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Applications of Biotechnology and Omics Tools in Brassicaceae Plants
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Applications of Biotechnology and Omics Tools in Brassicaceae Plants

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 December 2024) | Viewed by 4515

Special Issue Editors

Dr. Pu Chu

E-Mail Website
Guest Editor
College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: rapeseed (Brassica napus L.); plant physiology; plant molecular biology; plant omics
Prof. Dr. Chenlong Li

E-Mail Website
Guest Editor
School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
Interests: bioinformatics; epigenetics; molecular mechanism; chromosome remodeling

Special Issue Information

Dear Colleagues,

The Brassicaceae (formerly Cruciferae) family encompasses a wide range of economically important crops which are critical sources of food, feed, fiber, and biofuels for global populations. In recent decades, significant progress has been made in elucidating the genetic basis of the agronomic and economic traits in this family. This Special Issue of Plants primarily focuses on the exploration and application of genes related to important traits in the Brassicaceae plant, such as crop yield, oil content, oil quality, nutritional value, stress tolerance, disease resistance, etc. We welcome original research and incisive reviews that address the challenges and opportunities in this field. Contributions may cover a wide range of topics, including—but not limited to—gene discovery and functional characterization at all levels (e.g., genome, transcriptome, proteome, metabolome, and epigenome studies), genetic transformation and genome editing, and from model species to crop plants in the Brassicaceae family. By shedding light on this topic, we aim to provide insights into how genetic knowledge can be harnessed to enhance the performance of the Brassicaceae crops for higher yield, better quality, and improved tolerance to biotic and abiotic stresses.

Dr. Pu Chu
Prof. Dr. Chenlong Li
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Brassicaceae
  • functional genes
  • agronomic trait
  • economic traits
  • abiotic and biotic stress traits
  • QTL mapping
  • BSA-seq
  • GWAS
  • omics
  • transgenics
  • gene editing

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Published Papers (3 papers)

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Research

20 pages, 7153 KiB  
Article
Identification and Expression Analysis of Acid Phosphatase Gene (PAP) in Brassica napus: Effects of cis-Acting Elements on Two BnaPAP10 Genes in Response to Phosphorus Stress
by Hongyuan Du, Ruiqian Zhang, Qingxue Zhang, Xun Shi, Jiaxue Wang, Qian Peng, Asfa Batool and Shisheng Li
Plants 2025, 14(3), 461; https://doi.org/10.3390/plants14030461 - 5 Feb 2025
Viewed by 640
Abstract
Purple acid phosphatases (PAPs) play a key role in phosphorus (P) assimilation and redistribution in plants, catalyzing the hydrolysis of phosphate esters to produce inorganic phosphate (Pi). In this study, a total of 77 PAP genes were identified in B. napus. The [...] Read more.
Purple acid phosphatases (PAPs) play a key role in phosphorus (P) assimilation and redistribution in plants, catalyzing the hydrolysis of phosphate esters to produce inorganic phosphate (Pi). In this study, a total of 77 PAP genes were identified in B. napus. The candidate genes were divided into three groups and ten subgroups based on the phylogenetic analyses and exon-intron organization. Among these 77 BnaPAP proteins, 35 exhibit typical metal-ligating residues characteristic of known PAPs, whereas certain unaltered amino acid residues were absent or displaced in other BnaPAPs. A computational prediction was conducted, revealing that the majority of PAPs contain signal peptide motifs and display a range of N-glycosylation levels, as well as transmembrane helix motifs. An analysis of previously obtained RNA-seq data revealed that 55.84% (43 of 77) of the BnaPAPs responded to Pi deficiency. Moreover, we conducted a preliminary examination of the expression profiles of BnaPAP genes in response to salt stress, and discovered that 42.86% (33 of 77) of these genes were induced under salt stress, either in the shoots or in the roots. Further qRT-PCR and GUS analyses revealed that BnaC9.PAP10 and BnaA7.PAP10, two paralogs of BnaPAP10s, were induced by Pi deficiency. Notably, BnaC9.PAP10 exhibits robust induction, compared to the relatively mild induction observed in BnaA7.PAP10. Our research shows that BnaA7.PAP10 uniquely responds to Pi stress via the W-box, while BnaA7.PAP10 predominantly responds via the P1BS element, and the differences in cis-regulatory elements (CREs) within their promoter regions specifically contribute to their distinct expression levels under Pi stress. Our findings provide valuable insights and establish a foundation for future functional studies of BnaPAPs. Full article
(This article belongs to the Special Issue Applications of Biotechnology and Omics Tools in Brassicaceae Plants)
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19 pages, 3918 KiB  
Article
Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus
by Fang Qian, Dan Zuo, Tuo Zeng, Lei Gu, Hongcheng Wang, Xuye Du, Bin Zhu and Jing Ou
Plants 2024, 13(7), 950; https://doi.org/10.3390/plants13070950 - 25 Mar 2024
Cited by 1 | Viewed by 1711
Abstract
Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this [...] Read more.
Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes. Full article
(This article belongs to the Special Issue Applications of Biotechnology and Omics Tools in Brassicaceae Plants)
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14 pages, 1779 KiB  
Article
Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed (Brassica napus L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data
by Liang Chai, Haojie Li, Xiaoguang Zhao, Cheng Cui, Benchuan Zheng, Ka Zhang, Jun Jiang, Jinfang Zhang and Liangcai Jiang
Plants 2023, 12(13), 2429; https://doi.org/10.3390/plants12132429 - 23 Jun 2023
Cited by 2 | Viewed by 1489
Abstract
Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) [...] Read more.
Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) zws-217. Genes were studied on genome, transcriptome and proteome levels and then we focused on genes with non-synonymous single nucleotide polymorphism (SNP) or frame-shift insertion-deletion (InDel), finding some genes on the list which changes their sequences. Then, combined with their annotation and the information of their orthologs, certain genes such as BnaA09g05900D, ortholog of AGAMOUS-LIKE 42 (AGL42), which encodes an MADS-box protein, were assumed as probably responsible for the multi-silique trait. Also, we analyzed the Differentially Accumulated Proteins (DAPs) between zws-ms and zws-217, revealing some genes involved in homologous recombination and mismatch repair pathways. Since the development of flowers/siliques is crucial to crops and it influences the yield of rapeseed, this study paved a way to deeply understand the mechanism of the multi-pistil flower formation, which may facilitate researches on rapeseed production in future. Full article
(This article belongs to the Special Issue Applications of Biotechnology and Omics Tools in Brassicaceae Plants)
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