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Crop Omics
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Crop Omics

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (25 June 2022) | Viewed by 14262

Special Issue Editor

Prof. Dr. Chuyu Ye

E-Mail Website
Guest Editor
Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
Interests: crop genomics

Special Issue Information

Dear Colleagues,

Since the publication of the genomic sequence of Arabidopsis in 2000 and rice in 2002, reference genomes have been generated for hundreds of plant species, including major food and oil crops, horticultural and forestry plants, orphan crops, etc. Correspondingly, considerable progress has been achieved in crop omics research, including genomics, transcriptomics, proteomics, and metabolomics, as well as databases and bioinformatics methods and tools. During the last two decades, omics approaches have revolutionized how crop scientists understand crop evolution, explore mechanisms underlying the formation of agricultural traits, and accelerate crop breeding. Technological breakthroughs in sequencing have emerged, which include third-generation genome sequencing, single-cell sequencing, 3D genome sequencing, etc. Crop omics studies have stepped into the big-data era and will play an increasingly important role in future crop research. This Special Issue will cover a wide variety of omics areas in crops, aiming to contribute to the overall knowledge of crop evolution, gene discovery, and crop breeding with the help of omics research.

Dr. Chuyu Ye
Guest Editor

Manuscript Submission Information

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Keywords

  • Crop omics
  • Genomics
  • Transcriptomics
  • Bioinformatics
  • Database

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Published Papers (5 papers)

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Research

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16 pages, 553 KiB  
Article
Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Aspalathus linearis) Genome
by Yamkela Mgwatyu, Stephanie Cornelissen, Peter van Heusden, Allison Stander, Mary Ranketse and Uljana Hesse
Plants 2022, 11(16), 2156; https://doi.org/10.3390/plants11162156 - 19 Aug 2022
Cited by 6 | Viewed by 2926
Abstract
While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that [...] Read more.
While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that South Africa is home to the highly diverse Cape Floristic Region, local establishment of methods for plant genome analysis is essential. Long-read sequencing is becoming standard procedure for plant genome research, as these reads can span repetitive regions of the DNA, substantially facilitating reassembly of a contiguous genome. With the MinION, Oxford Nanopore offers a cost-efficient sequencing method to generate long reads; however, DNA purification protocols must be adapted for each plant species to generate ultra-pure DNA, essential for these analyses. Here, we describe a cost-effective procedure for the extraction and purification of plant DNA and evaluate diverse genome assembly approaches for the reconstruction of the genome of rooibos (Aspalathus linearis), an endemic South African medicinal plant widely used for tea production. We discuss the pros and cons of nine tested assembly programs, specifically Redbean and NextDenovo, which generated the most contiguous assemblies, and Flye, which produced an assembly closest to the predicted genome size. Full article
(This article belongs to the Special Issue Crop Omics)
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13 pages, 4471 KiB  
Article
Transcriptome Level Analysis of Genes of Exogenous Ethylene Applied under Phosphorus Stress in Chinese Fir
by Shuotian Huang, Lixia Zhang, Tingting Cai, Yuxuan Zhao, Jiao Liu, Pengfei Wu, Xiangqing Ma and Peng Shuai
Plants 2022, 11(15), 2036; https://doi.org/10.3390/plants11152036 - 4 Aug 2022
Viewed by 1665
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is a widely grown gymnosperm in China. Phosphorus (P) is an indispensable nutrient for the growth of Chinese fir. Inorganic phosphate (Pi) deficiency exists in soils of many Chinese fir planting area regions, and the trees [...] Read more.
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is a widely grown gymnosperm in China. Phosphorus (P) is an indispensable nutrient for the growth of Chinese fir. Inorganic phosphate (Pi) deficiency exists in soils of many Chinese fir planting area regions, and the trees themselves have limited efficiency in utilizing P from the soil. Ethylene is important in regulation responses to nutrient deficiencies. However, little is known about how ethylene signals participate in Pi stress in Chinese fir. A total of six different treatments were performed to reveal the transcript levels of Chinese fir under Pi, ethephon (an ethylene-releasing compound), and CoCl2 (cobalt chloride, an ethylene biosynthesis inhibitor) treatments. We assembled a full-length reference transcriptome containing 22,243 unigenes as a reference for UMI RNA-seq (Digital RNA-seq). There were 586 Differentially Expressed Genes (DEGs) in the Pi starvation (NP) group, while DEGs from additional ethephon or CoCl2 in NP were 708 and 292, respectively. Among the DEGs in each treatment, there were 83 TFs in these treatment groups. MYB (v-myb avian myeloblastosis viral oncogene homolog) family was the most abundant transcription factors (TFs). Three ERF (Ethylene response factor) family genes were identified when only ethylene content was imposed as a variable. Enrichment analysis indicated that the ascorbate and aldarate metabolism pathway plays a key role in resistance to Pi deficiency. This study provides insights for further elucidating the regulatory mechanism of Pi deficiency in Chinese fir. Full article
(This article belongs to the Special Issue Crop Omics)
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17 pages, 6564 KiB  
Article
Transcriptional Comparison of New Hybrid Progenies and Clone-Cultivars of Tea (Camellia sinensis L.) Associated to Catechins Content
by Hani Widhianata, Panjisakti Basunanda, Supriyadi Supriyadi and Taryono Taryono
Plants 2022, 11(15), 1972; https://doi.org/10.3390/plants11151972 - 29 Jul 2022
Cited by 4 | Viewed by 1979
Abstract
Heterosis or hybrid vigor is the improved performance of a desirable quality in hybrid progeny. Hybridization between high-productive Assam type and high-quality Chinese type clone-cultivar is expected to develop elite tea plant progenies with high quality and productivity. Comparative transcriptomics analyses of leaves [...] Read more.
Heterosis or hybrid vigor is the improved performance of a desirable quality in hybrid progeny. Hybridization between high-productive Assam type and high-quality Chinese type clone-cultivar is expected to develop elite tea plant progenies with high quality and productivity. Comparative transcriptomics analyses of leaves from the F1 hybrids and their parental clone-cultivars were conducted to explore molecular mechanisms related to catechin content using a high-throughput next-generation RNA-seq strategy and high-performance liquid chromatography (HPLC). The content of EGCG (epigallocatechin gallate) and C (catechin) was higher in ‘Kiara-8’ × ‘Sukoi’, ‘Tambi-2’ × ‘Suka Ati’, and ‘Tambi-2’ × ‘TRI-2025’ than the other hybrid and clone-cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analysis found that most pathways associated with catechins content were enriched. Significant differentially expressed genes (DEGs) mainly associated with phenylpropanoid, flavonoid, drug metabolism-cytochrome P450, and transcription factor (MYB, bHLH, LOB, and C2H2) pathways appeared to be responsible for the high accumulation of secondary metabolites in ‘Kiara-8’ × ‘Sukoi’, ‘Tambi-2’ × ‘Suka Ati’, and ‘Tambi-2’ × ‘TRI-2025’ as were detected in EGCG and catechin content. Several structural genes related to the above pathways have been obtained, which will be used as candidate genes in the screening of breeding materials. Full article
(This article belongs to the Special Issue Crop Omics)
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17 pages, 5866 KiB  
Article
Transcriptomic Characterization of Miscanthus sacchariflorus × M. lutarioriparius and Its Implications for Energy Crop Development in the Semiarid Mine Area
by Hui Feng, Cong Lin, Wei Liu, Liang Xiao, Xuhong Zhao, Lifang Kang, Xia Liu, Tao Sang, Zili Yi, Juan Yan and Hongmei Huang
Plants 2022, 11(12), 1568; https://doi.org/10.3390/plants11121568 - 14 Jun 2022
Cited by 5 | Viewed by 1817
Abstract
Miscanthus interspecific hybrids have been proved to have better adaptability in marginal lands than their parents. Miscanthus sacchariflorus and Miscanthus lutarioriparius were used as the parents to develop hybrids. We performed the transcriptome for 110 F1 hybrids of Miscanthus sacchariflorus × Miscanthus lutarioriparius [...] Read more.
Miscanthus interspecific hybrids have been proved to have better adaptability in marginal lands than their parents. Miscanthus sacchariflorus and Miscanthus lutarioriparius were used as the parents to develop hybrids. We performed the transcriptome for 110 F1 hybrids of Miscanthus sacchariflorus × Miscanthus lutarioriparius and their parents that had been established on the Loess Plateau mine area, to estimate the population’s genetic expression variation, and illuminate the adaptive mechanism of the F1 population. The result speculated that the F1 population has mainly inherited the stress response metabolic pathway of its female parent (M. sacchariflorus), which may be responsible for its higher environmental adaptability and biomass yield compared with male parents. Based on PopART, we assembled a leaf reference transcriptome for M. sacchariflorus (LRTMS) and obtained 8116 high-quality transcripts. When we analyze the differential expression of genes between F1 population and parent, 39 and 56 differentially expressed genes were screened out in the female parent and male parent, respectively. The enrichment analysis showed that pathways of carbohydrate metabolism, lipid metabolism, biosynthesis of secondary metabolites and circadian rhythm-plant played a key role in resisting the harsh environment. The carbohydrate metabolism and lipid metabolism were also significantly enriched, and the synthesis of these substances facilitated the yield. The results provided an insight into breeding Miscanthus hybrids more suited to the harsh environment of the Loess Plateau. Full article
(This article belongs to the Special Issue Crop Omics)
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Review

