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Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0

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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 April 2023) | Viewed by 13995

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Prof. Dr. Yuriy Lvovich Orlov

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Guest Editor

Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
Interests: medical genomics; e-health; bioinformatics; systems biology
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Ming Chen

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Guest Editor

College of Life Sciences, Zhejiang University, Hangzhou 310058, China
Interests: bioinformatics; systems biology
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications. It is in the focus of modern sequencing and bioinformatics research. Sequencing and systems biology approaches offer a comprehensive view of plant growth from molecular to cellular, organ, and population levels. Sequencing and microscopy technologies make it possible to model protein–protein and gene regulatory interactions in plant cells, providing a basis for better crop production and sustainability. Plant–pathogen interaction studies complement network modeling in this area. Based on the high demand, we announce this Special Issue on molecular informatics for plant biotechnology, continuing journal Special Issues on medical genomics and bioinformatics based on sequencing data analysis.

In this Special Issue we collect works on the following topics: 1) gene expression regulation in plants; 2) plant genomics and bioinformatics; 3) miRNA and molecular mechanisms studies in plants; 4) plant systems biology and digital phenotyping; 5) sequencing of model organisms for agro- and biotechnology.

Prof. Dr. Yuriy Lvovich Orlov
Prof. Dr. Ming Chen
Guest Editors

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Keywords

gene expression regulation in plants
molecular mechanisms of stress resistance in plants
ncRNA and gene editing in plants
plant–pathogen interactions
systems biology for agrobiology
next-generation sequencing in biotechnology
transcriptome analysis in plants
modeling of plant cell growth
gene networks in plants
digital applications in plant phenotyping

Published Papers (9 papers)

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Editorial

Jump to: Research

5 pages, 203 KiB

Open AccessEditorial

Special Issue on “Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0”

by Yuriy L. Orlov and Ming Chen

Int. J. Mol. Sci. 2023, 24(24), 17588; https://doi.org/10.3390/ijms242417588 - 18 Dec 2023

Viewed by 767

Abstract

The analysis of molecular mechanisms underlying plant adaptation to environmental changes and stress response is crucial for plant biotechnology [...] Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

Research

Jump to: Editorial

18 pages, 3436 KiB

Open AccessArticle

Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions

by Lidiia Samarina, Jaroslava Fedorina, Daria Kuzmina, Lyudmila Malyukova, Karina Manakhova, Tatyana Kovalenko, Alexandra Matskiv, Enhua Xia, Wei Tong, Zhaoliang Zhang, Alexey Ryndin, Yuriy L. Orlov and Elena K. Khlestkina

Int. J. Mol. Sci. 2023, 24(19), 14538; https://doi.org/10.3390/ijms241914538 - 26 Sep 2023

Viewed by 1152

Abstract

This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon–sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g⁻¹, and the L-theanine content varied from 0.2 to 5.8 mg g⁻¹ dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3′-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3′5′Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3′5′Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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10 pages, 1773 KiB

Open AccessArticle

Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly

by Yilian Zhao, Guangxin Liu, Ziyue Wang, Yihang Ning, Runxin Ni and Mengli Xi

Int. J. Mol. Sci. 2023, 24(12), 9950; https://doi.org/10.3390/ijms24129950 - 09 Jun 2023

Cited by 1 | Viewed by 1612

Abstract

Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of Populus simonii which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for P. simonii to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current P. simonii genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the P. simonii chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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26 pages, 4897 KiB

Open AccessArticle

Magnesium Nutrient Application Induces Metabolomics and Physiological Responses in Mulberry (Morus alba) Plants

by Xin Jin, Michael Ackah, Lei Wang, Frank Kwarteng Amoako, Yisu Shi, Lionnelle Gyllye Essoh, Jianbin Li, Qiaonan Zhang, Haonan Li and Weiguo Zhao

Int. J. Mol. Sci. 2023, 24(11), 9650; https://doi.org/10.3390/ijms24119650 - 02 Jun 2023

