The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 6...

Full description

Saved in:
Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2021-05, Vol.113 (3), p.1407-1415
Main Authors: Nosrati, Maryam, Asadollahpour Nanaei, Hojjat, Javanmard, Arash, Esmailizadeh, Ali
Format: Article
Language:English
Subjects:
Animals
Autozygosity
Cattle
Genome
Genomic inbreeding
Genomics
Genotype
Homozygote
Inbreeding
Polymorphism, Single Nucleotide
ROH hotspot
Runs of homozygosity
Sheep
Sheep - genetics
Swine
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923
cites cdi_FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923
container_end_page 1415
container_issue 3
container_start_page 1407
container_title Genomics (San Diego, Calif.)
container_volume 113
creator Nosrati, Maryam
Asadollahpour Nanaei, Hojjat
Javanmard, Arash
Esmailizadeh, Ali
description Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were
doi_str_mv 10.1016/j.ygeno.2021.03.005
format article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2501267646</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0888754321000860</els_id><sourcerecordid>2501267646</sourcerecordid><originalsourceid>FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923</originalsourceid><addsrcrecordid>eNp9kLtO7DAQhi0EguXyBEjIJU3CJHacpKA4QoeLhESzFY3lOJNdrxI72AloefrjZTmUVDPS_BfNR8hlBmkGmbjZpNsVWpfmkGcpsBSgOCCLDKo6qQQXh2QBVVUlZcHZCTkNYQMANavyY3LCWAlFPC7I63KNdFTThN5S11E_27Cbaze4z-3KBTNtqbIt3VUNRlNjG4_YGruKK_1wvm-TD9MiDWvEkY5unHs1GWfDOTnqVB_w4nuekeX93-XdY_L88vB09-c50Rz4lORVVSgldM14DUyUvBXAeaM7gCwvVQtCMdYUuhHYFDVgybnIOqhzZFrVOTsj1_vY0bu3GcMkBxM09r2y6OYg8yLmiDISiVK2l2rvQvDYydGbQfmtzEDumMqN_GIqd0wlMBmZRtfVd8HcDNj-eP5DjILbvQDjl-8GvQzaoNWRkkc9ydaZXwv-ATXFiV0</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2501267646</pqid></control><display><type>article</type><title>The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations</title><source>ScienceDirect Freedom Collection</source><creator>Nosrati, Maryam ; Asadollahpour Nanaei, Hojjat ; Javanmard, Arash ; Esmailizadeh, Ali</creator><creatorcontrib>Nosrati, Maryam ; Asadollahpour Nanaei, Hojjat ; Javanmard, Arash ; Esmailizadeh, Ali</creatorcontrib><description>Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were &lt;16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1–4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain. •The genome-wide pattern of Runs of Homozygosity (ROH) across world-wide sheep populations was evaluated.•.The sheep genome compared with other livestock such as cattle and pigs displays low homozygosity•A total of 465 ROH hotspots were detected surrounding 257 genes across the genome.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2021.03.005</identifier><identifier>PMID: 33705888</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Animals ; Autozygosity ; Cattle ; Genome ; Genomic inbreeding ; Genomics ; Genotype ; Homozygote ; Inbreeding ; Polymorphism, Single Nucleotide ; ROH hotspot ; Runs of homozygosity ; Sheep ; Sheep - genetics ; Swine</subject><ispartof>Genomics (San Diego, Calif.), 2021-05, Vol.113 (3), p.1407-1415</ispartof><rights>2021</rights><rights>Copyright © 2021. Published by Elsevier Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923</citedby><cites>FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33705888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nosrati, Maryam</creatorcontrib><creatorcontrib>Asadollahpour Nanaei, Hojjat</creatorcontrib><creatorcontrib>Javanmard, Arash</creatorcontrib><creatorcontrib>Esmailizadeh, Ali</creatorcontrib><title>The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were &lt;16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1–4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain. •The genome-wide pattern of Runs of Homozygosity (ROH) across world-wide sheep populations was evaluated.•.The sheep genome compared with other livestock such as cattle and pigs displays low homozygosity•A total of 465 ROH hotspots were detected surrounding 257 genes across the genome.