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Journal of Integrative Agriculture  2021, Vol. 20 Issue (9): 2483-2490    DOI: 10.1016/S2095-3119(20)63474-8
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing
WU Ping-xian1*, ZHOU Jie1*, WANG Kai1, CHEN De-juan1, YANG Xi-di1, LIU Yi-hui3, JIANG An-an1, SHEN Lin-yuan1, JIN Long1, XIAO Wei-hang1, JIANG Yan-zhi2, LI Ming-zhou1, ZHU Li1, ZENG Yang-shuang3, XU Xu3, QIU Xiao-tian4, LI Xue-wei1, TANG Guo-qing1 
1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 College of Life Science, Sichuan Agricultural University, Ya’an 625014, P.R.China
3 Sichuan Animal Husbandry Station, Chengdu 610041, P.R.China
4 National Animal Husbandry Service, Beijing 100125, P.R.China
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摘要  

旨在基于简化基因组测序(Genotyping-by-sequencing,GBS)技术进一步挖掘与大白猪初生重(Birth weight,BW)和达百公斤日龄(Days to 100 kg,D100)性状相关的分子遗传标记,并挖掘同时影响两个性状的多效基因。简化基因组测序数据相较于SNP芯片分型数据能够获得更多的SNP位点信息,能够有效的提高全基因组关联分析的检测力。本研究采集600头大白猪的耳组织样品,提取基因组DNA,并利用GBS测序技术进行测序,测序共获得487.34Gb Clean data,测序结果经质量控制和基因型填充后,利用全基因组关联分析(Genome-wide association study,GWAS)鉴定影响大白猪BW和D100的SNP位点和候选基因,采用GEMMA软件对大白猪BW和D100性状进行全基因组关联分析。结果显示,通过GATK软件初步检测共获得10 445 924个SNPs,经过严格的质量控制后共获得279 787个高质量的SNPs位点,并利用Beagle 5.1软件对该基因型数据进行基因型填充。基于填充后的GBS数据采用全基因组关联分析,在基因组显著水平上鉴定到30个SNPs(P<1.79E-07)与D100相关;在建议显著水平上鉴定到22和2个SNPs(P<3.57E-06)分别与D100和BW相关。通过全基因组关联分析筛选到一个显著的SNPs(SSC12: 46,226,512 bp)同时影响BW和D100,暗示了基因在不同性状间具有的一因多效性。本文依据候选基因的相关分子生物学功能,最终确定了2个基因(NSRP1DOCK7)作为影响猪生长性状的最有希望的候选基因。本研究结果为猪BW和D100性状提供了重要的遗传变异位点和候选基因,可以为猪生长性状基因组选择提供重要遗传信息。





Abstract  
Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes.  However, the genetic architecture of these quantitative traits is still elusive.  Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis.  To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology.  After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS).  A total of 30 genome-wide SNPs (P<1.79E–07) were identified for D100.  Furthermore, a total of 22 and 2 suggestive SNPs (P<3.57E–06) were detected for D100 and BW, respectively.  Of these, one locus located on SSC12 (position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits.  Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits.  Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.
 
Keywords:  genotyping-by-sequencing        GWAS        birth weight        days to 100 kg        Yorkshire pigs  
Received: 15 June 2020   Accepted:
Fund: This study was supported by grants from the Sichuan Science and Technology Program, China (2020YFN0024), the Sichuan Innovation Team of Pig, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province (sccxtd-2020-08), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (31530073 and C170102), and the the China Agricultural Research System of MOF and MARA (CARS-35-01A).
Corresponding Authors:  Correspondence TANG Guo-qing, E-mail: tyq003@163.com    
About author:  WU Ping-xian, E-mail: wupingxianxian@163.com; ZHOU Jie, E-mail: 1048185949@qq.com; * These authors contributed equally to this study.

Cite this article: 

WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing. 2021. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing. Journal of Integrative Agriculture, 20(9): 2483-2490.

