Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

ShuRu, Cheng; Zhang, Quanwei; He, Yuqin; Zhang, Xia; Yang, Lei; Shi, Jing

doi:10.3390/genes11020183

Cited by 26 publications

(24 citation statements)

References 40 publications

(66 reference statements)

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“…Recently the HEG1 gene was identified as one of several novel genes associated with human skeletal muscle growth, exhibiting a significant correlation with the percentage of change in lean mass [66,67]. In a comparative transcriptomic analysis aimed to identify differentially expressed genes related to product performance and meat quality from the longissimus dorsi in sheep, Cheng et al (2020) [68] identified six differentially expressed genes, including HEG1 [66].…”

Section: Discussionmentioning

confidence: 99%

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Yoshida

Yáñez

2021

BMC Genomics

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Background Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromis niloticus) using genotypes imputed to whole-genome sequences (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13 to 44%, depending on the trait analyzed. The better resolution of the WGS data, combined with the increased power of the mtGWAS approach, allowed the detection of significant markers which were not previously found in the stGWAS. Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions The high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

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Section: Discussionmentioning

confidence: 99%

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Yoshida

Yáñez

2021

BMC Genomics

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“…It was therefore inferred that the number of samples has no adverse effect on our results. Finally, in previous studies about the transcriptome profiles of the skeletal muscle in sheep ( Arora et al, 2019 ; Cheng et al, 2020 ), cattle ( Cassar-Malek et al, 2017 ; Zhang et al, 2018 ) and goats ( Lin et al, 2017 ; Wang et al, 2017 ; Zhan et al, 2018 ), the number of samples per condition was less than four.…”

Section: Discussionmentioning

confidence: 97%

“…The wingless-type MMTV integration site family (Wnt), mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-kinase (PI3K)-Akt signaling pathways have been reported to play key roles in myogenesis, muscle growth, regeneration and differentiation in mice ( Tajbakhsh et al, 1998 ; Liu et al, 2017 ), chicken ( Elia et al, 2007 ; Abu-Elmagd et al, 2010 ), and human ( Otto et al, 2008 ; Kornasio et al, 2009 ). In recent years, RNA-Seq has been widely used to analyze genetic mechanisms underlying skeletal muscle growth and development in pigs ( Óvilo et al, 2014 ; Xu et al, 2018 ), cattle ( Silva-Vignato et al, 2017 ; Zhang et al, 2018 ), and sheep ( Sun et al, 2016 ; Cheng et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

Hao

Wang

et al. 2021

Front. Genet.

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Carcass weight, meat quality and muscle components are important traits economically and they underpin most of the commercial return to goat producers. In this study, the Longissimus dorsi muscle tissues were collected from five Liaoning cashmere (LC) goats and five Ziwuling black (ZB) goats with phenotypic difference in carcass weight, some meat quality traits and muscle components. The histological quantitative of collagen fibers and the transcriptome profiles in the Longissimus dorsi muscle tissues were investigated using Masson-trichrome staining and RNA-Seq, respectively. The percentage of total collagen fibers in the Longissimus dorsi muscle tissues from ZB goats was less than those from LC goats, suggesting that these ZB goats had more tender meat. An average of 15,919 and 15,582 genes were found to be expressed in Longissimus dorsi muscle tissues from LC and ZB goats, respectively. Compared to LC goats, the expression levels of 78 genes were up-regulated in ZB goats, while 133 genes were down-regulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in GO terms related to the muscle growth and development and the deposition of intramuscular fat and lipid metabolism, hippo signaling pathway and Jak-STAT signaling pathway. The results provide an improved understanding of the genetic mechanisms regulating meat production performance in goats, and will help us improve the accuracy of selection for meat traits in goats using marker-assisted selection based on these differentially expressed genes obtained.

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“…MiRNAs are also essential for satellite cell function and muscle development, according to muscle-specific ablation of Dicer, a critical enzyme for the generation of precursor (pre)miRNAs (11). RNA-SEQ has been widely employed in recent years to investigate the genetic mechanisms of skeletal muscle growth and development in various domestic animals (12,13). Muscle-specific miRNAs, such as miR-1, miR-133, and miR-206, have been found to play an essential role in the proliferation, differentiation, and regeneration of skeletal muscle cells in studies (14-16).…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq Reveals miRNA and mRNA Co-regulate Muscle Differentiation in Fetal Leizhou Goats

Zhao

Xue

et al. 2022

Front. Vet. Sci.

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Muscle differentiation is an essential link in animal growth and development, and microRNA and mRNA are indispensable in skeletal muscle differentiation. To improve the meat quality and production of the Leizhou goat, it is vital to understand the molecular mechanism by which its skeletal muscle differentiates. By RNA sequencing (RNA-SEQ), we established miRNA-mRNA profiles of Leizhou goats at three stages: fetal day 70, 90, and 120. There were 991 differently expressed mRNAs and 39 differentially expressed miRNAs found, with the differentially expressed mRNAs mainly enriched in calcium ion binding, ECM-receptor interaction, and Focal adhesion. CKM and MYH3, two muscle differentiation markers, were significantly differentially expressed during this period. In addition, we found that chi-miR-129-5p, chi-miR-433, and chi-miR-24-3p co-regulate muscle differentiation with their target genes. Finally, we can confirm that muscle differentiation occurred in Leizhou goat between 90 and 120 days of the fetus. This study is helpful to better explore the molecular mechanism of goat muscle differentiation.

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Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

Cited by 26 publications

References 40 publications

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

RNA-Seq Reveals miRNA and mRNA Co-regulate Muscle Differentiation in Fetal Leizhou Goats

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