Application of Bioinformatics Technology in Fruit Trees Study

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (10 June 2022) | Viewed by 2626

Special Issue Editors

College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: genomics; fruit tree; genome-wide association study; gene regulatory networks; statistical genomics; comparative genomics; transcriptome

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Guest Editor
College of Forestry, Hainan University, Haikou 570228, China
Interests: bioinformatics; algorithm development; genomics and epigenomics; statistical genetics; proteomics

Special Issue Information

Dear Colleagues,

Fruit tree research, as an important branch of agriculture, provides people with rich fruits and nutrients, which has a deep impact on the quality of people's lives. The expectation of producing high-quality fruits is being met by acting at multiple levels, but mainly through the introduction of new technologies, such as bioinformatics. Bioinformatics, as a very useful tool combining statistics and computer science, can discover potential laws or determine the reasons for a particular appearance (phenotype). It has been used in humans and crops and is greatly promoting the development of research. Bioinformatics technology includes genome, transcriptome, proteome, epigenomics, database and other technologies. However, its application in fruit trees is still relatively new, with only 5–8 years of development.

For this reason, in order to better promote and develop the application and combination of bioinformation technology in fruit tree science, we set up this Special Issue. In our issue, we hope to collect high-quality research papers describing the application of bioinformatics technologies to fruit crops, including but not limited to pears, apples, grapes, oranges, strawberries, bananas and peaches. The analyses can be based on comparative genomics, genetic analysis, phylogenetics, molecular evolutionary modeling and gene regulatory networks determined using all kinds of bioinformatics technology.

Dr. Meng Li
Prof. Dr. Shang-Qian Xie
Guest Editors

Manuscript Submission Information

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Keywords

  • comparative genomics
  • genetic analysis
  • phylogenetics
  • epigenomics
  • molecular evolutionary modeling
  • gene regulatory networks
  • fruit trees
  • pear
  • apple
  • grape
  • orange
  • strawberry

Published Papers (1 paper)

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Research

19 pages, 6532 KiB  
Article
Genome-Wide Identification and Expression Analysis of WRKY Genes during Anthocyanin Biosynthesis in the Mango (Mangifera indica L.)
by Bin Shi, Hongxia Wu, Wencan Zhu, Bin Zheng, Songbiao Wang, Kaibing Zhou and Minjie Qian
Agriculture 2022, 12(6), 821; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12060821 - 07 Jun 2022
Cited by 8 | Viewed by 2089
Abstract
The WRKY family is one of the largest transcription factor (TF) families in plants and is involved in the regulation of plant physiological processes, such as anthocyanin accumulation. However, little information is known regarding the WRKY genes in the mango. In this study, [...] Read more.
The WRKY family is one of the largest transcription factor (TF) families in plants and is involved in the regulation of plant physiological processes, such as anthocyanin accumulation. However, little information is known regarding the WRKY genes in the mango. In this study, a total of 87 mango WRKY genes were identified and named MiWRKY1 to MiWRKY87. Phylogenetic results showed that the 87 MiWRKYs could be divided into three groups (I, II, III) and five subgroups of group II (II-a, II-b, II-c, II-d, II-e), with high similarity in exon–intron structures and WRKY domain and motif compositions within the same group and subgroup. One tandem duplication (MiWRKY76 and MiWRKY82) and 97 pairs of segmental duplicates were identified in the mango genome. Syntenic analysis showed that mango MiWRKY genes had 52 and 69 orthologous pairs with Arabidopsis and citrus, respectively. Promoter cis-acting element analysis revealed that MiWRKYs contain a large number of elements associated with light signaling, hormonal response, environmental stress, and plant development. Tissue specific expression profiles showed that the expression of MiWRKY genes displayed tissue preference. Quantitative-PCR analysis showed that high expression levels of MiWRKY1, MiWRKY3, MiWRKY5, MiWRKY81, and MiWRKY84 were detected in the skin of red mango cultivar, and the expressions of MiWRKY1 and MiWRKY81 were up-regulated during light-induced anthocyanin accumulation in the mango, indicating these genes might regulate anthocyanin biosynthesis in the mango. This study provides comprehensive genetic information on the MiWRKYs in mango fruit. Full article
(This article belongs to the Special Issue Application of Bioinformatics Technology in Fruit Trees Study)
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