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19 pages, 643 KiB  
Review
Multi-Omics Approaches to Study Molecular Mechanisms in Cannabis sativa
by Tiziana M. Sirangelo, Richard A. Ludlow and Natasha D. Spadafora
Plants 2022, 11(16), 2182; https://doi.org/10.3390/plants11162182 - 22 Aug 2022
Cited by 9 | Viewed by 5044
Abstract
Cannabis (Cannabis sativa L.), also known as hemp, is one of the oldest cultivated crops, grown for both its use in textile and cordage production, and its unique chemical properties. However, due to the legislation regulating cannabis cultivation, it is not a [...] Read more.
Cannabis (Cannabis sativa L.), also known as hemp, is one of the oldest cultivated crops, grown for both its use in textile and cordage production, and its unique chemical properties. However, due to the legislation regulating cannabis cultivation, it is not a well characterized crop, especially regarding molecular and genetic pathways. Only recently have regulations begun to ease enough to allow more widespread cannabis research, which, coupled with the availability of cannabis genome sequences, is fuelling the interest of the scientific community. In this review, we provide a summary of cannabis molecular resources focusing on the most recent and relevant genomics, transcriptomics and metabolomics approaches and investigations. Multi-omics methods are discussed, with this combined approach being a powerful tool to identify correlations between biological processes and metabolic pathways across diverse omics layers, and to better elucidate the relationships between cannabis sub-species. The correlations between genotypes and phenotypes, as well as novel metabolites with therapeutic potential are also explored in the context of cannabis breeding programs. However, further studies are needed to fully elucidate the complex metabolomic matrix of this crop. For this reason, some key points for future research activities are discussed, relying on multi-omics approaches. Full article
(This article belongs to the Special Issue Crop Omics)
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