Aulchenko Y S, Ripatti S, Lindqvist I, Boomsma D I, Heid I M, Pramstaller P P, Penninx B W J H, Janssens A C J W, Wilson J F, Spector T D. 2009. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nature Genetics, 41, 47–55.
Aulchenko Y S, Ripke S, Isaacs A, Van Duijn C M. 2007. GenABEL: An R library for genome-wide association analysis. Bioinformatics, 23, 1294–1296.
Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.
Beaulieu A D, Aalhus J L, Williams N H, Patience J F. 2010. Impact of piglet birth weight, birth order, and litter size on subsequent growth performance, carcass quality, muscle composition, and eating quality of pork. Journal of Animal Science, 88, 2767–2778.
Bidanel J P, Milan D, Iannuccelli N, Amigues Y, Boscher M Y, Bourgeois F, Caritez J C, Gruand J, Le Roy P, Lagant H. 2001. Detection of quantitative trait loci for growth and fatness in pigs. Genetics Selection Evolution, 33, 289–309.
Brett K, Ferraro Z, Yockell-Lelievre J, Gruslin A, Adamo K. 2014. Maternal–fetal nutrient transport in pregnancy pathologies: The role of the placenta. International Journal of Molecular Sciences, 15, 16153–16185.
Browning B L, Zhou Y, Browning S R. 2018. A one-penny imputed genome from next-generation reference panels. The American Journal of Human Genetics, 103, 338–348.
Do D N, Ostersen T, Strathe A B, Mark T, Jensen J, Kadarmideen H N. 2014. Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs. BMC Genetics, 15, 27.
Edea Z, Hong J K, Jung J H, Kim D W, Kim Y M, Kim E S, Shin S S, Jung Y C, Kim K S. 2017. Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip. Animal Genetics, 48, 473–477.
Fernandez A I, Perezmontarelo D, Barragan C, Ramayocaldas Y, Ibanezescriche N, Castello A, Noguera J L, Silio L, Folch J M, Rodriguez M C. 2012. Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genetics, 13, 41–41.
Fix J S, Cassady J P, Holl J W, Herring W O, Culbertson M S, See M T. 2010. Effect of piglet birth weight on survival and quality of commercial market swine. Livestock Science, 132, 98–106.
Gabriel S B, Schaffner S F, Nguyen H, Moore J M, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero S N, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander E S, Daly M J, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science, 296, 2225–2229.
Guo T, Yin R, Huang F, Yao L, Lin W, Pan S. 2016. Association between the DOCK7, PCSK9 and GALNT2 gene polymorphisms and serum lipid levels. Scientific Reports, 6, 19079–19079.
Guo Y, Hou L, Zhang X, Huang M, Mao H, Chen H, Ma J, Chen C, Ai H, Ren J. 2015. A meta analysis of genome-wide association studies for limb bone lengths in four pig populations. BMC Genetics, 16, 95–95.
Guo Y M, Lee G J, Archibald A L, Haley C S. 2008. Quantitative trait loci for production traits in pigs: A combined analysis of two Meishan×Large White populations. Animal Genetics, 39, 486–495.
Jeemon P, Pettigrew K, Sainsbury C, Prabhakaran D, Padmanabhan S. 2011. Implications of discoveries from genome-wide association studies in current cardiovascular practice. World Journal of Cardiology, 3, 230–247.
Jiang Y, Tang S, Wang C, Wang Y, Qin Y, Wang Y, Zhang J, Song H, Mi S, Yu F, Xiao W, Zhang Q, Ding X. 2018. A genome-wide association study of growth and fatness traits in two pig populations with different genetic backgrounds. Journal of Animal Science, 96, 806–816.
Johnson J, Wittgenstein H, Mitchell S, Hyma K, Temnykh S, Kharlamova A. 2015. Genotyping-by-sequencing (GBS) detects genetic structure and confirms behavioral QTL in tame and aggressive foxes (Vulpes vulpes). PLoS ONE, 10, e0127013.
Kim J J, Zhao H, Thomsen H, Rothschild M F, Dekkers J C. 2005. Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genetical Research, 85, 235–248.
Kim K, Larsen N J, Short T H, Plastow G, Rothschild M F. 2000. A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth, and feed intake traits. Mammalian Genome, 11, 131–135.
Kim Y D, Lee J Y, Oh K M, Araki M, Araki K, Yamamura K, Jun C D. 2011. NSrp70 is a novel nuclear speckle-related protein that modulates alternative pre-mRNA splicing in vivo. Nuclc Acids Research, 39, 4300–4314.
Knott S A, Marklund L, Haley C S, Andersson K, Davies W, Ellegren H, Fredholm M, Hansson I, Hoyheim B, Lundstrom K, Moller M, Andersson L. 1998. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics, 149, 1069–1080.
