WGVD: an integrated web-database for wheat genome variation and selective signatures

Area of Science:

• Agricultural Science
• Genomics
• Bioinformatics

Background:

• Bread wheat is a globally significant crop, with advancements in sequencing technology yielding extensive genomic data.
• Accessing and utilizing this vast amount of genomic information for wheat genetics research and breeding is challenging.

Purpose of the Study:

• To establish an integrated web-database, the Wheat Genome Variation Database (WGVD), for convenient access to bread wheat genomic variations.
• To incorporate genomic variations, selective signatures of domestication, and associated analytical tools for wheat research.

Main Methods:

• Compiled and integrated whole-genome resequencing and exome-capture data for bread wheat and its progenitors.
• Analyzed millions of single nucleotide polymorphisms (SNPs) and indels, focusing on genic and regulatory regions.
• Applied statistical tests (FST and Pi) to identify selective footprints during wheat domestication and improvement.

Main Results:

• WGVD contains over 7.3 million SNPs and 1 million indels, with allele frequency distributions for various wheat groups.
• Provides variant annotations, genotypes for two reference genome versions, and evaluated selective footprints.
• Includes a Genome Browser for visualization and a Blast tool for sequence alignment.

Conclusions:

• WGVD serves as a comprehensive resource for wheat genomic variations and domestication studies.
• The database and its integrated tools are expected to significantly advance functional genomics and wheat breeding efforts.