Whole genome SNPs discovery in Nero Siciliano pig

D’Alessandro, Enrico; Giosa, Domenico; Sapienza, Irene; Giuffrè, Letterio; Cigliano, Riccardo Aiese; Romeo, Orazio; Zumbo, Alessandro

doi:10.1590/1678-4685-GMB-2018-0169

Enrico D’Alessandro Send correspondence to Enrico D’Alessandro. Department of Veterinary Sciences, Division of Animal Production, University of Messina. Polo Universitario dell’Annunziata, 98168 Messina, Italy. E-mail: edalessandro@unime.it

Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy.

http://orcid.org/0000-0002-2282-0267

Domenico Giosa

Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.

http://orcid.org/0000-0002-3893-5296

Irene Sapienza

Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy.

Letterio Giuffrè

Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy.

http://orcid.org/0000-0001-5091-3017

Riccardo Aiese Cigliano

Sequentia Biotech SL, Barcelona, Spain.

Orazio Romeo

Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.

Scientific Institute for Research, Hospitalization and Health Care (IRCCS) - Centro Neurolesi “Bonino-Pulejo”, Messina, Italy.

http://orcid.org/0000-0001-5093-2525

Alessandro Zumbo

Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy.

http://orcid.org/0000-0002-5174-8583

Send correspondence to Enrico D’Alessandro. Department of Veterinary Sciences, Division of Animal Production, University of Messina. Polo Universitario dell’Annunziata, 98168 Messina, Italy. E-mail: edalessandro@unime.it

