NDLI: A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application

Content Provider	Springer Nature : BioMed Central
Author	Grant, Jason R. Herman, Emily K. Barlow, Lael D. Miglior, Filippo Schenkel, Flavio S. Baes, Christine F. Stothard, Paul
Abstract	Background Structural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation. Results In this work we produced a large and deeply characterized collection of SVs in Holstein cattle using two popular SV callers (Manta and Smoove) and publicly available Illumina whole-genome sequence (WGS) read sets from 310 samples (290 male, 20 female, mean 20X coverage). Manta and Smoove identified 31 K and 68 K SVs, respectively. In total the SVs cover 5% (Manta) and 6% (Smoove) of the reference genome, in contrast to the 1% impacted by SNPs and indels. SV genotypes from each caller were confirmed to accurately recapitulate animal relationships estimated using WGS SNP genotypes from the same dataset, with Manta genotypes outperforming Smoove, and deletions outperforming duplications. To support efforts to link the SVs to phenotypic variation, overlapping and tag SNPs were identified for each SV, using genotype sets extracted from the WGS results corresponding to two bovine SNP chips (BovineSNP50 and BovineHD). 9% (Manta) and 11% (Smoove) of the SVs were found to have overlapping BovineHD panel SNPs, while 21% (Manta) and 9% (Smoove) have BovineHD panel tag SNPs. A custom interactive database ( https://svdb-dc.pslab.ca ) containing the identified sequence variants with extensive annotations, gene feature information, and BAM file content for all SVs was created to enable the evaluation and prioritization of SVs for further study. Illustrative examples involving the genes POPDC3, ORM1, G2E3, FANCI, TFB1M, FOXC2, N4BP2, GSTA3, and COPA show how this resource can be used to find well-supported genic SVs, determine SV breakpoints, design genotyping approaches, and identify processed pseudogenes masquerading as deletions. Conclusions The resources developed through this study can be used to explore sequence variation in Holstein cattle and to develop strategies for studying SVs of interest. The lack of overlapping and tag SNPs from commonly used SNP chips for most of the SVs suggests that other genotyping approaches will be needed (for example direct genotyping) to understand their potential contributions to phenotype. The included SV genotype assessments point to challenges in characterizing SVs, especially duplications, using short-read data and support ongoing efforts to better characterize cattle genomes through long-read sequencing. Lastly, the identification of previously known functional SVs and additional CDS-overlapping SVs supports the phenotypic relevance of this dataset.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10812-2.pdf
Ending Page	18
Page Count	18
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-10812-2
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-09-30
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Cattle Holstein Structural variants SNPs Indels Visualization Database
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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