Please wait a minute...
Journal of Integrative Agriculture  2018, Vol. 17 Issue (11): 2528-2535    DOI: 10.1016/S2095-3119(18)61984-7
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide detection of selective signatures in a Duroc pig population
DIAO Shu-qi1*, LUO Yuan-yu1, 2*, MA Yun-long3, DENG Xi1, HE Ying-ting1, GAO Ning1, ZHANG Hao1, LI Jia-qi1, CHEN Zan-mou1, ZHANG Zhe1 
1 Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.China
2 Liupanshui Academy of Agricultural Sciences, Liupanshui 553001, P.R.China
3 Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education/College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide.  Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome.  In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip.  The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure.  In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness.  Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1.  These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes.  This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.
Keywords:  Duroc        selective signature        candidate genes        REHH  
Received: 30 September 2017   Accepted:
Fund: This research was supported by the earmarked fund for the China Agriculture Research System (CARS-35), the National Natural Science Foundation of China (31772556), the Basic Work of Science and Technology Project, China (2014FY120800), the Pearl River S&T Nova Program of Guangzhou, China (201506010027), and the Guangdong S&T Project, China (2017A020208043).
Corresponding Authors:  Correspondence CHEN Zan-mou, E-mail:    
About author:  DIAO Shu-qi, E-mail:; * These authors contributed equally to this study.

Cite this article: 

DIAO Shu-qi, LUO Yuan-yu, MA Yun-long, DENG Xi, HE Ying-ting, GAO Ning, ZHANG Hao, LI Jia-qi, CHEN Zan-mou, ZHANG Zhe. 2018. Genome-wide detection of selective signatures in a Duroc pig population. Journal of Integrative Agriculture, 17(11): 2528-2535.

Ai H S, Huang L S, Ren J. 2013. Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers. PLoS ONE, 8, e56001.
Ai H S, Yang B, Li J, Xie X H, Chen H, Ren J. 2014. Population history and genomic signatures for high-altitude adaptation in Tibetan pigs. BMC Genomics, 15, 834.
Amaral A J, Megens H J, Crooijmans R P, Heuven H C, Groenen M A. 2008. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics, 179, 569.
Ashburner M, Ball C A, Blake J A, Botstein D, Butler H, Cherry J M, Davis A P, Dolinski K, Dwight S S, Eppig J T, Harris M A, Hill D P, Issel-Tarver L, Kasarskis A, Lewis S, Matese J C, Richardson J E, Ringwald M, Rubin G M, Sherlock G. 2000. Gene ontology: Tool for the unification of biology. Nature Genetics, 25, 25–29.
Bosse M, Megens H J, Frantz L A, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans R P, Groenen M A. 2014. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nature Communications, 5, 4392.
Browning S R, Browning B L. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. American Journal of Human Genetics, 81, 1084.
Choi J W, Chung W H, Lee K T, Cho E S, Lee S W, Choi B H, Lee S H, Lim W, Lim D, Lee Y G, Hong J K, Kim D W, Jeon H J, Kim J, Kim N, Kim T H. 2015. Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds. DNA Research, 22, 259–267.
Fang M Y, Larson G, Ribeiro H S, Li N, Andersson L. 2009. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genetics, 5, e1000341.
Fay J C, Wu C I. 2000. Hitchhiking under positive Darwinian selection. Genetics, 155, 1405–1413.
Freund C L, Mcinnes R R. 1995. Guidebook to the Homeobox Genes. Oxford University Press, Oxford.
Groenen M A, Archibald A L, Uenishi H, Tuggle C K, Takeuchi Y, Rothschild M F, Rogel-Gaillard C, Park C, Milan D, Megens H J, Li S T, Larkin D M, Kim H, Frantz L A, Caccamo M, Ahn H, Aken B L, Anselmo A, Anthon C, Auvil L, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393–398.
Hu Z L, Park C A, Reecy J M. 2016. Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44, D827–D833.
Huang D W, Sherman B T, Lempicki R A. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44–57.
Kanehisa M, Goto S. 1999. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 27, 29–34.