Chr	Gene symbol	Gene function or putative association with QTLs	Start	End	Reference
1	ESR1	total newborn, newborn alive	14217032	14604906	*Rothschild et al., 1996*Rothschild M, Jacobson C, Vaske D, Tuggle C, Wang L, Short T, Eckardt G, Sasaki S, Vincent A, McLaren D et al. (1996) The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci U S A 93:201–205.
1	VPS13A	maintenance of thermostatic status, blood circulation	230069339	230331343	Groenen, 2016Groenen MAM (2016) A decade of pig genome sequencing: A window on pig domestication and evolution. Genet Sel Evol 48:23.
1	NR6A1	body size	265320597	265570941	Groenen, 2016Groenen MAM (2016) A decade of pig genome sequencing: A window on pig domestication and evolution. Genet Sel Evol 48:23.
2	FSHB	total newborn, newborn alive	30395769	30399282	*Zhao et al., 1998*Zhao Y,Li N,Xiao L,Cao G,Chen Y,Zhang S,Chen Y,Wu C, Zhang J,Sun S et al. (1998). FSHBsubunitgeneis associated with majorgenecontrolling litter size in commercial pig breeds. Sci China C Life Sci 1(6):664-668. Domestic Animal Diversity Information System (DAD-IS), http://dad.fao.org/. http://dad.fao.org/...
3	EIF2AK3	gene overlaps with QTLs for osteochondrosis score and feet and leg conformation	57423894	57506247	*Laenoi et al., 2011*Laenoi W, Uddin MJ, Cinar MU, Grosse-Brinkhaus C, Tesfaye D, Jonas E, Scholz AM, Tholen E, Looft C, Wimmers K et al. (2011) Quantitative trait loci analysis for leg weakness related traits in a Duroc Pietrain crossbred population. Genet Sel Evol 43:13.
3	AZGP1	adaptation to environment	7867521	7874857	*Beeckmann et al., 2003Beeckmann P, Schroffel J, Moser G, Bartenschlager H, Reiner G and Geldermann H (2003) Linkage and QTL mapping for Sus scrofa chromosome 3. J Anim Breed Genet 120:20–27.; Ma et al., 2009Ma J, Qi W, Ren D, Duan Y, Qiao R, Guo Y, Yang Z, Li L, Milan D, Ren J and Huang L (2009) A genome scan for quantitative trait loci affecting three ear traits in a White Duroc x Chinese Erhualian resource population. Anim Genet 40:463–467.; Harmegnies et al., 2006*Harmegnies N, Davin F, De Smet S, Buys N, Georges M and Coppieters W (2006) Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross. Anim Genet 37:543–553.
4	PLAG1	body size	75646585	75696718	*Rubin et al., 2012*Rubin CJ, Megens HJ, Barrio AM, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jørgensen CB et al. (2012) Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A 109:19529–19536.
6	IL12RB2	immune related gene	145210251	145292399	*Koch et al., 2012Koch MA, Thomas KR, Perdue NR, Smigiel KS, Srivastava S and Campbell DJ (2012) T-bet(+) Treg cells undergo abortive Th1 cell differentiation due to impaired expression of IL-12 receptor β2. Immunity 37:501–510.; Herrero-Medrano et al., 2014*Herrero-Medrano JM, Megens HJ, Groenen M, Bosse M, Pérez-Enciso M and Crooijmans R (2014) Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds. BMC Genomics 15:601.
6	FUT1	resistance to disease	54077431	54080475	*Meijerink et al., 1997Meijerink E, Fries R, Vögeli P, Masabanda J, Wigger G, Stricker C, Neuenschwander S, Bertschinger HU and Stranzinger G (1997) Two α(1,2) fucosyltransferase genes on porcine Chromosome 6q11 are closely linked to the blood group inhibitor (S) and Escherichia coli F18 receptor (ECF18R) loci. Mamm Genome 8:736–741., 2000Meijerink E, Neuenschwander S, Fries R, Dinter A, Bertschinger GS and Vögeli P (2000) A DNA polymorphism influencing α(1,2)fucosyltransferase activity of the pig FUT1 enzyme determines susceptibility of small intestinal epithelium to Escherichia coli F18 adhesion. Immunogenetics 52:129–136.; Bao et al., 2012Bao WB, Ye L, Zi C, Su XM, Pan Zy, Zhu J, Zhu GQ, Huang XG and Wu SL (2012) Study on the age-dependent tissue expression of FUT1 gene in porcine and its relationship to E. coli F18 receptor. Gene 497:336-339.; Zhang et al., 2015Zhang Y, Wang M, Yu XQ, Ye CR and Zhu JG (2015) Analysis of polymorphisms in the FUT1 and TAP1 genes and their influence on immune performance in Pudong White pigs. Genet Mol Res 14:17193-17203.; Fernández et al., 2017*Fernández AI, Muñoz M, García F, Núñez Y, Geracci C, Crovetti A, García-Casco J, Alves E, Skrlep M, Riquet J et al. (2017) Distribution of polymorphisms in major and candidate genes for productive and domestication-related traits in European local pig breeds. 36th International Society for Animal Genetics Conference, Dublin.
8	GNRHR	Ovulation rate	65470206	65488900	*Jiang et al., 2001*Jiang Z, Gibson JP, Archibald AL and Haley CS (2001) The porcine gonadotropin-releasing hormone receptor gene (GNRHR): Genomic organization, polymorphisms, and association with the number of corpora lutea. Genome 44:7-12.
8	LCORL	body size	12806878	12969370	*Rubin et al., 2012*Rubin CJ, Megens HJ, Barrio AM, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jørgensen CB et al. (2012) Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A 109:19529–19536.
9	AHR	litter size	86511866	86555950	*Bosse et al., 2014*Bosse M, Megens HJ, Frantz LAF, Madsen O, Larson G, Paudel Y, Duijvensteijn N, Harlizius B, Hagemeijer Y, Crooijmans RP et al. (2014) Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat Comm 5:4392.
12	PPP1R1B	candidate genes affecting behaviour	22681244	22690978	Groenen, 2016Groenen MAM (2016) A decade of pig genome sequencing: A window on pig domestication and evolution. Genet Sel Evol 48:23.
13	STAB1	immune related gene, defence against bacterial infection	34630448	34659371	*Herrero-Medrano et al., 2014Herrero-Medrano JM, Megens HJ, Groenen M, Bosse M, Pérez-Enciso M and Crooijmans R (2014) Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds. BMC Genomics 15:601.; Kzhyshkowska, 2010*Kzhyshkowska J (2010) Multifunctional receptor stabilin-1 in homeostasis and disease. Sci World J 10:2039–2053.
13	GPR149	potential effect on fertility, prolificacy	94356371	94419917	*Choi et al., 2015*Choi JW, Chung WH, Lee KT, Cho ES, Lee SW, Choi BH, Lee SH, Lim W, Lee YG, Hong JK et al. (2015) Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds. DNA Res 22:259–267.
13	CLDN1	potential effect on fertility	127714857	127730628	*Choi et al., 2015*Choi JW, Chung WH, Lee KT, Cho ES, Lee SW, Choi BH, Lee SH, Lim W, Lee YG, Hong JK et al. (2015) Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds. DNA Res 22:259–267.
14	RBP4	total newborn, newborn alive	105037360	105044552	*Rothschild et al., 2000*Rothschild M, Messer L, Day A, Wales R, Short T, Southwood O and Plastow G (2000) Investigation of the retinol-binding protein 4 (RBP4) gene as a candidate gene for increased litter size in pigs. Mamm Genome 11:75–77.
14	JMJD1C	potential effect on fertility	66640845	66966911	*Choi et al., 2015*Choi JW, Chung WH, Lee KT, Cho ES, Lee SW, Choi BH, Lee SH, Lim W, Lee YG, Hong JK et al. (2015) Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds. DNA Res 22:259–267.
15	DCAF17	maintenance of thermostatic status, hair growth	77564629	77603913	*Groenen et al., 2016*Groenen MAM (2016) A decade of pig genome sequencing: A window on pig domestication and evolution. Genet Sel Evol 48:23.
16	PRLR	involved in several reproductive traits, including litter size	20637568	20655881	Vincent et al., 1998Vincent AL, Tuggle CK, Rothschild MF, Evans G, Short TH, Southwood OI and Plastow GS (1998) The prolactin receptor gene is associated with increased litter size in pigs. Swine Research Report, 1997.; *van Rens et al., 2003van Rens BTTM, Evans GJ and Van Der Lende T (2003) Components of litter size in gilts with different prolactin receptor genotypes. Theriogenology 59:915–926.; Tomás et al., 2006*Tomás A, Casellas J, Ramírez O, Muñoz G, Noguera J and Sánchez A (2006) High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits. J Anim Sci 84:1991–1998.
18	TAS2R40	adaptation to specific dietary repertoires and environment	7024418	7027197	*Dong et al., 2009Dong D, Jones G and Zhang S (2009) Dynamic evolution of bitter taste receptor genes in vertebrates. BMC Evol Biol 9:12.; Fischer et al.,2005Fischer A, Gilad Y, Man O and Pääbo S (2005) Evolution of bitter taste receptors in humans and apes. Mol Biol Evol 22:432–436.,Ribani et al., 2017*Ribani A, Bertolini F, Schiavo G, Scotti E, Utzeri VJ, Dall’Olio S, Trevisi P, Bosi P and Fontanesi L (2017) Next generation semiconductor based sequencing of bitter taste receptor genes in different pig populations and association analysis using a selective DNA pool-seq approach. Anim Genet 48:97–102.

