Effects of LEP, GYS1, MYOD1, and MYF5 polymorphisms on pig economic traits

Park, Sang-Je; Ha, Ji Hee; Kim, Il-Suk; Kwon, Seul Gi; Hwang, Jung Hye; Park, Da Hye; Kang, Dong Jin; Kim, Tae Wan; Kim, Sam Woong; Kim, Chul Wook

doi:10.1515/aoas-2015-0022

Cited by 5 publications

(4 citation statements)

References 19 publications

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“…Examining the transcription factor sub-network, many of the key transcription factor hubs have been linked with feed efficiency, growth, intake, or carcass traits across species. Genes linked directly to feed efficiency include IRX3 in Australian Angus cattle [ 41 ], LHX3 in crossbred U.S. beef cattle [ 42 ], MYOD1 in Landrace swine [ 43 ], and ETS1 in Duroc swine [ 44 ] and commercial broiler chickens [ 45 ]. Other genes have been linked to muscle hypertrophy and lean growth, which was observed in this study to be enhanced in progeny of the low RFI sire.…”

Section: Discussionmentioning

confidence: 99%

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

et al. 2016

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Improvement in feed conversion efficiency can improve the sustainability of beef cattle production, but genomic selection for feed efficiency affects many underlying molecular networks and physiological traits. This study describes the differences between steer progeny of two influential Angus bulls with divergent genomic predictions for residual feed intake (RFI). Eight steer progeny of each sire were phenotyped for growth and feed intake from 8 mo. of age (average BW 254 kg, with a mean difference between sire groups of 4.8 kg) until slaughter at 14–16 mo. of age (average BW 534 kg, sire group difference of 28.8 kg). Terminal samples from pituitary gland, skeletal muscle, liver, adipose, and duodenum were collected from each steer for transcriptome sequencing. Gene expression networks were derived using partial correlation and information theory (PCIT), including differentially expressed (DE) genes, tissue specific (TS) genes, transcription factors (TF), and genes associated with RFI from a genome-wide association study (GWAS). Relative to progeny of the high RFI sire, progeny of the low RFI sire had -0.56 kg/d finishing period RFI (P = 0.05), -1.08 finishing period feed conversion ratio (P = 0.01), +3.3 kg^0.75 finishing period metabolic mid-weight (MMW; P = 0.04), +28.8 kg final body weight (P = 0.01), -12.9 feed bunk visits per day (P = 0.02) with +0.60 min/visit duration (P = 0.01), and +0.0045 carcass specific gravity (weight in air/weight in air—weight in water, a predictor of carcass fat content; P = 0.03). RNA-seq identified 633 DE genes between sire groups among 17,016 expressed genes. PCIT analysis identified >115,000 significant co-expression correlations between genes and 25 TF hubs, i.e. controllers of clusters of DE, TS, and GWAS SNP genes. Pathway analysis suggests low RFI bull progeny possess heightened gut inflammation and reduced fat deposition. This multi-omics analysis shows how differences in RFI genomic breeding values can impact other traits and gene co-expression networks.

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Section: Discussionmentioning

confidence: 99%

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

et al. 2016

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“…It can be recommended as a marker for PCR-RFLP, but need to shift 250 bp target sequence to the right (down stream). Park et al (2015) reported that LEP/HindIII polymorphisms were significantly different for the average daily gain (ADG) in Duroc pigs (P<0.05). Kurlyana (2022) reported that detection of the leptin gene in Bali cattle found 3 SNP at positions g.2913 C>T, g.3260 T>C and g.3549 G>A and resulted in seven types of Bali cattle.…”

Section: Discussionmentioning

confidence: 99%

Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database

ERMAWATI

PANJONO²,

BINTARA³

et al. 2022

Biodiversitas

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Abstract. Ermawati D, Panjono, Bintara S, Hartatik T. 2022. Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database. Biodiversitas 23: 5614-5620. Genetic marker method that is often used to select cattle is Single Polymorphism Nucleotide (SNP). Single Polymorphisms Nucleotide (SNP) has been found in various candidate genes, one of which is the leptin gene. Leptin is a gene that affects reproduction and cattle weight. Therefore, this research aims to identify SNP of the leptin gene (exon 3) in Crossbred cattle by comparison with GenBank data. A sample of Crossbred cattle was taken from Klaten in Central Java, Indonesia. Afterward, DNA sequencing results were analyzed with BioEdit to identify SNP. BioEdit software was used for DNA sequencing alignment part of intron 2, exon 3 and 3'UTR. The MEGA 11.1.1 program was used to analyze and edit the genetic distance and phylogenetic tree based on the SNP leptin gene. The result shows that nine variations of SNPs were found in exon 3. The phylogenetic tree shows that the Crossbred cattle, Bos taurus, Bos indicus, Hereford, Friesian Holstein and Bali, were in the same cluster. HindIII restriction enzyme can be recommended for genotyping Crossbred cattle using PCR RFLP. This research provides information on SNP in the leptin gene so that it can be used for further research on the association of the leptin gene to growth and reproduction.

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“…Moreover, LEP was also shown as a core gene that connects main pathways such as lipid catabolic process, inositol lipid-mediated signaling, and protein kinase B signaling in network analysis ( Figure 4 A). LEP has been associated with adipose tissue causing polymorphisms and regulating porcine hormones [ 41 , 42 , 43 ]. In addition, LEP has been found to prevent obesity by contributing to lipolysis metabolism [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

Regulation of Swine Growth by Backfat Tissue during Growing and Finishing Stages

Seo

Lim

Kim

et al. 2021

Animals

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Recently, interest in the function of pig backfat (BF) has increased in the field of livestock animals, and many transcriptome-based studies using commercial pig breeds have been conducted. However, there is a lack of comprehensive studies regarding the biological mechanisms of Korean native pigs (KNPs) and Yorkshire pig crossbreeds. In this study, therefore, BF samples of F1 crossbreeds of KNPs and Yorkshire pigs were investigated to identify differentially expressed genes (DEGs) and their related terms using RNA-sequencing analysis. DEG analysis identified 611 DEGs, of which 182 were up-regulated and 429 were down-regulated. Lipid metabolism was identified in the up-regulated genes, whereas growth and maturation-related terminologies were identified in the down-regulated genes. LEP and ACTC1 were identified as highly connected core genes during functional gene network analysis. Fat tissue was observed to affect lipid metabolism and organ development due to hormonal changes driven by transcriptional alteration. This study provides a comprehensive understanding of BF contribution to crossbreeds of KNPs and Yorkshire pigs during growth periods.

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Effects of LEP, GYS1, MYOD1, and MYF5 polymorphisms on pig economic traits

Cited by 5 publications

References 19 publications

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database

Regulation of Swine Growth by Backfat Tissue during Growing and Finishing Stages

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