposed to heat stress. The information provided in this study may be useful for further exploring the genes associated with high-temperature resistance in potato cultivars. Full article
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