Estimation & Prediction

Contribution of X-chromosome to the genetic variance of average daily gain and backfat thickness in pigs

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Abstract

Although genomic selection is well-established, not all available information is accounted for by current methods. Information on the sex chromosomes has been overlooked in genomic prediction. To exploit the X-chromosome (SSCX) information, it is essential to consider its differences from autosomes, which can be achieved through a specific relationship matrix for SSCX. We aimed to develop software to build HX, the ssGBLUP relationship matrix for SNP on SSCX, and estimate the genetic variance explained by SSCX on average daily gain (ADG) and backfat thickness (BF). The phenotypic dataset included information on 235,686 animals for BF and 238,651 for ADG. There were 244,739 animals in the pedigree, of which 30,000 were genotyped for 41,494 SNPs, including 1,435 in SSCX. Three different approaches were used to estimate variance components for both traits. In the first approach, only SNPs in the autosomes were used and the model included the additive genetic (u), litter (l), and residual (e) random effects. In the second approach, the same model was adopted; however, the data included SNPs in the autosomes and in SSCX. For both models, it was assumed that u|σ2u ~ N(0, Hσ2u), e|σ2e ~ N(0, Iσ2e), and l|σ2l ~ N(0, Iσ2l), wherein H is the ssGBLUP realized relationship matrix. In the third approach, the random additive genetic effects associated with SSCX (s) were included in the model described before. Then, it was assumed that s|σ2s ~ N(0, HXσ2s), where σ2s is the additive genetic variance associated with the SSCX. All models included systematic effects of contemporary group for both traits and end test weight for BF. All analyses were carried out using GIBBSF90+. For both traits, variance components were similar across approaches 1 and 2, with overlapping HPD intervals. In these approaches, heritabilities of 0.30 for ADG and 0.55 for BF were observed. Thus, including SSCX SNPs on the marker set without any special treatment did not provide extra benefit compared to using only autosomal SNPs. On the other hand, using the SSCX SNPs to build HX revealed that SSCX accounts for a significant part of the total additive genetic variance. It accounted for 23% of total additive variance (σ2u + σ2s) for ADG and 15% for BF. The heritabilities for SSCX were 0.08 and 0.09 for ADG and BF, and heritabilities only for the autosomal part were 0.26 and 0.50 for ADG and BF, respectively. We observed a reduction of h2u in comparison with approaches 1 and 2. Including the X chromosome as a separate effect and using HX as a covariance matrix showed that SNPs on SSCX contribute to the additive variance of ADG and BF. Considering this effect may provide extra benefit in genomic predictions for the evaluated traits.

Keywords: 2026

How to Cite:

Veroneze, R., Chen, C., Holl, J., Misztal, I., Bermann, M. & Lourenco, D., (2026) “Contribution of X-chromosome to the genetic variance of average daily gain and backfat thickness in pigs”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285765. doi: https://doi.org/10.31274/wcgalp.23788

Rights: 1