Cited by 6 | Viewed by 1559

Abstract

Mulberry (Morus alba) is a significant plant with numerous economic benefits; however, its growth and development are affected by nutrient levels. A high level of magnesium (Mg) or magnesium nutrient starvation are two of the significant Mg factors affecting plant growth and development. Nevertheless, M. alba’s metabolic response to different Mg concentrations is unclear. In this study, different Mg concentrations, optimal (3 mmol/L), high (6 mmol/L and 9 mmol/L), or low (1 and 2 mmol/L) and deficient (0 mmol/L), were applied to M. alba for three weeks to evaluate their effects via physiological and metabolomics (untargeted; liquid chromatography–mass spectrometry (LC-MS)) studies. Several measured physiological traits revealed that Mg deficiency and excess Mg altered net photosynthesis, chlorophyll content, leaf Mg content and fresh weight, leading to remarkable reductions in the photosynthetic efficiency and biomass of mulberry plants. Our study reveals that an adequate supply of the nutrient Mg promoted the mulberry’s physiological response parameters (net photosynthesis, chlorophyll content, leaf and root Mg content and biomass). The metabolomics data show that different Mg concentrations affect several differential metabolite expressions (DEMs), particularly fatty acyls, flavonoids, amino acids, organic acid, organooxygen compounds, prenol lipids, coumarins, steroids and steroid derivatives, cinnamic acids and derivatives. An excessive supply of Mg produced more DEMs, but negatively affected biomass production compared to low and optimum supplies of Mg. The significant DEMs correlated positively with mulberry’s net photosynthesis, chlorophyll content, leaf Mg content and fresh weight. The mulberry plant’s response to the application of Mg used metabolites, mainly amino acids, organic acids, fatty acyls, flavonoids and prenol lipids, in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. These classes of compounds were mainly involved in lipid metabolism, amino acid metabolism, energy metabolism, the biosynthesis of other secondary metabolites, the biosynthesis of other amino acids, the metabolism of cofactors and vitamin pathways, indicating that mulberry plants respond to Mg concentrations by producing a divergent metabolism. The supply of Mg nutrition was an important factor influencing the induction of DEMs, and these metabolites were critical in several metabolic pathways related to magnesium nutrition. This study provides a fundamental understanding of DEMs in M. alba’s response to Mg nutrition and the metabolic mechanisms involved, which may be critical to the mulberry genetic breeding program. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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18 pages, 4322 KiB

Open AccessArticle

Genome-Wide Identification of Histone Deacetylases and Their Roles Related with Light Response in Tartary Buckwheat (Fagopyrum tataricum)

by Huiling Yan, Hongxu Chen, Qingxia Liao, Mengying Xia, Tian Yao, Lianxin Peng, Liang Zou, Gang Zhao, Jianglin Zhao and Ding-Tao Wu

Int. J. Mol. Sci. 2023, 24(9), 8090; https://doi.org/10.3390/ijms24098090 - 30 Apr 2023

Cited by 1 | Viewed by 1237

Abstract

Histone deacetylases (HDACs), known as histone acetylation erasers, function crucially in plant growth and development. Although there are abundant reports focusing on HDACs of Arabidopsis and illustrating their important roles, the knowledge of HDAC genes in Tartary buckwheat (Polygonales Polygonaceae Fagopyrum tataricum (L.) Gaertn) is still scarce. In the study, a total of 14 HDAC genes were identified and divided into three main groups: Reduced Potassium Dependency-3/His-52 tone Deacetylase 1 (RPD3/HDA1), Silent Information Regulator 2 (SIR2), and the plant-53 specific HD2. Domain and motif composition analysis showed there were conserved domains and motifs in members from the same subfamilies. The 14 FtHDACs were distributed asymmetrically on 7 chromosomes, with three segmental events and one tandem duplication event identified. The prediction of the cis-element in promoters suggested that FtHDACs probably acted in numerous biological processes including plant growth, development, and response to environmental signals. Furthermore, expression analysis based on RNA-seq data displayed that all FtHDAC genes were universally and distinctly expressed in diverse tissues and fruit development stages. In addition, we found divergent alterations in FtHDACs transcript abundance in response to different light conditions according to RNA-seq and RT-qPCR data, indicating that five FtHDACs might be involved in light response. Our findings could provide fundamental information for the HDAC gene family and supply several targets for future function analysis of FtHDACs related with light response of Tartary buckwheat. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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16 pages, 5536 KiB

Open AccessArticle

Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus Oryza

by Wen Duan, Baoping Xue, Yaqian He, Shenghao Liao, Xuemei Li, Xueying Li and Yun-Kuan Liang

Int. J. Mol. Sci. 2023, 24(8), 7189; https://doi.org/10.3390/ijms24087189 - 13 Apr 2023

Cited by 3 | Viewed by 1417

Abstract

Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus Oryza. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species Oryza sativa has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for DIR genes’ evolution in Oryza, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that OsjDIR genes respond to a wide range of environmental factors, and most OsjDIR genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of OsjDIR genes to the undersupply of mineral elements, the excess of heavy metals and the infection of Rhizoctonia solani. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of DIR genes in rice. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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18 pages, 4724 KiB

Open AccessArticle

Overexpression of the Wheat TaPsb28 Gene Enhances Drought Tolerance in Transgenic Arabidopsis

by Yuexia Wang, Menghan Zhang, Xiaoyan Li, Ruixiang Zhou, Xinyu Xue, Jing Zhang, Nana Liu, Ruili Xue and Xueli Qi

