This study was conducted to estimate the genetic parameters of different feeding pattern traits, including average daily feed intake (ADFI), average occupation time per day (AOTD), average occupation time per visit (AOTV), average daily feeding rate (ADFR), average feeding rate per feeding visit (AFRV), average feed intake per feeding visit (AFIV), and average number of visits per day (ANVD), and their genetic relationship to production traits, such as on-test average daily gain (ADG), backfat thickness (BFT), loin muscle area (LMA), lean percentage (LP), and feed efficiency traits, such as feed conversion ratio (FCR) and five measures of residual feed intake (RFI1 to RFI5), in Duroc pigs (DD). The non-heritable common spatial pen effect was also estimated in all studied traits. The feeding pattern traits used in this study were derived from filtered feeding visits of 602 DD pigs. Using three animal models and the REML method, the genetic parameters revealed low to moderate heritability for ADFI (0.19 to 0.32) and AFIV (0.18 to 0.33), moderate heritability for ANVD (0.28 to 0.35) and AOTV (0.21 to 0.31), and high heritability for AOTD (0.73), ADFR (0.62 to 0.64), and AFRV (0.59 to 0.63). The addition of a common spatial pen effect in models 2 and 3 had a substantial impact, ranging from 8% to 23%, on the total variability of most feeding pattern traits, with the exception of AOTD, which only had a percentage variance of 0.30% due to the pen effect. The genetic and phenotypic correlation revealed that ADFI had consistent moderate to high genetic and phenotypic correlation with production and feed efficiency (FE) traits. However, selection against ADFI would negatively affect on-test ADG. Interestingly, the AOTD had no genetic correlation with ADG (0.04), low to moderate positive genetic correlation with FCR (0.27) and all RFI measures (0.24 to 0.33), and moderate negative correlation with LP (−0.39), indicating that selection for DD pigs with lower AOTD would not influence on-test ADG but may increase LP and improve feed efficiency by lowering FCR and all RFI measures. However, the corresponding phenotypic correlation of AOTD with production and feed efficiency traits was mostly weak, which can be attributed to the low residual or environmental correlation between these correlated traits. At the genetic level, the feeding pattern traits showed potential in improving feed efficiency and production traits. However, further studies are needed to evaluate their impact at phenotypic level.

Residual feed intake (RFI) gained attention as a potential alternative to the feed conversion ratio (FCR). Thus, this study aimed to estimate genetic parameters for different feed efficiency (FE) traits (FCR, RFI1 to RFI5) and their genetic correlation to on-test daily weight gain (ADG), backfat (BFT), loin muscle area (LMA), lean percentage (LP), and total feed intake (FI) for 603 Male Duroc (DD), 295 Landrace (LL), and 341 Yorkshire (YY). The common spatial pen effect was also estimated in these traits. Five RFI measures were estimated by regressing daily feed intake on initial testing age (ITA), initial testing weight (IBW), and ADG for RFI1; other models were the same as RFI1 except for additional BFT for RFI2; LMA for RFI3; BFT and LMA for RFI4; BFT, LMA, and average metabolic body weight (AMBW) instead of IBW for RFI5. Genetic parameters estimated using two animal models and the REML method showed moderate heritability for FCR in all breeds (0.22 and 0.28 for DD, 0.31 and 0.39 for LL, 0.17 and 0.22 for YY), low heritability for the majority of RFI measures in DD (0.15 to 0.23) and YY (0.14 to 0.20) and moderate heritability for all RFI measures in LL (0.31 to 0.34). Pen variance explained 7% to 22% for FE and 0% to 9% for production traits’ phenotypic variance. The genetic correlation revealed that selection against less complex RFI1 in DD and LL and RFI2 in YY would bring the most advantageous reduction to FI (0.71 for DD, 0.49 for LL, 0.43 YY) without affecting ADG in all breeds (0.06 for DD, −0.11 for LL, 0.05 for YY), decrease in BFT, and increase in LP in DD (0.51 in BFT, −0.77 in LP) and LL (0.45 in BFT, −0.83 in LP). Therefore, inclusion of these breed-specific RFI measures in the future selection criteria would help improve feed efficiency in the swine industry.

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD (r(2)) of 3.698 million SNP pairs was 0.135 +/- 0.204. The mean r(2) decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the r(2) calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (+/- standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals. We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current Ne as well as ancestral Ne. We identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current Ne of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical Ne of Yorkshire pigs suggests that the ancestor Ne has decreased by 99.6% over the last 10,000 generations. To maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of Ne. The best way to preserve a sustainable population is to maintain a sufficient Ne.