From genomes to gardens: introducing the HortGenome Search Engine for horticultural crops

As genomics profoundly reshapes our understanding of horticultural crops, researchers often grapple with dispersed and complex genomic data. This fragmentation significantly hinders effective analysis and application, presenting a clear demand for more cohesive research tools. Addressing this need is crucial for unlocking the full potential of genomic insights to enhance crop quality, diversity, and resilience in the face of growing agricultural demands.

Researchers from Beijing University of Agriculture, in collaboration with international scientists, have announced the development of HortGenome Search Engine (HSE), published in the prestigious journal Horticulture Research on April 8, 2024. The study (DOI: 10.1093/hr/uhae100) introduces a novel search engine designed to query and analyze genomic data of over 500 horticultural crops, enhancing our understanding of gene functions and crop improvement.

HSE consolidates genomic data from a diverse array of over 500 horticultural crops into a unified platform, providing easy access and efficient comparison of genetic information. Equipped with advanced tools like Basic Local Alignment Search Tool (BLAST) and Synteny Viewer, HSE streamlines gene querying and functional annotation processes. Features such as batch query interfaces and enrichment analysis simplify data navigation, boosting research efficiency. The engine’s capability to identify crucial gene families, like the TCP transcription factors in tomatoes, highlights its essential role in driving forward genomic research and agricultural innovation.

Dr. Zhangjun Fei, co-developer of HSE, states, “The HortGenome Search Engine is a vital breakthrough in horticultural genomics, providing unparalleled access to extensive genomic data. This tool revolutionizes plant genomic research, significantly speeding up crop improvement discoveries and applications.”

The HSE not only streamlines genomic research but also profoundly impacts crop breeding and genetic conservation. By simplifying genomic data access and analysis, HSE enables researchers to quickly pinpoint genes associated with desirable traits, thus accelerating the breeding of crop varieties that are more nutritious, resilient, and compatible with sustainable agricultural practices.

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References

DOI

10.1093/hr/uhae100

Original Source URL

https://doi.org/10.1093/hr/uhae100

Funding information

This work was supported by grants from the Beijing University of Agriculture (Start-up fund) to Y.Z., Young Teachers’ Research and Innovation Capacity Enhancement Program QJKC2022044 and Beijing Municipal Education Commission Scientific Research Plan Project KM202310020010 to S.Wang. The computing power was supported by the Alibaba Cloud.

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.