A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

다국어 초록 (Multilingual Abstract)

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB).
Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multi-trait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874).
Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits.
Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

참고문헌 (Reference)

1 Höglund JK, "Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle" 15 : 8-, 2014

2 Rattikan Suwannasing, "The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study" 아세아·태평양축산학회 31 (31): 1852-1862, 2018

3 Rothschild M, "The estrogen receptor locus is associated with a major gene influencing litter size in pigs" 93 : 201-205, 1996

4 Choi JW, "Spindlin 1 is essential for metaphase II stage maintenance and chromosomal stability in porcine oocytes" 23 : 166-176, 2017

5 Janecki DM, "SPIN1 is a proto-oncogene and SPIN3 is a tumor suppressor in human seminoma" 9 : 32466-32477, 2018

6 Ptacek T, "Physical mapping of distinct 7q22 deletions in uterine leiomyoma and analysis of a recently annotated 7q22 candidate gene" 174 : 116-120, 2007

7 Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses" 81 : 559-575, 2007

8 MaríaMuñoz, "Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line" 42 : 23-, 2010

9 Price AL, "New approaches to population stratification in genome-wide association studies" 11 : 459-463, 2010

10 Nallasamy S, "Msx homeobox genes critically regulate embryo implantation by controlling paracrine signaling between uterine stroma and epithelium" 8 : e1002500-, 2012

11 Evangelou E, "Meta-analysis methods for genome-wide association studies and beyond" 14 : 379-389, 2013

12 Willer CJ, "METAL : fast and efficient meta-analysis of genomewide association scans" 26 : 2190-2191, 2010

13 Janss L, "Inferences from genomic models in stratified populations" 192 : 693-704, 2012

14 Tucker G, "Improving the power of GWAS and avoiding confounding from population stratification with PC-select" 197 : 1045-1049, 2014

15 Wu P, "Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs" 50 : 1026-1035, 2018

16 Bosse M, "Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression" 5 : 4392-, 2014

17 Zhang LC, "Genome-wide study refines the quantitative trait locus for number of ribs in a Large White x Minzhu intercross pig population and reveals a new candidate gene" 291 : 1885-1890, 2016

18 Sell-Kubiak E, "Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population" 16 : 1049-, 2015

19 Le TH, "Genome-wide association study for conformation traits in three Danish pig breeds" 49 : 12-, 2017

20 Guo X, "Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs" 17 : 468-, 2016

21 Qiao R, "Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations" 47 : 17-, 2015

22 Wang C, "Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs" 15 : 414-424, 2014

23 Liu A, "Genome-wide Association studies for female fertility traits in Chinese and Nordic Holsteins" 7 : 8487-, 2017

24 Taeheon Lee, "Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed" 아세아·태평양축산학회 27 (27): 303-309, 2014

25 Jiaying Wang, "Genome wide association study on feed conversion ratio using imputed sequence data in chickens" 아세아·태평양축산학회 32 (32): 494-500, 2019

26 Minozzi1 G, "Genome wide analysis of fertility and production traits in Italian Holstein cattle" 8 : e80219-, 2013

27 Yang J, "GCTA : a tool for genome-wide complex trait analysis" 88 : 76-82, 2011

28 Fangmann A, "Empirical comparison between different methods for genomic prediction of number of piglets born alive in moderate sized breeding populations" 95 : 1434-1443, 2017

29 VanRaden PM, "Efficient methods to compute genomic predictions" 91 : 4414-4423, 2008

30 Chen X, "Differential gene expression in uterine endometrium during implantation in pigs" 92 : 52-, 2015

31 Daikoku T, "Conditional deletion of Msx homeobox genes in the uterus inhibits blastocyst implantation by altering uterine receptivity" 21 : 1014-1025, 2011

32 Wotton KR, "Analysis of lamprey clustered Fox genes : insight into Fox gene evolution and expression in vertebrates" 489 : 30-40, 2011

33 Ogaki S, "An expression profile analysis of ES cell-derived definitive endodermal cells and Pdx1-expressing cells" 11 : 13-, 2011

34 Onteru SK, "A whole-genome association study for pig reproductive traits" 43 : 18-26, 2012

35 Cha J, "A new role for muscle segment homeobox genes in mammalian embryonic diapause" 3 : 130035-, 2013

36 Bolormaa S, "A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle" 10 : e1004198-, 2014

37 Guo Y, "A meta analysis of genome-wide association studies for limb bone lengths in four pig populations" 16 : 95-, 2015

38 Joon-ki Hong, "A genome-wide association study of social genetic effects in Landrace pigs" 아세아·태평양축산학회 31 (31): 784-790, 2018