Kijas J M, Wales R, Törnsten A, Chardon P, Moller M, Andersson L. 1998. Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics, 150, 1177–1185.
Li M Z, Tian S L, Yeung C K L, Meng X H, Tang Q Z, Niu L L, Wang X, Jin L, Ma J D, Long K, Zhou C W, Cao Y C, Zhu L, Bai L, Tang G Q, Gu Y R, Jiang A A, Li X W, Li R Q, et al. 2014. Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication. Scientific Reports, 4, 4678.
Li X L, Yang S B, Tang Z L, Li K, Rothschild M F, Liu B, Fan B. 2014. Genome-wide scans to detect positive selection in Large White and Tongcheng pigs. Animal Genetics, 45, 329–339.
Ma Y L, Wei J L, Zhang Q, Chen L, Wang J Y, Liu J F, Ding X D. 2015. A genome scan for selection signatures in pigs. PLoS ONE, 10, e0116850.
Ma Y L, Zhang H H, Zhang Q, Ding X D. 2014. Identification of selection footprints on the X chromosome in pig. PLoS ONE, 9, e94911.
Min F G, Pan J C, Wang X L, Chen R A, Wang F G, Luo S M, Ye J C. 2014. Biological characteristics of captive Chinese Wuzhishan minipigs (Sus scrofa). International Scholarly Research Notices, 2014, 1–9.
Moon S, Kim T H, Lee K T, Kwak W, Lee T, Lee S W, Kim M J, Cho K, Kim N, Chung W H, Sung S, Park T, Cho S, Groenen M A, Nielsen R, Kim Y, Kim H, et al. 2015. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics, 16, 130.
Nsengimana J, Baret P, Haley C S, Visscher P M. 2004. Linkage disequilibrium in the domesticated pig. Genetics, 166, 1395–1404.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J, Sham P C. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559–575.
Qanbari S, Pimentel E C, Tetens J, Thaller G, Lichtner P, Sharifi A R, Simianer H. 2010. A genome-wide scan for signatures of recent selection in Holstein cattle. Animal Genetics, 41, 377–389.
Ramos A M, Crooijmans R P M A, Affara N A, Amaral A J, Archibald A L, Beever J E, Bendixen C, Churcher C, Clark R, Dehais P, Hansen M S, Hedegaard J, Hu Z L, Kerstens H H, Law A S, Megens H J, Milan D, Nonneman D J, Rohrer G A, Rothschild M F. 2009. Design of a high density SNP genotyping assay in the pig using SNPs Identified and characterized by next generation sequencing technology. PLoS ONE, 4, e6524.
Regulski M, Harding K, Kostriken R, Karch F, Levine M, Mcginnis W. 1985. Homeo box genes of the Antennapedia and Bithorax Complexes of Drosophila. Cell, 43, 71–80.
Sabeti P C, Reich D E, Higgins J M, Levine H Z P, Richter D J, Schaffner S F, Gabriel S B, Platko J V, Patterson N J, McDonald G J, Ackerman H C, Campbell S J, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander E S. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832–837.
Sanchez M P, Iannuccelli N, Basso B, Bidanel J P, Billon Y, Gandemer G, Gilbert H, Larzul C, Legault C, Riquet J, Milan D, Le Roy P. 2007. Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc×Large White cross. BMC Genetics, 8, 55.
Strecker T R, Lengyel J A. 1988. Anterior-posterior pattern formation: an evolutionary perspective on genes specifying terminal domains. Bioessays News & Reviews in Molecular Cellular & Developmental Biology, 9, 3.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.
Tummaruk P, Tantasuparuk W, Kunavongkrit A. 2014. Age at puberty in landrace, yorkshire, duroc and crossbred Landrace×Yorkshire gilts kept in evaporative cooling system in a commercial herd in Thailand. In: Proceedings of the 15th congress of the Federation of Asian Veterinary Associations. FAVA-OIE Joint Symposium on Emerging Diseases,Thailand. pp. 185–188.
Uemoto Y, Soma Y, Sato S, Ishida M, Shibata T, Kadowaki H, Kobayashi E, Suzuki K. 2012. Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Animal Genetics, 43, 27–34.
