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Advances in Horticultural Research Based on Multi-Omics and Computational Biology

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 14510

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Dr. Yunpeng Cao

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Guest Editor

CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: plant science; evolution; genomics

Prof. Dr. Jen-Tsung Chen

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Guest Editor

Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
Interests: bioactive compounds; chromatography techniques; medicinal plants; phytochemicals; plant biotechnology; plant growth regulators; plant secondary metabolites
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Dear Colleagues,

Horticultural plants play an important role for humans as a source of herbal medicines, beverages, vegetables, fruits, and ornamentals. High-throughput technologies have revolutionised the time scale and power of detecting physiological changes and thus achieving insights into the biological mechanisms functioning in plants. All manner of sequencing data and tools have helped us better understand the evolutionary histories of horticultural plants and provided genotype and phenotype resources for molecular studies on economically important traits. Integration of these omics technologies (e.g., genomics, transcriptomics, proteomics, metabolomics, lipidomics, ionomics, and redoxomics) currently lies at the forefront of plant research. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and polyploidy. Thus, novel computational methods must be developed to take advantage of state-of-the-art genomic technologies. As a result, the mining of multiomics data and the development of new computational biology approaches for the reliable and efficient analysis of plant traits is necessary. Multiomics and computational biology approaches allow understanding of the biochemical mechanisms involved in determining plant traits. The integration of multi-omics data and computational biology technologies allows construction of biological networks to identify traits that can be further applied towards horticultural crop breeding in developing more productive crop varieties.

This Research Topic aims to combine high-throughput omics and computational biology technologies in identifying coherently matching geno–pheno relationships or associations in horticultural crops research. We encourage manuscripts dedicated to improving our understanding of biological mechanisms, from the genotype to phenotype level.

Prof. Dr. Yunpeng Cao
Dr. Jen-Tsung Chen
Guest Editors

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Keywords

multi-omics analysis
bioinformatics
genomics
phenomics
regulation of gene expression
gene network
quantitative genetics

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Published Papers (4 papers)

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Research

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29 pages, 3962 KiB

Open AccessArticle

Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study

by Dejana Milić, Ana Pantelić, Bojana Banović Đeri, Jelena Samardžić and Marija Vidović

Int. J. Mol. Sci. 2023, 24(6), 5288; https://doi.org/10.3390/ijms24065288 - 9 Mar 2023

Cited by 4 | Viewed by 2854

Abstract

The photosynthetically active green leaf (GL) and non-active white leaf (WL) tissues of variegated Pelargonium zonale provide an excellent model system for studying processes associated with photosynthesis and sink-source interactions, enabling the same microenvironmental conditions. By combining differential transcriptomics and metabolomics, we identified the main differences between these two metabolically contrasting tissues. Genes related to photosynthesis and associated pigments, the Calvin–Benson cycle, fermentation, and glycolysis were strongly repressed in WL. On the other hand, genes related to nitrogen and protein metabolism, defence, cytoskeletal components (motor proteins), cell division, DNA replication, repair and recombination, chromatin remodelling, and histone modifications were upregulated in WL. A content of soluble sugars, TCA intermediates, ascorbate, and hydroxybenzoic acids was lower, while the concentration of free amino acids (AAs), hydroxycinnamic acids, and several quercetin and kaempferol glycosides was higher in WL than in GL. Therefore, WL presents a carbon sink and depends on photosynthetic and energy-generating processes in GL. Furthermore, the upregulated nitrogen metabolism in WL compensates for the insufficient energy from carbon metabolism by providing alternative respiratory substrates. At the same time, WL serves as nitrogen storage. Overall, our study provides a new genetic data resource for the use of this excellent model system and for ornamental pelargonium breeding and contributes to uncovering molecular mechanisms underlying variegation and its adaptive ecological value. Full article

(This article belongs to the Special Issue Advances in Horticultural Research Based on Multi-Omics and Computational Biology)

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15 pages, 3809 KiB

Open AccessArticle

PollenDetect: An Open-Source Pollen Viability Status Recognition System Based on Deep Learning Neural Networks

by Zhihao Tan, Jing Yang, Qingyuan Li, Fengxiang Su, Tianxu Yang, Weiran Wang, Alifu Aierxi, Xianlong Zhang, Wanneng Yang, Jie Kong and Ling Min

Int. J. Mol. Sci. 2022, 23(21), 13469; https://doi.org/10.3390/ijms232113469 - 3 Nov 2022

