Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Peng, Hongyang; Hu, Mingyue; Liu, Zhengxi; Lai, Weining; Shi, Lulu; Zhao, Zhenghua; Ma, Huiqin; Li, Yumei; Yan, Shouqing

doi:10.3389/fgene.2022.868717

Cited by 10 publications

(7 citation statements)

References 57 publications

(62 reference statements)

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“…WC populations are well known for their juiciness and for the flavour of their meat, and the SNPs identified in this study may help explain the genetic mechanisms underlying these favorable qualities. We also found that the SNPs identified in WC populations were related to developmental growth, which has been hypothesized to be involved in the growth and development of muscles (Peng et al, 2022). In addition, the GO terms of GO:0001525 – angiogenesis and GO:0005524 – ATP binding found in WC populations have been reported to be associated with the tolerance of ultraviolet radiation.…”

Section: Discussionsupporting

confidence: 56%

Genome‐wide re‐sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China

Shuaishuai

Zhong

et al. 2023

Animal Genetics

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Wenchang (WC) chicken, the only indigenous chicken breed listed in Chinese genetic resources in Hainan province, is well known for its excellent meat quality and is sold all over southeast Asia. In recent years, the number of WC has decreased sharply with considerable variability in the quality at market. To explore the genetic diversity and population structure of WC chickens, the whole‐genome data of 235 WC individuals from three conservation farms were obtained using the Illumina 150 bp paired‐end platform and used in conjunction with the sequencing data from 123 individuals from other chicken breeds (including eight Chinese indigenous chicken breeds and three foreign or commercial breeds) downloaded from a public database. A total of 12 111 532 SNPs were identified, of which 11 541 878 SNPs were identified in WC. The results of gene enrichment analyses revealed that the SNPs harbored in WC genomes are mainly related to environmental adaptation, disease resistance and meat quality traits. Genetic diversity statistics, quantified by expected heterozygosity, observed heterozygosity, linkage disequilibrium, nucleotide diversity and fixation statistics, indicated that WC displays high genetic diversity compared with other Chinese indigenous chicken breeds. Genetic structure analyses showed that each population displayed great differentiation between WC and the other breeds, indicating the uniqueness of WC. In conclusion, the results of our study provide the first genomic overview of genetic variants, genetic diversity and population structure of WC from three conservation farms. This information will be valuable for the future breeding and conservation of WC and other surveyed populations.

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Section: Discussionsupporting

confidence: 56%

Genome‐wide re‐sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China

Shuaishuai

Zhong

et al. 2023

Animal Genetics

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“…Peng, et al (2022) found that 2188 DEGs were markedly up or downregulated between muscle and liver. There were 950,160 upregulated and 100,771 downregulated genes in the liver and muscle, respectively [ 23 ]. In the current study, 1346 genes were found to be differentially expressed in the subcutaneous fat of sheep fed different levels of wheat diets of Tibetan sheep.…”

Section: Discussionmentioning

confidence: 99%

The impact of different levels of wheat diets on hepatic oxidative stress, immune response, and lipid metabolism in Tibetan sheep (Ovis aries)

Ma,

Raza,

Pant

et al. 2024

BMC Vet Res

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Background Compared with corn, wheat contains higher crude protein, amino acids concentration. However, wheat contains a mass of anti-nutritional factors, resulting in increased of the digesta viscosity and impaired the intestinal function in ruminant. Objective This study aimed to investigate the effects of substitution of different amounts of wheat for corn on hepatic metabolism in the Tibetan lamb. Methods Ninety Tibetan lambs (Body weight = 12.37 ± 0.92 kg) were randomly assigned to three groups: 0% wheat diet (Control), 10% wheat diet (Low group), and 15% wheat diet (High group). The feeding trial lasted for 130 d, including a 10 d adaption period. Hepatic gene expression profiling was performed via RNA sequencing after the conclusion of the feeding trials. Results Results showed that greater level of glutathione peroxidase levels in L group compared with those of the C and H groups (P < 0.05). The immune indexes, including interleukin-1β (IL-1β), immunoglobulin A (IgA), and IgM were also elevated in L group compared with the other groups (P < 0.05). Compared with H group, the hepatocytes were arranged radially, and hepatic plates anastomosed with each other to form a labyrinth-like structure in L group. Transcriptomic analysis showed 872 differentially expressed genes (DEG) between H and L group, of which 755 were down-regulated and 117 were up-regulated. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 32 pathways were significantly enriched (Q-value < 0.05), such as the cAMP signaling pathway, Th1 and Th2 cell differentiation, leukocyte transendothelial migration, platelet activation and adipocytokine signaling pathway. Additionally, the expression of comment DEGs were verified via quantitative reverse-transcription polymerase chain reaction. Conclusion In summary, our findings suggest that wheat can be supplemented up to 10% in Tibetan sheep, contributing to improve the hepatic oxidative stress, immune response and lipid metabolism through regulating the expression of related genes.

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“…Several studies have revealed that the FABP3 gene is involved in muscle development and meat marbling [29,30]. FABP3 had been identified as a positive effect on the intramuscular fat content or fat deposition in the muscle of pigs or sheep [31][32][33]. The evidence including the validation results of RT-qPCR indicated a high correlation between this gene and the growth and meat production performance phenotypes of the goat population, suggesting that this FABP3 as an important candidate gene for grow period of our crossbred Chongming white goat population.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance

Lin,

Sun,

et al. 2024

BMC Genomics

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Background The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). Results A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. Conclusion This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.

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Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Cited by 10 publications

References 57 publications

Genome‐wide re‐sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China

Genome‐wide re‐sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China

The impact of different levels of wheat diets on hepatic oxidative stress, immune response, and lipid metabolism in Tibetan sheep (Ovis aries)

Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance

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