Analyses of Lysin-Motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the Brassica LysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The Brassica LysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

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In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Plants ◽

10.3390/plants9101393 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1393

Author(s):

Elham Mehri Eshkiki ◽

Zahra Hajiahmadi ◽

Amin Abedi ◽

Mojtaba Kordrostami ◽

Cédric Jacquard

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Genetic Manipulation ◽

Expression Patterns ◽

Rna Seq ◽

Brassica Napus L ◽

Genome Wide ◽

A Genome ◽

Ssr Loci ◽

Post Transcriptional Regulation

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

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Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

BMC Plant Biology ◽

10.1186/s12870-017-1165-5 ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 10

Author(s):

Haitao Li ◽

Bo Wang ◽

Qinghua Zhang ◽

Jing Wang ◽

Graham J. King ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Indoleacetic Acid ◽

Brassica Napus L ◽

Genome Wide Analysis ◽

Genome Wide

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The extensin gene family in oilseed rape (Brassica napus L.): Characterisation of sequences of representative members of the family

MGG Molecular & General Genetics ◽

10.1007/bf00265064 ◽

1990 ◽

Vol 223 (2) ◽

pp. 273-287 ◽

Cited By ~ 21

Author(s):

I. Marta Evans ◽

Laurence N. Gatehouse ◽

John A. Gatehouse ◽

Jennifer N. Yarwood ◽

Donald Boulter ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Oilseed Rape ◽

Brassica Napus L ◽

The Family

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Identification and comprehensive analysis of the CLV3 / ESR‐ related ( CLE ) gene family in Brassica napus L.

Plant Biology ◽

10.1111/plb.13117 ◽

2020 ◽

Vol 22 (4) ◽

pp. 709-721 ◽

Cited By ~ 1

Author(s):

S. Han ◽

M. H. U. Khan ◽

Y. Yang ◽

K. Zhu ◽

H. Li ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Comprehensive Analysis ◽

Brassica Napus L

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Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽

10.3390/genes12070981 ◽

2021 ◽

Vol 12 (7) ◽

pp. 981

Author(s):

Jichun Xia ◽

Dong Wang ◽

Yuzhou Peng ◽

Wenning Wang ◽

Qianqian Wang ◽

...

Keyword(s):

Brassica Napus ◽

Expression Patterns ◽

Purifying Selection ◽

Brassica Species ◽

Pcr Analysis ◽

Sequencing Data ◽

Functional Identification ◽

Brassica Napus L ◽

Intron Structure ◽

Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

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Peer Review #1 of "Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors (v0.3)"

10.7287/peerj.7511v0.3/reviews/1 ◽

2019 ◽

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Peer Review ◽

Hsp70 Gene ◽

Brassica Napus L ◽

Genome Wide ◽

Identification And Characterization

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Peer Review #2 of "Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors (v0.1)"

10.7287/peerj.7511v0.1/reviews/2 ◽

2019 ◽

Author(s):

M Ratnaparkhe

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Peer Review ◽

Hsp70 Gene ◽

Brassica Napus L ◽

Genome Wide ◽

Identification And Characterization

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Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling

Antioxidants ◽

10.3390/antiox10091481 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1481

Author(s):

Wei Li ◽

Xuemin Huai ◽

Peitao Li ◽

Ali Raza ◽

Muhammad Salman Mubarik ◽

...

Keyword(s):

Abiotic Stress ◽

Brassica Napus ◽

Gene Family ◽

Antioxidant Defense ◽

Main Role ◽

Brassica Napus L ◽

Group I ◽

Genome Wide ◽

A Genome ◽

Antioxidant Defense Systems

Plant glutathione peroxidases (GPXs) are the main enzymes in the antioxidant defense system that sustain H2O2 homeostasis and normalize plant reaction to abiotic stress conditions. To understand the major roles of the GPX gene family in rapeseed (Brassica napus L.), for the first time, a genome-wide study identified 25 BnGPX genes in the rapeseed genome. The phylogenetic analysis discovered that GPX genes were grouped into four major groups (Group I–Group IV) from rapeseed and three closely interrelated plant species. The universal investigation uncovered that the BnGPXs gene experienced segmental duplications and positive selection pressure. Gene structure and motifs examination recommended that most of the BnGPX genes demonstrated a comparatively well-maintained exon-intron and motifs arrangement within the identical group. Likewise, we recognized five hormones-, four stress-, and numerous light-reactive cis-elements in the promoters of BnGPXs. Five putative bna-miRNAs from two families were also prophesied, targeting six BnGPXs genes. Gene ontology annotation results proved the main role of BnGPXs in antioxidant defense systems, ROS, and response to stress stimulus. Several BnGPXs genes revealed boosted expression profiles in many developmental tissues/organs, i.e., root, seed, leaf, stem, flower, and silique. The qRT-PCR based expression profiling exhibited that two genes (BnGPX21 and BnGPX23) were suggestively up-regulated against different hormones (ABA, IAA, and MeJA) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. In short, our discoveries provide a basis for additional functional studies on the BnGPX genes in future rapeseed breeding programs.

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