Gene symbol	Length	Variants (SNPs and short INDEL) classified by impact				Total	%Variants/length	Structural variants
		High	Low	Moderate	Modifier
ESR1	387875	0	14	0	2891	2905	0.749	102
VPS13A	262005	1	1	1	370	373	0.142	36
NR6A1	250345	0	0	1	9	10	0.004	13
FSHB	3514	0	0	0	0	0	0.000	0
EIF2AK3	82354	0	1	0	410	411	0.499	24
AZGP1	7337	2	4	7	66	79	1.077	2
PLAG1	50134	0	0	0	3	3	0.006	1
IL12RB2	82149	0	4	4	318	326	0.397	11
FUT1	3045	2	0	0	3	5	0.164	1
GNRHR	18695	0	0	0	25	25	0.134	3
LCORL	162493	1	4	1	422	428	0.263	30
AHR	44085	0	8	9	494	511	1.159	20
PPP1R1B	9735	0	0	0	13	13	0.134	2
STAB1	28924	0	1	3	9	13	0.045	1
GPR149	63547	0	9	4	370	383	0.603	10
CLDN1	15772	0	0	0	8	8	0.051	0
RBP4	7193	0	1	0	56	57	0.792	2
JMJD1C	326067	0	5	0	762	767	0.235	62
DCAF17	39285	0	1	2	178	181	0.461	10
PRLR	18314	1	1	3	240	245	1.338	15
TAS2R40	2780	0	0	0	4	4	0.144	0
TOTAL	1865648	7	54	35	6651	6747	0.362	345

[1] Send correspondence to Enrico D’Alessandro. Department of Veterinary Sciences, Division of Animal Production, University of Messina. Polo Universitario dell’Annunziata, 98168 Messina, Italy. E-mail: edalessandro@unime.it

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Whole genome SNPs discovery in Nero Siciliano pig

Abstract