Genetic dissection of 26 meat cut, meat quality and carcass traits in four pig populations

Abstract

Background Currently, meat cut traits are integrated in pig breeding objectives to gain extra profit. However, little is known about the heritability of meat cut proportions (MCP) and their correlations with other traits. The aims of this study were to assess the heritability and genetic correlation of MCP with carcass and meat quality traits using single nucleotide polymorphism chips and conduct a genome-wide association study (GWAS) to identify candidate genes for MCP. Results Seventeen MCP, 12 carcass, and seven meat quality traits were measured in 2012 pigs from four populations (Landrace; Yorkshire; Landrace and Yorkshire hybrid pigs; Duroc, and Landrace and Yorkshire hybrid pigs). Estimates of the heritability for MCP ranged from 0.10 to 0.55, with most estimates being moderate to high and highly consistent across populations. In the combined population, the heritability estimates for the proportions of scapula bone, loin, back fat, leg bones, and boneless picnic shoulder were 0.44 ± 0.04, 0.36 ± 0.04, 0.44 ± 0.04, 0.38 ± 0.04, and 0.39 ± 0.04, respectively. Proportion of middle cuts was genetically significantly positively correlated with intramuscular fat content and backfat depth. Proportion of ribs was genetically positively correlated with carcass oblique length and straight length (0.35 ± 0.08 to 0.45 ± 0.07) and negatively correlated with backfat depth (− 0.26 ± 0.10 to − 0.45 ± 0.10). However, weak or nonsignificant genetic correlations were observed between most MCP, indicating their independence. Twenty-eight quantitative trait loci (QTL) for MCP were detected by GWAS, and 24 new candidate genes related to MCP were identified, which are involved with growth, height, and skeletal development. Most importantly, we found that the development of the bones in different parts of the body may be regulated by different genes, among which HMGA1 may be the strongest candidate gene affecting forelimb bone development. Moreover, as previously shown, VRTN is a causal gene affecting vertebra number, and BMP2 may be the strongest candidate gene affecting hindlimb bone development. Conclusions Our results indicate that breeding programs for MCP have the potential to enhance carcass composition by increasing the proportion of expensive cuts and decreasing the proportion of inexpensive cuts. Since MCP are post-slaughter traits, the QTL and candidate genes related to these traits can be used for marker-assisted and genomic selection.

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

“…It is worth noting that cannon bone circumference is wellestablished for its role in enhancing body size traits, including the ability to support excessive body weight, engage in strenuous physical activity, and exhibit resistance to injuries. 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.…”

“…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.…”

“…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].…”

“…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.…”

Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS

“…Notably, the VRTN gene, associated with vertebral development, has undergone extensive investigation and emerged as a promising candidate gene for regulating rib number. It is localized within the quantitative trait loci (QTL) region of swine chromosome 7 [6,[9][10][11][12][13]. Additionally, previous studies have shed light on other factors influencing rib growth, including the LTBP2 gene, which has demonstrated its capability to enhance rib number in knockout mice [5].…”