Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis

Abstract

This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.

Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs

“…Genes activated by HIF-1 can enhance the oxygen delivery to tissues and promote cell metabolism to adapt to low oxygen levels, and HIF-1 negatively regulates the transcriptional regulation of various glycolytic pathway enzymes [ 42 ]. HIF-1 overexpression in hypoxic environments reduces the expression level of the myodifferentiation factor and myoietin, thus inhibiting myoblast differentiation [ 43 ]. Li et al [ 44 ] found that HIF-1α is important in the transition from oxidative metabolism to glycolysis in muscles.…”

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

“…The association of the HMGA gene with growth and body weight has also been found in pigs and dogs. It was found that it is activated during early development, participates in the processes of cell division, and the body weight of the animal is highly correlated with HMGA expression [64][65][66]. The MSRB3 gene is an important member of the MSL gene family, which regulates the catalyzing effect of methionine-R-sulfoxide to methionine [67].…”

“…The GG genotype is associated with a larger live weight of animals, increased carcass yield, and the content of the pulp part in it, but also the ratio of protein and adipose tissue in meat preferred for dietary nutrition. The data obtained seem to be explained by the fact that the SNP at the rs268269710 position is located in close proximity to the HMGA2 and MSRB3 genes, for which a more pronounced association with growth energy in young animals has been described [62][63][64][65][66][67][68][69].…”

Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review

“…It is also characterised by slow growth, high intramuscular fat content, and superior meat quality [59] and is appreciated for its low feed consumption, convenient operation and management, and docile temperament. It is often studied in human medical research since it shows anatomical and physiological traits similar to humans [55,57,60]. Its SDG local risk status is "unknown".…”