Short communication: Including genomic information increases accuracy of breeding value estimation in a small outdoor organic pig population

TY - JOUR

T1 - Short communication: Including genomic information increases accuracy of breeding value estimation in a small outdoor organic pig population

AU - Zaalberg, Roos Marina

AU - Buitenhuis, Albert Johannes

AU - Jensen, Just

AU - Chu, Thinh Tuan

AU - Villumsen, Trine Michelle

PY - 2025/3

Y1 - 2025/3

N2 - To optimise organic pig breeding, we studied the effect of including genomic information for predicting breeding values (EBVs) in a small organic pig population. The recorded traits were the number of functional teats (n = 16 494), BW at birth (n = 36 995) and on day 10 (n = 29 744), and litter size on day 0, 4, or 11 (n ≈ 5 900 litters). Genomic information from 18 929 SNPs was available for 1 394 pigs, including Landrace sows and boars, and Yorkshire x Landrace crossbred sows. Throughout the study, a purebred- and crossbred correlation of 1 was assumed. Univariate mixed models that either included pedigree information or both pedigree and genomic information were used to estimate parameters and EBV. The prediction accuracy of the EBV was based on a forward prediction of data from the final 11 months of data. For the number of functional teats, the direct additive genetic component was considered, whereas for the other traits, the maternal genetic component was considered. The accuracy of predicting EBV for individuals without their own phenotype increased for all traits when genomic information was included, especially when the heritability was low. In conclusion, including genomic information can improve EBV prediction accuracy, which can optimise the genetic improvement in small breeding programmes.

AB - To optimise organic pig breeding, we studied the effect of including genomic information for predicting breeding values (EBVs) in a small organic pig population. The recorded traits were the number of functional teats (n = 16 494), BW at birth (n = 36 995) and on day 10 (n = 29 744), and litter size on day 0, 4, or 11 (n ≈ 5 900 litters). Genomic information from 18 929 SNPs was available for 1 394 pigs, including Landrace sows and boars, and Yorkshire x Landrace crossbred sows. Throughout the study, a purebred- and crossbred correlation of 1 was assumed. Univariate mixed models that either included pedigree information or both pedigree and genomic information were used to estimate parameters and EBV. The prediction accuracy of the EBV was based on a forward prediction of data from the final 11 months of data. For the number of functional teats, the direct additive genetic component was considered, whereas for the other traits, the maternal genetic component was considered. The accuracy of predicting EBV for individuals without their own phenotype increased for all traits when genomic information was included, especially when the heritability was low. In conclusion, including genomic information can improve EBV prediction accuracy, which can optimise the genetic improvement in small breeding programmes.

KW - Breeding plan

KW - Genomic breeding value

KW - Genomics

KW - Outdoor

KW - Sus scrofa

UR - http://www.scopus.com/inward/record.url?scp=85217902558&partnerID=8YFLogxK

U2 - 10.1016/j.animal.2025.101434

DO - 10.1016/j.animal.2025.101434

M3 - Journal article

SN - 1751-7311

VL - 19

JO - Animal

JF - Animal

IS - 3

M1 - 101434

ER -