De Koning D J, Harlizius B, Rattink A P, Groenen M A, Brascamp E W, van Arendonk J A. 2001. Detection and characterization of quantitative trait loci for meat quality traits in pigs. Journal of Animal Science, 79, 2812–2819.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754–1760.
Liu G, Jennen D G, Tholen E, Juengst H, Kleinwachter T, Holker M, Tesfaye D, Un G, Schreinemachers H J, Murani E, Ponsuksili S, Kim J J, Schellander K, Wimmers K. 2007. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics, 38, 241–252.
Liu G, Kim J J, Jonas E, Wimmers K, Ponsuksili S, Murani E, Phatsara C, Tholen E, Juengst H, Tesfaye D, Chen J L, Schellander K. 2008. Combined line-cross and half-sib QTL analysis in Duroc-Pietrain population. Mammalian Genome, 19, 429–438.
Malek M, Dekkers J C, Lee H K, Baas T J, Rothschild M F. 2001. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mammalian Genome, 12, 630–636.
NRC (National Research Council). 2012. Nutrient Requirements of Swine. 11th revised ed. National Academic Press, Washington, D.C. pp. 226–227.
De Passille A M, Rushen J, Foxcroft G R, Aherne F X, Schaefer A. 1993. Performance of young pigs: Relationships with periparturient progesterone, prolactin, and insulin of sows. Journal of Animal Science, 71, 179–184.
Pearson T A. 2008. How to interpret a genome-wide association study. Jama - Journal of the American Medical Association, 299, 1335.
De Pristo M A, Banks E, Poplin R, Garimella K V, Maguire J R, Hartl C, Philippakis A A, del Angel G, Rivas M A, Hanna M, McKenna A, Fennell T J, Kernytsky A M, Sivachenko A Y, Cibulskis K, Gabriel S B, Altshuler D, Daly M J. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43, 491–498.
Quintanilla R, Milan D, Bidanel J P. 2002. A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations. Genetics Selection Evolution, 34, 193–210.
Roehe R. 1999. Genetic determination of individual birth weight and its association with sow productivity traits using Bayesian analyses. Journal of Animal Science, 77, 330–343.
Sakiroglu M, Brummer E C. 2017. Identification of loci controlling forage yield and nutritive value in diploid alfalfa using GBS-GWAS. Theoretical & Applied Genetics, 130, 261–268.
Sell-Kubiak E, Duijvesteijn N, Lopes M S, Janss L L, Knol E F, Bijma P, Mulder H A. 2015. Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population. BMC Genomics, 16, 1049.
Tan C, Wu Z, Ren J, Huang Z, Liu D, He X, Prakapenka D, Zhang R, Li N, Da Y, Hu X. 2017. Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing. Genetics Selection Evolution, 49, 35.
Turner S D. 2014. qqman: An R package for visualizing GWAS results using Q-Q and manhattan plots. Biorxiv, doi: 10.1101/005165.
Wang K, Liu D, Hernandez-Sanchez J, Chen J, Liu C, Wu Z, Fang M, Li N. 2015. Genome wide association analysis reveals new production trait genes in a male duroc population. PLoS ONE, 10, e0139207.
Wang L, Zhang Y, Zhang T, Zhang L, Yan H, Liu X, Wang L. 2017. Genotyping by sequencing reveals a new locus for pig teat number. Animal Genetics, 48, 470–472.
Wang Y, Ding X, Tan Z, Ning C, Xing K, Yang T, Pan Y, Sun D, Wang C. 2017. Genome-wide association study of piglet uniformity and farrowing interval. Frontiers in Genetics, 8, 194.
Van Wijk H J, Buschbell H, Dibbits B, Liefers S C, Harlizius B, Heuven H C, Knol E F, Bovenhuis H, Groenen M A. 2007. Variance component analysis of quantitative trait loci for pork carcass composition and meat quality on SSC4 and SSC11. Journal of Animal Science, 85, 22–30.
Woollett L A. 2011. Review: Transport of maternal cholesterol to the fetal circulation. Placenta, 32, 218–221.
Yang Q, Wu P, Wang K, Chen D, Zhou J, Ma J, Li M, Xiao W, Jiang A, Jiang Y, Bai L, Zhu L, Li X, Tang G. 2018. SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study. Genomics, 111, 1583–1589.
Yoo C K, Park H B, Lee J B, Jung E J, Kim B M, Kim H I, Ahn S J, Ko M S, Cho I C, Lim H T. 2014. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs. Animal Genetics, 45, 589–592.
Zhang Z, Chen Z, Diao S, Ye S, Li J. 2021. Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population. Journal of Integrative Agriculture, 20, 1607–1614.
Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics, 44, 821–824.
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