Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts

Abstract

Background: Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits.

Results: Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0.08 ± 0.06, respectively. Genetic correlations within VS traits were very high for both breeds, with the lowest of 0.67 ± 0.29 for VH and VW for Landrace. Genome-wide association studies (GWAS) for Landrace, reveled genomic region associated with VS traits on Sus scrofa chromosome (SSC) 2 (154-157 Mb), 7 (107-110 Mb), 8 (4-6 Mb), and 10 (8-19 Mb). For Yorkshire, genomic regions on SSC 1 (87-91 and 282-287 Mb) and 5 (67 Mb) were identified. All regions explained at least 3.4% of the genetic variance. Accuracies of genomic prediction were moderate in Landrace, ranging from 0.30 (VH) to 0.61 (VA), and lower for Yorkshire, with 0.07 (VW) to 0.11 (VH). Between-breed and multi-breed genomic prediction accuracies were low.

Conclusions: Our findings suggest that VS traits are heritable in Landrace and Yorkshire gilts. Genomic analyses show that major QTL control these traits, and they differ between breed. Genomic information can be used to increase genetic gains for these traits in gilts. Additional research must be done to validate the GWAS and genomic prediction results reported in our study.

Keywords: GWAS; Genetic parameters; Genomic prediction; Gilts; Reproduction; Vulva size.

Fig. 1

Manhattan plot for vulva size traits by breed. Each data point represents a 1-Mb SNP window plotted against the percentage of total genetic variance accounted for by the markers (TGVM, %). The chromosomes (1 to 18) and 1-Mb SNP window locations are ordered from left to right. Plots a, b, and c represent results for vulva area (VA), height (VH), and width (VW), respectively, for Landrace breed. Plots d, e and f represent results for VA, VH, and VW, respectively, for Yorkshire breed

Fig. 2

Genomic prediction accuracies (GPA) for vulva area (VA), vulva height (VH), and vulva width (VW). The x-axis represents the breed used as the validation group: Landrace (LA; red) and Yorkshire (YO, yellow). a Within-breed GPA, using 4- and 6-fold cross-validation for LA and YO, respectively, b Between-breed GPA, and c Multi-breed GPA, using 10-fold cross-validation, using one-fold per breed for validation at a time. Error bars represent the standard deviation of the GPA across folds

Fig. 3

Genomic prediction accuracies (GPA) based on different sets of SNPs based on the GWAS results. Results for Landrace and Yorkshire breeds are in a and b, respectively, for vulva area (VA), vulva height (VH), and vulva width (VW). Within each panel, color bars represent GPA across SNP datasets. a For Landrace, Sus scrofa chromosome (SSC) 2, SSC 7, SSC 8, and SSC 10 represent the SNP datasets based on QTL identified on SSC 2 (154–157 Mb), 7 (107–110 Mb), 8 (4–6 Mb), and 10 (8–19 Mb), respectively. b For Yorkshire, SSC 1a, SSC 1b, and SSC 5 represent the SNP datasets based on QTLs on SSC 1 (87–91 Mb), SSC 1 (282–287 Mb), and SSC 5 (67 Mb), respectively. ALL represents all markers used for analysis (as presented in Fig. 1), QTL represents the SNP dataset based on all QTL identified for a given trait per breed, and REST represents the SNP dataset based on ALL minus the SNPs outside the QTL and neighboring upstream and downstream 3-Mb regions. Error bars represent the standard deviation of accuracies across cross-validation folds

Fig. 4

Heatmap of the average genomic relationships within (diagonal) and between (off-diagonals) cross-validation folds. Folds (F) F1 to F6 belong to Yorkshire, and F7 to F10 to Landrace breeds. Each number represents the average genomic relationships of individuals within (diagonal) and between (off-diagonals) folds, with boxes with positive and negative numbers in red and purple, respectively