Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array

Abstract

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the “giant panda” (very precious) in the world’s pig species by Chinese animal husbandry.Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs.Results: We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4–112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16–0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p < 3.8 × 10−7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits.Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.

Genome-Wide Association Study for Meat Quality Traits in a Multi-Breed Pig Population

“…It has to be noted however, that these teams analysed traits much more simpler to measure (meat conductivity, marbling score, moisture, meat color, pH and intramuscular fat) which were recorded by automatic measurements. GP measured in our experiment relies on sophisticated biochemical tests which limits the number of samples simultaneously analysed as it is also shown in GWAS for GP in which Xie et al (2023) used 301 pigs.…”

A novel QTL region for pH and meat color in Duroc pigs

“…Particularly in pork, but also in other livestock species, abnormal muscle pH declines can generate protein‐denaturing conditions, which produce meat defects such as pale, soft, and exudative (PSE) meat (Barbut et al., 2008). The genetic component of ultimate pH has been well documented (Chung et al., 2015; Verardo et al., 2017; Xie et al., 2023), with low heritability estimates (0.14–0.27; De Vries et al., 1994; Gjerlaug‐Enger et al., 2010; Lo et al., 1992; Tian et al., 2023). A noteworthy gene that has been associated with PSE phenotypes is the ryanodine receptor ( RYR1 ) gene, commonly known as the halothane gene.…”

Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color

“…It has a vast territory and a wide distribution of local pig breeds, forming many excellent pig breeds. For example, Meishan pigs [ 2 ] and Erhualian pigs [ 3 ] in East China have large litter sizes, and Erhualian pig breed is one of the famous high-yielding pig breeds in China; Luchuan pigs and Bama pigs in South China have thin skin and excellent heat resistance [ 4 , 5 ]; Min pigs [ 6 ] and Tibetan pigs [ 7 ] have strong cold tolerance; and there are varieties resistant to rough feeding, with strong adaptability and excellent meat quality. These pig breeds play a key role in the Chinese pig industry and contribute to the development of international commercial breeds.…”