CitGVD: a comprehensive database of citrus genomic variations

Citrus is one of the most important commercial fruit crops worldwide. With the vast genomic data currently available for citrus fruit, genetic relationships, and molecular markers can be assessed for the development of molecular breeding and genomic selection strategies. In this study, to permit the...

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Bibliographic Details
Published in:Horticulture research 2020, Vol.7 (1), p.12, Article 12
Main Authors: Li, Qiang, Qi, Jingjing, Qin, Xiujuan, Dou, Wanfu, Lei, Tiangang, Hu, Anhua, Jia, Ruirui, Jiang, Guojin, Zou, Xiuping, Long, Qin, Xu, Lanzhen, Peng, Aihong, Yao, Lixiao, Chen, Shanchun, He, Yongrui
Format: Article
Language:English
Subjects:
631/181/457/649/2157
631/208/721
Agriculture
Annotations
Bioinformatics
Biomedical and Life Sciences
Breeding
Citrinae
Citrus fruits
Ecology
Fruit crops
Fruits
Genetic analysis
Genetic relationship
Genetic structure
Genome-wide association studies
Genomes
Life Sciences
Nucleotides
Phenotypes
Phenotypic variations
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Plant Sciences
Single-nucleotide polymorphism
Structural analysis
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Summary:Citrus is one of the most important commercial fruit crops worldwide. With the vast genomic data currently available for citrus fruit, genetic relationships, and molecular markers can be assessed for the development of molecular breeding and genomic selection strategies. In this study, to permit the ease of access to these data, a web-based database, the citrus genomic variation database (CitGVD, http://citgvd.cric.cn/home ) was developed as the first citrus-specific comprehensive database dedicated to genome-wide variations including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs). The current version (V1.0.0) of CitGVD is an open-access resource centered on 1,493,258,964 high-quality genomic variations and 84 phenotypes of 346 organisms curated from in-house projects and public resources. CitGVD integrates closely related information on genomic variation annotations, related gene annotations, and details regarding the organisms, incorporating a variety of built-in tools for data accession and analysis. As an example, CitGWAS can be used for genome-wide association studies (GWASs) with SNPs and phenotypic data, while CitEVOL can be used for genetic structure analysis. These features make CitGVD a comprehensive web portal and bioinformatics platform for citrus-related studies. It also provides a model for analyzing genome-wide variations for a wide range of crop varieties.
ISSN:2662-6810
2052-7276
2052-7276
DOI:10.1038/s41438-019-0234-3