Читать книгу Genotyping by Sequencing for Crop Improvement - Группа авторов - Страница 31

SNP databases correspond to a publically available archive of genetic information of economically important species. Recent developments in genome sequencing technologies have ushered the era of cost‐effective, high‐throughput genomics resulting in the creation of huge datasets of sequence information. In a similar manner, developments in computing facilities and data sciences had enabled us to compare, categorize, and compute relationship matrices among and between species leading to the creation of databases. As numerous labs are working on the same species, collaborative consortiums were established to avoid redundancy leading to high‐quality SNP databases containing a range of molecular variations constituting SNP’s, insertions, and deletions (InDels), trait‐specific characterized SNP’s and called variants. Table 1.3 enlists some important SNP databases corresponding to humans, model genetic organisms, and important crop species. These public databases serve as an important resource for crop improvement for genetic diversity analysis, establishing a genetic association and linkage disequilibrium studies.

Table 1.3 List of important online SNP databases.

SNP database	Organism	URL
dbSNP	Human	http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp
Ensembl	Human	http://www.ensembl.org/Homo_sapiens/index.html
1001 Genomes	Arabidopsis	https://1001genomes.org/
CropSNPdb	Brassica crops, wheat	http://snpdb.appliedbioinformatics.com.au
SNP‐Seek Database	Rice 3K panel	https://snp‐seek.irri.org/
MaizeSNPDB	1210 Maize inbred lines	http://150.109.59.144:3838/MaizeSNPDB/
CerealDB	Wheat	http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php