The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs

被引：18

作者：

Ding, Rongrong ^{[1
,2
,3
]}

Savegnago, Rodrigo ^{[2
,10
]}

Liu, Jinding ^{[2
,4
]}

Long, Nanye ^{[5
]}

Tan, Cheng ^{[3
,6
]}

Cai, Gengyuan ^{[1
,6
]}

Zhuang, Zhanwei ^{[1
]}

Wu, Jie ^{[1
]}

Yang, Ming ^{[1
]}

Qiu, Yibin ^{[1
]}

Ruan, Donglin ^{[1
]}

Quan, Jianping ^{[1
,2
]}

Zheng, Enqin ^{[1
]}

Yang, Huaqiang ^{[1
]}

Li, Zicong ^{[1
,7
]}

Tan, Suxu ^{[2
,11
]}

Bedhane, Mohammed ^{[2
]}

Schnabel, Robert ^{[8
]}

Steibel, Juan ^{[2
,9
]}

Gondro, Cedric ^{[2
]}

Yang, Jie ^{[1
,7
]}

Huang, Wen ^{[2
]}

Wu, Zhenfang ^{[1
,3
]}

机构：

[1] South China Agr Univ, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, Guangzhou, Guangdong, Peoples R China

[2] Michigan State Univ, Dept Anim Sci, E Lansing, MI 48824 USA

[3] Yunfu Subctr Guangdong Lab Lingnan Modern Agr, Yufu, Guandong, Peoples R China

[4] Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Nanjing, Jiangsu, Peoples R China

[5] Michigan State Univ, Inst Cyber Enabled Res, E Lansing, MI USA

[6] Guangdong Zhongxin Breeding Technol Co Ltd, Guangzhou, Guangdong, Peoples R China

[7] South China Agr Univ, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou, Guangdong, Peoples R China

[8] Univ Missouri, Div Anim Sci, Columbia, MO USA

[9] Michigan State Univ, Dept Fisheries & Wildlife, E Lansing, MI USA

[10] Genus IntelliGen Technol, De Forest, WI USA

[11] Qingdao Univ, Coll Life Sci, Qingdao, Shandong, Peoples R China

来源：

COMMUNICATIONS BIOLOGY | 2023年 / 6卷 / 01期

关键词：

GENOTYPE IMPUTATION; VARIANT; GROWTH; QTL;

D O I：

10.1038/s42003-023-04933-9

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The SWine IMputation (SWIM) haplotype reference panel and web server offer a vast public resource to improve sequence-level imputation and genetic discoveries in pigs. Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r(2) of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.

引用

页数：10

共 44 条

[1] Fast model-based estimation of ancestry in unrelated individuals [J].

Alexander, David H. ;

Novembre, John ;

Lange, Kenneth .

GENOME RESEARCH, 2009, 19 (09) :1655-1664

[2]

[Anonymous], 2023, ZENODO, DOI [10.5281/zenodo.7900470, DOI 10.5281/ZENODO.7900470]

[3] Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection [J].

Boddicker, Nicholas J. ;

Bjorkquist, Angelica ;

Rowland, Raymond R. R. ;

Lunney, Joan K. ;

Reecy, James M. ;

Dekkers, Jack C. M. .

GENETICS SELECTION EVOLUTION, 2014, 46

[4] Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression [J].

Bosse, Mirte ;

Megens, Hendrik-Jan ;

Frantz, Laurent A. F. ;

Madsen, Ole ;

Larson, Greger ;

Paudel, Yogesh ;

Duijvesteijn, Naomi ;

Harlizius, Barbara ;

Hagemeijer, Yanick ;

Crooijmans, Richard P. M. A. ;

Groenen, Martien A. M. .

NATURE COMMUNICATIONS, 2014, 5

[5] Fast two-stage phasing of large-scale sequence data [J].

Browning, Brian L. ;

Tian, Xiaowen ;

Zhou, Ying ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2021, 108 (10) :1880-1890

[6] Second-generation PLINK: rising to the challenge of larger and richer datasets [J].

Chang, Christopher C. ;

Chow, Carson C. ;

Tellier, Laurent C. A. M. ;

Vattikuti, Shashaank ;

Purcell, Shaun M. ;

Lee, James J. .

GIGASCIENCE, 2015, 4

[7] Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle [J].

Daetwyler, Hans D. ;

Capitan, Aurelien ;

Pausch, Hubert ;

Stothard, Paul ;

Van Binsbergen, Rianne ;

Brondum, Rasmus F. ;

Liao, Xiaoping ;

Djari, Anis ;

Rodriguez, Sabrina C. ;

Grohs, Cecile ;

Esquerre, Diane ;

Bouchez, Olivier ;

Rossignol, Marie-Noelle ;

Klopp, Christophe ;

Rocha, Dominique ;

Fritz, Sebastien ;

Eggen, Andre ;

Bowman, Phil J. ;

Coote, David ;

Chamberlain, Amanda J. ;

Anderson, Charlotte ;

VanTassell, Curt P. ;

Hulsegge, Ina ;

Goddard, Mike E. ;

Guldbrandtsen, Bernt ;

Lund, Mogens S. ;

Veerkamp, Roel F. ;

Boichard, Didier A. ;

Fries, Ruedi ;

Hayes, Ben J. .

NATURE GENETICS, 2014, 46 (08) :858-865

[8] Twelve years of SAMtools and BCFtools [J].

Danecek, Petr ;

Bonfield, James K. ;

Liddle, Jennifer ;

Marshall, John ;

Ohan, Valeriu ;

Pollard, Martin O. ;

Whitwham, Andrew ;

Keane, Thomas ;

McCarthy, Shane A. ;

Davies, Robert M. ;

Li, Heng .

GIGASCIENCE, 2021, 10 (02)

[9] The variant call format and VCFtools [J].

Danecek, Petr ;

Auton, Adam ;

Abecasis, Goncalo ;

Albers, Cornelis A. ;

Banks, Eric ;

DePristo, Mark A. ;

Handsaker, Robert E. ;

Lunter, Gerton ;

Marth, Gabor T. ;

Sherry, Stephen T. ;

McVean, Gilean ;

Durbin, Richard .

BIOINFORMATICS, 2011, 27 (15) :2156-2158

[10] Next-generation genotype imputation service and methods [J].

Das, Sayantan ;

Forer, Lukas ;

Schoenherr, Sebastian ;

Sidore, Carlo ;

Locke, Adam E. ;

Kwong, Alan ;

Vrieze, Scott I. ;

Chew, Emily Y. ;

Levy, Shawn ;

McGue, Matt ;

Schlessinger, David ;

Stambolian, Dwight ;

Loh, Po-Ru ;

Iacono, William G. ;

Swaroop, Anand ;

Scott, Laura J. ;

Cucca, Francesco ;

Kronenberg, Florian ;

Boehnke, Michael ;

Abecasis, Goncalo R. ;

Fuchsberger, Christian .

NATURE GENETICS, 2016, 48 (10) :1284-1287

← 1 2 3 4 5 →