Int. J. Mol. Sci. 2023, 24(6), 5226; https://doi.org/10.3390/ijms24065226 - 09 Mar 2023

Cited by 2 | Viewed by 1474

Abstract

Psb28 is a soluble protein in the photosystem II (PSII) complex, but its role in the drought stress response of wheat remains unclear. Here, we functionally characterized the TaPsb28 gene, which positively regulates drought tolerance in wheat. When the full-length 546-bp TaPsb28 cDNA was transferred into Arabidopsis thaliana, it was located in the guard cell chloroplast around the stroma. Overexpression of TaPsb28 conferred drought tolerance, as exhibited by the increases in the survival rate. Transgenic plants maintained lower MDA content and higher chlorophyll content by inducing chlorophyll synthase (ChlG) gene transcription. The content of abscisic acid (ABA) and zeatin increased significantly in wild-type (WT) plants under drought stress, and the transcriptional expression levels of RD22, dihydroflavonol 4-reductase (DFR) and anthocyanin reductase (ANR) genes were induced, thus enhancing the contents of endogenous cyanidin, delphinidin, and proanthocyanidins. However, in transgenic plants, although anthocyanins were further aggregated, the ABA increase was inhibited, zeatin was restored to the control level under drought stress, and stomatal closure was promoted. These findings indicate ABA and zeatin have opposite synergistic effects in the process of drought tolerance caused by TaPsb28 because only after the effect of zeatin is alleviated can ABA better play its role in promoting anthocyanin accumulation and stomatal closure, thus enhancing the drought tolerance of transgenic plants. The results suggest that overexpression of TaPsb28 exerts a positive role in the drought response by influencing the functional metabolism of endogenous hormones. The understanding acquired through the research laid a foundation for further in-depth investigation of the function of TaPsb28 in drought resistance in wheat, especially its relationship with anthocyanidin accumulation. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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22 pages, 11576 KiB

Open AccessArticle

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

by Serafima V. Novikova, Vadim V. Sharov, Natalia V. Oreshkova, Evgeniy P. Simonov and Konstantin V. Krutovsky

Int. J. Mol. Sci. 2023, 24(5), 4530; https://doi.org/10.3390/ijms24054530 - 25 Feb 2023

Cited by 4 | Viewed by 1739

Abstract

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (F_ST = 0.036) and all 25,143 SNPs (F_ST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (F_ST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001). Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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21 pages, 4624 KiB

Open AccessArticle

Genome-Wide Identification, Classification, and Expression Analyses of the CsDGAT Gene Family in Cannabis sativa L. and Their Response to Cold Treatment

by Bowei Yan, Chuanyi Chang, Yingnan Gu, Nan Zheng, Yuyan Fang, Ming Zhang, Guijiang Wang and Liguo Zhang

Int. J. Mol. Sci. 2023, 24(4), 4078; https://doi.org/10.3390/ijms24044078 - 17 Feb 2023

Cited by 2 | Viewed by 2173

Abstract

Hempseed is a nutrient-rich natural resource, and high levels of hempseed oil accumulate within hemp seeds, consisting primarily of different triglycerides. Members of the diacylglycerol acyltransferase (DGAT) enzyme family play critical roles in catalyzing triacylglycerol biosynthesis in plants, often governing the rate-limiting step in this process. As such, this study was designed to characterize the Cannabis sativa DGAT (CsDGAT) gene family in detail. Genomic analyses of the C. sativa revealed 10 candidate DGAT genes that were classified into four families (DGAT1, DGAT2, DGAT3, WS/DGAT) based on the features of different isoforms. Members of the CsDGAT family were found to be associated with large numbers of cis-acting promoter elements, including plant response elements, plant hormone response elements, light response elements, and stress response elements, suggesting roles for these genes in key processes such as development, environmental adaptation, and abiotic stress responses. Profiling of these genes in various tissues and varieties revealed varying spatial patterns of CsDGAT expression dynamics and differences in expression among C. sativa varieties, suggesting that the members of this gene family likely play distinct functional regulatory functions CsDGAT genes were upregulated in response to cold stress, and significant differences in the mode of regulation were observed when comparing roots and leaves, indicating that CsDGAT genes may play positive roles as regulators of cold responses in hemp while also playing distinct roles in shaping the responses of different parts of hemp seedlings to cold exposure. These data provide a robust basis for further functional studies of this gene family, supporting future efforts to screen the significance of CsDGAT candidate genes to validate their functions to improve hempseed oil composition. Full article

(This article belongs to the Special Issue Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0)

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