Voight B F, Kudaravalli S, Wen X, Pritchard J K. 2006. A map of recent positive selection in the human genome. PLoS Biology, 4, e72.
Walsh E C, Sabeti P, Hutcheson H B, Fry B, Schaffner S F, de Bakker P I, Varilly P, Palma A A, Roy J, Cooper R, Winkler C, Zeng Y, de The G, Lander E S, O’Brien S, Altshuler D. 2006. Searching for signals of evolutionary selection in 168 genes related to immune function. Human Genetics, 119, 92–102.
Wang Z, Chen Q, Yang Y M, Yang H J, He P F, Zhang Z, Chen Z L, Liao R R, Tu Y Y, Zhang X Z, Wang Q S, Pan Y C. 2014. A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data. Animal Genetics, 45, 808–816.
Warriss P D, Kestin S C, Brown S N, Nute G R. 1996. The quality of pork from traditional pig breeds. Meat Focus International, 5, 179–182.
Wei H D, Sherman B T, Lempicki R A. 2009. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37, 1–13.
Weir B S, Cockerham C C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370.
Westerberg R, Mansson J E, Golozoubova V, Shabalina I G, Backlund E C, Tvrdik P, Retterstol K, Capecchi M R, Jacobsson A. 2006. ELOVL3 is an important component for early onset of lipid recruitment in brown adipose tissue. Journal of Biological Chemistry, 281, 4958–4968.
Wilkinson S, Lu Z H, Megens H J, Archibald A L, Haley C, Jackson I J, Groenen M A, Crooijmans R P, Ogden R, Wiener P. 2013. Signatures of diversifying selection in European pig breeds. PLoS Genetics, 9, e1003453.
Yang S B, Li X L, Li K, Fan B, Tang Z L. 2014. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genetics, 15, 7.
Zhang C, Bailey D K, Awad T, Liu G Y, Xing G L, Cao M Q, Valmeekam V, Retief J, Matsuzaki H, Taub M, Seielstad M, Kennedy G C. 2006. A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations. Bioinformatics, 22, 2122–2128.
[1] ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying. Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2521-2537.
[2] JIA Jia, WANG Huan, CAI Zhan-dong, WEI Ru-qian, HUANG Jing-hua, XIA Qiu-ju, XIAO Xiao-hui, MA Qi-bin, NIAN Hai, CHENG Yan-bo. Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycine max (L.) Merr.][J]. >Journal of Integrative Agriculture, 2022, 21(11): 3169-3184.
[3] DING Xiao-yu, XU Jin-song, HUANG He, QIAO Xing, SHEN Ming-zhen, CHENG Yong, ZHANG Xue-kun. Unraveling waterlogging tolerance-related traits with QTL analysis in reciprocal intervarietal introgression lines using genotyping by sequencing in rapeseed (Brassica napus L.)[J]. >Journal of Integrative Agriculture, 2020, 19(8): 1974-1983.
[4] XU Zhong, SUN Hao, ZHANG Zhe, Zhao Qing-bo, Babatunde Shittu Olasege, Li Qiu-meng, Yue Yang, Ma Pei-pei, Zhang Xiang-zhe, Wang Qi-shan, Pan Yu-chun .
Genome-wide detection of selective signatures in a Jinhua pig population
[J]. >Journal of Integrative Agriculture, 2020, 19(5): 1314-1322.
[5] XIA Ning, YAN Wen-bing, WANG Xiao-qi, SHAO Yu-peng, YANG Ming-ming, WANG Zhi-kun, ZHAN Yu-hang, TENG Wei-li, HAN Ying-peng, SHI Yan-guo. Genetic dissection of hexanol content in soybean seed through genome-wide association analysis[J]. >Journal of Integrative Agriculture, 2019, 18(6): 1222-1229.
[6] ZHAO Jie, QIN Jing-jing, SONG Qian, SUN Chuan-qing, LIU Feng-xia. Combining QTL mapping and expression profile analysis to identify candidate genes of cold tolerance from Dongxiang common wild rice (Oryza rufipogon Griff.)[J]. >Journal of Integrative Agriculture, 2016, 15(9): 1933-1943.
No Suggested Reading articles found!