Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig

Abstract

Background As pre-cut and pre-packaged chilled meat becomes increasingly popular, integrating the carcass-cutting process into the pig industry chain has become a trend. Identifying quantitative trait loci (QTLs) of pork cuts would facilitate the selection of pigs with a higher overall value. However, previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts, neglecting the investigation of QTLs influencing these traits. This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips. Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values (GEBVs) for pork cuts. Results We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes, respectively. Specifically, we found that HMGA1, VRTN and BMP2 were associated with body length and weight. Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones, VRTN primarily affects the number of vertebrates, and BMP2 primarily affects the length of vertebrae and the size of hind leg bones. The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population, divided by the square root of the trait's heritability. The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693. Notably, ribs, boneless picnic shoulder, tenderloin, hind leg bones, and scapula bones exhibited prediction accuracies exceeding 0.600. Employing better models, increasing marker density through genotype imputation, and pre-selecting markers significantly improved the prediction accuracy of GEBVs. Conclusions We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes. These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection. Additionally, we have constructed the first reference populations for genomic selection of pork cuts in pigs.

Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China

“…This effect has also been observed in Duroc × (Landrace × Yorkshire) crossbreeds. Furthermore, a separate investigation reported that this SNP influences the length of vertebral structures and the size and development of hind leg bones in pigs [31,32].…”

“…Multiple studies have reported this association [31,[74][75][76], with consistent findings. Similarly, Xie L et al [31,32] identified key candidate genes, including HMGA1, VRTN, and BMP2, linked to body length and size in pigs. They observed a positive correlation of HMGA1 with leg bone size, VRTN with the number of vertebrae, and BMP2 with the length of vertebrae.…”

“…Notably, Western commercial breeds such as Large White, Duroc, and Landrace feature a higher number of thoracic-lumbar vertebrae (n = 21 to 23) due to rigorous selective breeding [13,15]. In pigs, some causal or tightly linked genes affecting crucial vertebral traits and used in practical production have been reported in previous studies [29][30][31][32]. In practical pig production, the integration of genetic knowledge regarding vertebral traits allows producers to make informed breeding decisions.…”