G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data

Abstract

Maintaining duplicate germplasms in genebanks hampers effective conservation and utilization of genebank resources. The redundant germplasm adds to the cost of germplasm conservation by requiring a large proportion of the genebank financial resources towards conservation rather than enriching the diversity. Besides, genome-wide-association analysis using an association panel with over-represented germplasms can be biased resulting in spurious marker-trait associations. The conventional methods of germplasm duplicate removal using passport information suffer from incomplete or missing passport information and data handling errors at various stages of germplasm enrichment. This limitation is less likely in the case of genotypic data. Therefore, we developed a web-based tool, Germplasm Duplicate Identification and Removal Tool (G-DIRT), which allows germplasm duplicate identification based on identity-by-state analysis using single-nucleotide polymorphism genotyping information along with pre-processing of genotypic data. A homozygous genotypic difference threshold of 0.1% for germplasm duplicates has been determined using tetraploid wheat genotypic data with 94.97% of accuracy. Based on the genotypic difference, the tool also builds a dendrogram that can visually depict the relationship between genotypes. To overcome the constraint of high-dimensional genotypic data, an offline version of G-DIRT in the interface of R has also been developed. The G-DIRT is expected to help genebank curators, breeders and other researchers across the world in identifying germplasm duplicates from the global genebank collections by only using the easily sharable genotypic data instead of physically exchanging the seeds or propagating materials. The web server will complement the existing methods of germplasm duplicate identification based on passport or phenotypic information being freely accessible at http://webtools.nbpgr.ernet.in/gdirt/.

Whole-genome resequencing-based characterization of a durum wheat landrace showing similarity to ‘Senatore Cappelli’

“…To further investigate the placement of ‘TB2018’ among the ‘Cappelli’ accessions described in [ 45 ] we performed an analysis with the G-DIRT software [ 54 ], a tool for the identification and removal of duplicate germplasm based on identity-by-state analysis using SNP data. The results indicate, out of the 3,509 SNP loci left from the genotyping test described above, that 613 markers were retained after linkage disequilibrium (LD) pruning, and 511 markers were retained after applying the Hardy-Weinberg Equilibrium (HWE) data filtration threshold of 0.05 and Heterozygosity threshold of 0.1.…”

“…To further investigate the placing of ‘TB2018’ against the five “Cappelli” entries from [ 45 ], the G-DIRT software [ 54 ] was run using the set of 3,509 SNP loci retained from the above analysis and formatted according to the instructions ( S2 Text ) with the parameters shown in S3 Text .…”

Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data

“…Even for cultivars like Riebesel st. 47-51 , neither the accession number nor the accession name can be used to identify duplicates, as demonstrated here. For these reasons, computational methods based on single-nucleotide polymorphisms (SNPs) and genetic distances have been proposed ( Singh et al., 2019 ; Cseh et al., 2021 ; Sahu et al., 2022 ; Schulthess et al., 2022a ). Still, these methods might have problems with introgressions leading to missing variant calls due to low coverage in the corresponding genomic regions as described above.…”