NDLI: Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

Content Provider	Springer Nature : BioMed Central
Author	Olasege, Babatunde S. Porto-Neto, Laercio R. Tahir, Muhammad S. Gouveia, Gabriela C. Cánovas, Angela Hayes, Ben J. Fortes, Marina R. S.
Abstract	Although the genetic correlations between complex traits have been estimated for more than a century, only recently we have started to map and understand the precise localization of the genomic region(s) that underpin these correlations. Reproductive traits are often genetically correlated. Yet, we don’t fully understand the complexities, synergism, or trade-offs between male and female fertility. In this study, we used reproductive traits in two cattle populations (Brahman; BB, Tropical Composite; TC) to develop a novel framework termed correlation scan (CS). This framework was used to identify local regions associated with the genetic correlations between male and female fertility traits. Animals were genotyped with bovine high-density single nucleotide polymorphisms (SNPs) chip assay. The data used consisted of ~1000 individual records measured through frequent ovarian scanning for age at first corpus luteum (AGECL) and a laboratory assay for serum levels of insulin growth hormone (IGF1 measured in bulls, IGF1b, or cows, IGF1c). The methodology developed herein used correlations of 500-SNP effects in a 100-SNPs sliding window in each chromosome to identify local genomic regions that either drive or antagonize the genetic correlations between traits. We used Fisher’s Z-statistics through a permutation method to confirm which regions of the genome harboured significant correlations. About 30% of the total genomic regions were identified as driving and antagonizing genetic correlations between male and female fertility traits in the two populations. These regions confirmed the polygenic nature of the traits being studied and pointed to genes of interest. For BB, the most important chromosome in terms of local regions is often located on bovine chromosome (BTA) 14. However, the important regions are spread across few different BTA’s in TC. Quantitative trait loci (QTLs) and functional enrichment analysis revealed many significant windows co-localized with known QTLs related to milk production and fertility traits, especially puberty. In general, the enriched reproductive QTLs driving the genetic correlations between male and female fertility are the same for both cattle populations, while the antagonizing regions were population specific. Moreover, most of the antagonizing regions were mapped to chromosome X. These results suggest regions of chromosome X for further investigation into the trade-offs between male and female fertility. We compared the CS with two other recently proposed methods that map local genomic correlations. Some genomic regions were significant across methods. Yet, many significant regions identified with the CS were overlooked by other methods.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-022-08898-7.pdf
Ending Page	20
Page Count	20
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-022-08898-7
Journal	BMC Genomics
Issue Number	1
Volume Number	23
Language	English
Publisher	BioMed Central
Publisher Date	2022-10-05
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genomic correlation Drivers Antagonizing RHOGDI Pathway analysis QTLs Correlation scan
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

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs

Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes

Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study

The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits

Microbial genomic taxonomy

Genomic variations and association study of agronomic traits in flax

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle

Integrating biological pathways and genomic profiles with ChiBE 2

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

Similar Documents

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs

Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes

Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study

The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits

Microbial genomic taxonomy

Genomic variations and association study of agronomic traits in flax

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle

Integrating biological pathways and genomic profiles with ChiBE 2

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits