A genome-wide association study for gestation length in swine

G. M. See, M. D. Trenhaile-Grannemann, M. L. Spangler, Daniel C Ciobanu, B. E. Mote

Research output: Contribution to journalArticle

Abstract

Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska–Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1–GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.

Original languageEnglish (US)
Pages (from-to)539-542
Number of pages4
JournalAnimal Genetics
Volume50
Issue number5
DOIs
StatePublished - Oct 1 2019

Fingerprint

Genome-Wide Association Study
Swine
pregnancy
piglets
Pregnancy
swine
genomics
Litter Size
parity (reproduction)
Parity
litter size
Multifactorial Inheritance
Insemination
Homozygote
farrowing
homozygosity
selection criteria
breeding value
insemination
Patient Selection

Keywords

  • Bayesian
  • GWAS
  • reproduction

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

See, G. M., Trenhaile-Grannemann, M. D., Spangler, M. L., Ciobanu, D. C., & Mote, B. E. (2019). A genome-wide association study for gestation length in swine. Animal Genetics, 50(5), 539-542. https://doi.org/10.1111/age.12822

A genome-wide association study for gestation length in swine. / See, G. M.; Trenhaile-Grannemann, M. D.; Spangler, M. L.; Ciobanu, Daniel C; Mote, B. E.

In: Animal Genetics, Vol. 50, No. 5, 01.10.2019, p. 539-542.

Research output: Contribution to journalArticle

See, GM, Trenhaile-Grannemann, MD, Spangler, ML, Ciobanu, DC & Mote, BE 2019, 'A genome-wide association study for gestation length in swine', Animal Genetics, vol. 50, no. 5, pp. 539-542. https://doi.org/10.1111/age.12822
See GM, Trenhaile-Grannemann MD, Spangler ML, Ciobanu DC, Mote BE. A genome-wide association study for gestation length in swine. Animal Genetics. 2019 Oct 1;50(5):539-542. https://doi.org/10.1111/age.12822
See, G. M. ; Trenhaile-Grannemann, M. D. ; Spangler, M. L. ; Ciobanu, Daniel C ; Mote, B. E. / A genome-wide association study for gestation length in swine. In: Animal Genetics. 2019 ; Vol. 50, No. 5. pp. 539-542.
@article{1d83b12da07b4988843ee25164f9b4b6,
title = "A genome-wide association study for gestation length in swine",
abstract = "Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska–Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1–GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.",
keywords = "Bayesian, GWAS, reproduction",
author = "See, {G. M.} and Trenhaile-Grannemann, {M. D.} and Spangler, {M. L.} and Ciobanu, {Daniel C} and Mote, {B. E.}",
year = "2019",
month = "10",
day = "1",
doi = "10.1111/age.12822",
language = "English (US)",
volume = "50",
pages = "539--542",
journal = "Animal Genetics",
issn = "0268-9146",
publisher = "Wiley-Blackwell",
number = "5",

}

TY - JOUR

T1 - A genome-wide association study for gestation length in swine

AU - See, G. M.

AU - Trenhaile-Grannemann, M. D.

AU - Spangler, M. L.

AU - Ciobanu, Daniel C

AU - Mote, B. E.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska–Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1–GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.

AB - Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska–Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1–GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.

KW - Bayesian

KW - GWAS

KW - reproduction

UR - http://www.scopus.com/inward/record.url?scp=85068916389&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85068916389&partnerID=8YFLogxK

U2 - 10.1111/age.12822

DO - 10.1111/age.12822

M3 - Article

VL - 50

SP - 539

EP - 542

JO - Animal Genetics

JF - Animal Genetics

SN - 0268-9146

IS - 5

ER -