NDLI: Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

Content Provider	Springer Nature : BioMed Central
Author	Sallam, Ahmed M. Reyer, Henry Wimmers, Klaus Bertolini, Francesca Aboul-Naga, Adel Braz, Camila U. Rabee, Alaa Emara
Abstract	Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-023-09679-6.pdf
Ending Page	16
Page Count	16
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-023-09679-6
Journal	BMC Genomics
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-09-26
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Adaptation Local breeds Selection signature Inbreeding Homozygosity
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

Examination of homozygosity runs and selection signatures in native goat breeds of Henan, China

Genome-wide detection of runs of homozygosity in Ding’an pigs revealed candidate genes relating to meat quality traits

Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Runs of homozygosity and distribution of functional variants in the cattle genome

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Genome-wide scan for runs of homozygosity in South American Camelids

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

Similar Documents

Examination of homozygosity runs and selection signatures in native goat breeds of Henan, China

Genome-wide detection of runs of homozygosity in Ding’an pigs revealed candidate genes relating to meat quality traits

Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Runs of homozygosity and distribution of functional variants in the cattle genome

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Genome-wide scan for runs of homozygosity in South American Camelids

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds