NDLI: The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

Content Provider	Springer Nature : BioMed Central
Author	Nel, Cornelius Gurman, Phillip Swan, Andrew van der Werf, Julius Snyman, Margaretha Dzama, Kennedy Gore, Klint Scholtz, Anna Cloete, Schalk
Abstract	Background South Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resources could facilitate development for across country selection, but the influence of population structures could be important to the compatability of genomic data from varying origins. The genetic structure within and across breeds, countries and strains was evaluated in this study by population genomic parameters derived from SNP-marker data. Populations were first analysed by breed and country of origin and then by subpopulations of South African and Australian Merinos. Results Mean estimated relatedness according to the genomic relationship matrix varied by breed (-0.11 to 0.16) and bloodline (-0.08 to 0.06) groups and depended on co-ancestry as well as recent genetic links. Measures of divergence across bloodlines (FST: 0.04–0.12) were sometimes more distant than across some breeds (FST: 0.05–0.24), but the divergence of common breeds from their across-country equivalents was weak (FST: 0.01–0.04). According to mean relatedness, FST, PCA and Admixture, the Australian Ultrafine line was better connected to the SA Cradock Fine Wool flock than with other AUS bloodlines. Levels of linkage disequilibrium (LD) between adjacent markers was generally low, but also varied across breeds (r2: 0.14–0.22) as well as bloodlines (r2: 0.15–0.19). Patterns of LD decay was also unique to breeds, but bloodlines differed only at the absolute level. Estimates of effective population size (Ne) showed genetic diversity to be high for the majority of breeds (Ne: 128–418) but also for bloodlines (Ne: 137–369). Conclusions This study reinforced the genetic complexity and diversity of important sheep breeds, especially the Merino breed. The results also showed that implications of isolation can be highly variable and extended beyond breed structures. However, knowledge of useful links across these population substructures allows for a fine-tuned approach in the combination of genomic resources. Isolation across country rarely proved restricting compared to other structures considered. Consequently, research into the accuracy of across-country genomic prediction is recommended.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-021-08020-3.pdf
Ending Page	19
Page Count	19
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-021-08020-3
Journal	BMC Genomics
Issue Number	1
Volume Number	23
Language	English
Publisher	BioMed Central
Publisher Date	2022-01-04
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Across-country Genetic variation Merino Population genetics Sheep SNP markers
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

Genomic population structure and prevalence of copy number variations in South African Nguni cattle

Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array

Genomic landscape of rat strain and substrain variation

Correction: Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep

Genomic predictions combining SNP markers and copy number variations in Nellore cattle

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Identifying low-density, ancestry-informative SNP markers through whole genome resequencing in Indian, Chinese, and wild yak

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

Similar Documents

Genomic population structure and prevalence of copy number variations in South African Nguni cattle

Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array

Genomic landscape of rat strain and substrain variation

Correction: Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep

Genomic predictions combining SNP markers and copy number variations in Nellore cattle

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Identifying low-density, ancestry-informative SNP markers through whole genome resequencing in Indian, Chinese, and wild yak

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations