Subcutaneous and intramuscular fat transcriptomes show large differences in network organization and associations with adipose traits in pigs

Molecular Biology and Evolution

Yang

et al. 2021

Self Cite

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We re-sequenced 80 Eurasian pigs from 9 different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene-flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y-chromosomes.

Section: Resultsmentioning

confidence: 99%

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Molecular Biology and Evolution

Yang

et al. 2021

Self Cite

“…Jinhua pig and Landrace pig intramuscular fat transcriptome sequencing revealed the differences in fat and protein metabolism at the transcriptional level of the two pigs 9 . Sequencing of subcutaneous fat and IMF of 100 pigs identified 215 subcutaneous fat genes and 90 IMF genes 10 . The mechanism of subcutaneous fat and IMF deposition has not only been studied in different breeds of pigs, but also in Italian Great White pigs or Duroc pigs 11 of the same breed with different phenotypes 6 .…”

Section: Introductionmentioning

confidence: 99%

Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

et al. 2022

Sci Rep

Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.

“…RNA sequencing (RNA-Seq) is a transcript quanti cation technology widely used to measure gene expression in tissues. Although RNA-Seq has been used to analyze the transcriptome pro les of subcutaneous and intramuscular fat in pigs, most of these studies have been conducted using different pig breeds [9,10]. Some researchers have used pigs of the same breed with different phenotypes to study the mechanism of subcutaneous or intramuscular fat deposition [6,11]; however, there are few reports on the simultaneous study of subcutaneous and intramuscular fat.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Genes that Specifically Regulate Subcutaneous and Intramuscular Fat Deposition Using Transcriptomic and Proteomic Profiles in Dingyuan Pigs

et al. 2021

Preprint

Background: Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. The Dingyuan pig is a local pig breed in Anhui Province, China, that has great potential for fat deposition. Individuals with extreme subcutaneous fat and intramuscular fat content can be found in this breed, which provides a good study system for investigating the molecular mechanisms regulating these two types of fat deposit.Results: In this study, we used RNA-Seq and tandem mass tags-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high backfat thickness (HBF) and low backfat thickness (LBF) groups. In the high intramuscular fat and low intramuscular fat groups, we found 85 DEGs and 12 DAPs. The gene ontology and KEGG pathway enrichment analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in various metabolic pathways, such as those related to carbohydrates, amino acids, esters, and fatty acids, whereas the DEGs and DAPs of the IMF groups were involved in a wide range of signaling pathways, including metabolic pathways, the insulin pathway, ketone body synthesis and degradation, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters, and fatty acids, we found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes that specifically regulate IMF deposition in Dingyuan pigs.Conclusion: Our data show that subcutaneous fat deposition and IMF deposition are regulated by the same genes, but there are also genes that specifically regulate these two fat depositions. Our data provide insights into the mechanisms of pig fat deposition.