</description><subject>Animals</subject><subject>Autozygosity</subject><subject>Cattle</subject><subject>Genome</subject><subject>Genomic inbreeding</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Homozygote</subject><subject>Inbreeding</subject><subject>Polymorphism, Single Nucleotide</subject><subject>ROH hotspot</subject><subject>Runs of homozygosity</subject><subject>Sheep</subject><subject>Sheep - genetics</subject><subject>Swine</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kLtO7DAQhi0EguXyBEjIJU3CJHacpKA4QoeLhESzFY3lOJNdrxI72AloefrjZTmUVDPS_BfNR8hlBmkGmbjZpNsVWpfmkGcpsBSgOCCLDKo6qQQXh2QBVVUlZcHZCTkNYQMANavyY3LCWAlFPC7I63KNdFTThN5S11E_27Cbaze4z-3KBTNtqbIt3VUNRlNjG4_YGruKK_1wvm-TD9MiDWvEkY5unHs1GWfDOTnqVB_w4nuekeX93-XdY_L88vB09-c50Rz4lORVVSgldM14DUyUvBXAeaM7gCwvVQtCMdYUuhHYFDVgybnIOqhzZFrVOTsj1_vY0bu3GcMkBxM09r2y6OYg8yLmiDISiVK2l2rvQvDYydGbQfmtzEDumMqN_GIqd0wlMBmZRtfVd8HcDNj-eP5DjILbvQDjl-8GvQzaoNWRkkc9ydaZXwv-ATXFiV0</recordid><startdate>202105</startdate><enddate>202105</enddate><creator>Nosrati, Maryam</creator><creator>Asadollahpour Nanaei, Hojjat</creator><creator>Javanmard, Arash</creator><creator>Esmailizadeh, Ali</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>202105</creationdate><title>The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations</title><author>Nosrati, Maryam ; Asadollahpour Nanaei, Hojjat ; Javanmard, Arash ; Esmailizadeh, Ali</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Autozygosity</topic><topic>Cattle</topic><topic>Genome</topic><topic>Genomic inbreeding</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Homozygote</topic><topic>Inbreeding</topic><topic>Polymorphism, Single Nucleotide</topic><topic>ROH hotspot</topic><topic>Runs of homozygosity</topic><topic>Sheep</topic><topic>Sheep - genetics</topic><topic>Swine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nosrati, Maryam</creatorcontrib><creatorcontrib>Asadollahpour Nanaei, Hojjat</creatorcontrib><creatorcontrib>Javanmard, Arash</creatorcontrib><creatorcontrib>Esmailizadeh, Ali</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nosrati, Maryam</au><au>Asadollahpour Nanaei, Hojjat</au><au>Javanmard, Arash</au><au>Esmailizadeh, Ali</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2021-05</date><risdate>2021</risdate><volume>113</volume><issue>3</issue><spage>1407</spage><epage>1415</epage><pages>1407-1415</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were &lt;16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1–4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain. •The genome-wide pattern of Runs of Homozygosity (ROH) across world-wide sheep populations was evaluated.•.The sheep genome compared with other livestock such as cattle and pigs displays low homozygosity•A total of 465 ROH hotspots were detected surrounding 257 genes across the genome.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>33705888</pmid><doi>10.1016/j.ygeno.2021.03.005</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0888-7543
ispartof Genomics (San Diego, Calif.), 2021-05, Vol.113 (3), p.1407-1415
issn 0888-7543
1089-8646
language eng
recordid cdi_proquest_miscellaneous_2501267646
source ScienceDirect Freedom Collection
subjects Animals
Autozygosity
Cattle
Genome
Genomic inbreeding
Genomics
Genotype
Homozygote
Inbreeding
Polymorphism, Single Nucleotide
ROH hotspot
Runs of homozygosity
Sheep
Sheep - genetics
Swine
title The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-26T02%3A26%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20pattern%20of%20runs%20of%20homozygosity%20and%20genomic%20inbreeding%20in%20world-wide%20sheep%20populations&rft.jtitle=Genomics%20(San%20Diego,%20Calif.)&rft.au=Nosrati,%20Maryam&rft.date=2021-05&rft.volume=113&rft.issue=3&rft.spage=1407&rft.epage=1415&rft.pages=1407-1415&rft.issn=0888-7543&rft.eissn=1089-8646&rft_id=info:doi/10.1016/j.ygeno.2021.03.005&rft_dat=%3Cproquest_cross%3E2501267646%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c404t-2885aa6c934903674d6044bcf00127ad06a33b5cb6eb590e74461f092e3ca923%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2501267646&rft_id=info:pmid/33705888&rfr_iscdi=true