Cited by 5 | Viewed by 4590

Abstract

Pollen grains, the male gametophytes for reproduction in higher plants, are vulnerable to various stresses that lead to loss of viability and eventually crop yield. A conventional method for assessing pollen viability is manual counting after staining, which is laborious and hinders high-throughput screening. We developed an automatic detection tool (PollenDetect) to distinguish viable and nonviable pollen based on the YOLOv5 neural network, which is adjusted to adapt to the small target detection task. Compared with manual work, PollenDetect significantly reduced detection time (from approximately 3 min to 1 s for each image). Meanwhile, PollenDetect can maintain high detection accuracy. When PollenDetect was tested on cotton pollen viability, 99% accuracy was achieved. Furthermore, the results obtained using PollenDetect show that high temperature weakened cotton pollen viability, which is highly similar to the pollen viability results obtained using 2,3,5-triphenyltetrazolium formazan quantification. PollenDetect is an open-source software that can be further trained to count different types of pollen for research purposes. Thus, PollenDetect is a rapid and accurate system for recognizing pollen viability status, and is important for screening stress-resistant crop varieties for the identification of pollen viability and stress resistance genes during genetic breeding research. Full article

(This article belongs to the Special Issue Advances in Horticultural Research Based on Multi-Omics and Computational Biology)

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16 pages, 27285 KiB

Open AccessArticle

PbUGT72AJ2-Mediated Glycosylation Plays an Important Role in Lignin Formation and Stone Cell Development in Pears (Pyrus bretschneideri)

by Han Wang, Xiaofeng Feng, Yingjie Zhang, Dongyi Wei, Yang Zhang, Qing Jin and Yongping Cai

Int. J. Mol. Sci. 2022, 23(14), 7893; https://doi.org/10.3390/ijms23147893 - 18 Jul 2022

Cited by 7 | Viewed by 2140

Abstract

Glycosylation is necessary for many processes of plant secondary metabolism. It can maintain plant homeostasis and is of great significance to normal plant growth and development. At present, the significance of glycosylation for lignin biosynthesis has been proven in some plants, but it has not yet been reported in pears. We used in situ hybridization, in vitro expression, substrate catalysis, transgenic Arabidopsisthaliana, and transient transformation of pear fruit in our investigation, which was predicated on the identification of a gene PbUGT72AJ2 that may be involved in lignin monolignol glycosylation according to our previous work. These results revealed that PbUGT72AJ2 transcripts were localized to some pulp cell walls, lignin deposition, and stone cell areas of pear fruit. The recombinant PbUGT72AJ2-pGEX4T-1 protein had activity against coniferyl alcohol and sinapyl alcohol, and its catalytic efficiency against coniferyl alcohol was higher than that against sinapyl alcohol. When PbUGT72AJ2 was transferred into Arabidopsisthaliana mutants, it was found that some characteristics of Arabidopsisthalianaugt72e3 mutants were restored. In Arabidopsisthaliana, overexpression of PbUGT72AJ2 enhanced the contents of coniferin and syringin, whereas lignification did not change significantly. Transient transformation of pear fruit showed that when PbUGT72AJ2 in pear fruit was silenced by RNA interference, the content of lignin and stone cells in pear fruit increased, whereas the gene PbUGT72AJ2 was overexpressed in pear fruit, and there was almost no change in the pear fruit compared with the control. Lignin deposition in pear fruit was closely related to stone cell development. In this study, we proved that PbUGT72AJ2 plays an important role in lignin deposition and stone cell development in pear fruit, which provides a molecular biological basis for improving pear fruit quality at the molecular level. Full article

(This article belongs to the Special Issue Advances in Horticultural Research Based on Multi-Omics and Computational Biology)

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Review

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15 pages, 1600 KiB

Open AccessReview

Universal Stress Proteins: From Gene to Function

by Dan Luo, Zilin Wu, Qian Bai, Yong Zhang, Min Huang, Yajiao Huang and Xiangyang Li

Int. J. Mol. Sci. 2023, 24(5), 4725; https://doi.org/10.3390/ijms24054725 - 1 Mar 2023

Cited by 12 | Viewed by 3213

Abstract

Universal stress proteins (USPs) exist across a wide range of species and are vital for survival under stressful conditions. Due to the increasingly harsh global environmental conditions, it is increasingly important to study the role of USPs in achieving stress tolerance. This review discusses the role of USPs in organisms from three aspects: (1) organisms generally have multiple USP genes that play specific roles at different developmental periods of the organism, and, due to their ubiquity, USPs can be used as an important indicator to study species evolution; (2) a comparison of the structures of USPs reveals that they generally bind ATP or its analogs at similar sequence positions, which may underlie the regulatory role of USPs; and (3) the functions of USPs in species are diverse, and are generally directly related to the stress tolerance. In microorganisms, USPs are associated with cell membrane formation, whereas in plants they may act as protein chaperones or RNA chaperones to help plants withstand stress at the molecular level and may also interact with other proteins to regulate normal plant activities. This review will provide directions for future research, focusing on USPs to provide clues for the development of stress-tolerant crop varieties and for the generation of novel green pesticide formulations in agriculture, and to better understand the evolution of drug resistance in pathogenic microorganisms in medicine. Full article

(This article belongs to the Special Issue Advances in Horticultural Research Based on Multi-Omics and Computational Biology)

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