Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

C. Reimer, C.J. Rubin, A.R. Sharifi, Ngoc Thuy Ha, S. Weigend, K.H. Waldmann, O. Distl, Sameer Pant, Merete Fredholm, M. Schlather, H. Simianer

Research output: Contribution to journalArticle

1 Citation (Scopus)
2 Downloads (Pure)

Abstract

Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. © 2018 The Author(s).
Original languageEnglish
Article number687
Pages (from-to)1-17
Number of pages17
JournalBMC Genomics
Volume19
Issue number1
DOIs
Publication statusPublished - 19 Sep 2018

Fingerprint

Miniature Swine
Body Size
Swine
X Chromosome
Genes
Single Nucleotide Polymorphism
Miniaturization
Molecular Sequence Annotation
Domestic Animals
Androgen Receptors
Haplotypes
Insulin Resistance
Growth
Population

Cite this

Reimer, C., Rubin, C. J., Sharifi, A. R., Ha, N. T., Weigend, S., Waldmann, K. H., ... Simianer, H. (2018). Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. BMC Genomics, 19(1), 1-17. [687]. https://doi.org/10.1186/s12864-018-5009-y
Reimer, C. ; Rubin, C.J. ; Sharifi, A.R. ; Ha, Ngoc Thuy ; Weigend, S. ; Waldmann, K.H. ; Distl, O. ; Pant, Sameer ; Fredholm, Merete ; Schlather, M. ; Simianer, H. / Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. In: BMC Genomics. 2018 ; Vol. 19, No. 1. pp. 1-17.
@article{ba7868f63e4245e78c6511f1013006e9,
title = "Analysis of porcine body size variation using re-sequencing data of miniature and large pigs",
abstract = "Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in {"}SweepFinder{"}, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3{\%} in F2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3{\%} on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. {\circledC} 2018 The Author(s).",
keywords = "Goettingen Minipig, Whole genome sequencing, body size, X-chromosomal QTL",
author = "C. Reimer and C.J. Rubin and A.R. Sharifi and Ha, {Ngoc Thuy} and S. Weigend and K.H. Waldmann and O. Distl and Sameer Pant and Merete Fredholm and M. Schlather and H. Simianer",
year = "2018",
month = "9",
day = "19",
doi = "10.1186/s12864-018-5009-y",
language = "English",
volume = "19",
pages = "1--17",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

Reimer, C, Rubin, CJ, Sharifi, AR, Ha, NT, Weigend, S, Waldmann, KH, Distl, O, Pant, S, Fredholm, M, Schlather, M & Simianer, H 2018, 'Analysis of porcine body size variation using re-sequencing data of miniature and large pigs', BMC Genomics, vol. 19, no. 1, 687, pp. 1-17. https://doi.org/10.1186/s12864-018-5009-y

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. / Reimer, C.; Rubin, C.J.; Sharifi, A.R.; Ha, Ngoc Thuy; Weigend, S.; Waldmann, K.H.; Distl, O.; Pant, Sameer; Fredholm, Merete; Schlather, M.; Simianer, H.

In: BMC Genomics, Vol. 19, No. 1, 687, 19.09.2018, p. 1-17.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

AU - Reimer, C.

AU - Rubin, C.J.

AU - Sharifi, A.R.

AU - Ha, Ngoc Thuy

AU - Weigend, S.

AU - Waldmann, K.H.

AU - Distl, O.

AU - Pant, Sameer

AU - Fredholm, Merete

AU - Schlather, M.

AU - Simianer, H.

PY - 2018/9/19

Y1 - 2018/9/19

N2 - Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. © 2018 The Author(s).

AB - Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. © 2018 The Author(s).

KW - Goettingen Minipig

KW - Whole genome sequencing

KW - body size

KW - X-chromosomal QTL

U2 - 10.1186/s12864-018-5009-y

DO - 10.1186/s12864-018-5009-y

M3 - Article

C2 - 30231878

VL - 19

SP - 1

EP - 17

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 687

ER -

Reimer C, Rubin CJ, Sharifi AR, Ha NT, Weigend S, Waldmann KH et al. Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. BMC Genomics. 2018 Sep 19;19(1):1-17. 687. https://doi.org/10.1186/s12864-018-5009-y