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

Abstract

Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding.

Database url: http://animal.nwsuaf.edu.cn/code/index.php/Wheat.

Figure 1.

Data sources and analysis pipeline used to build the database.

Figure 2.

Population structure of 968 accessions.

Figure 3.

Screenshots of a SNP data search.

Figure 4.

The result display by searching a SNP data for example.

Figure 5.

Screenshots of a search for genomic selection data and the result display for example.

Figure 6.

The read coverage depth on the region of gene TraesCS5D01G548500 in eight bread wheat accessions. The gene is absent in three landrace (C21, C23 and C29) as indicated by the few reads alignment, while it is present in the other five accessions.

Figure 7.

Three haplotypes (Hap1, Hap2 and Hap3) for gene TraesCS4A01G132700 region among wild emmer, domesticated emmer, landrace and variety based on the genotype pattern with homozygous reference in gray, heterozygous variant in yellow and homozygous variant in green.

Figure 8.

Two haplotypes (Hap1 and Hap2) for gene TraesCS2B01G534200 region among bread wheat based on the genotype pattern with homozygous reference in gray, heterozygous variant in yellow and homozygous variant in green.

Figure 9.

Two haplotypes (Hap1 and Hap2) for gene TraesCS4D01G347800 region among Ae. tauschii, landrace and variety based on the genotype pattern with homozygous reference in gray, heterozygous variant in yellow and homozygous variant in green.