Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.

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Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle)

PLoS ONE ◽

10.1371/journal.pone.0241848 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0241848

Author(s):

Hyo Jun Lee ◽

Yoon Ji Chung ◽

Sungbong Jang ◽

Dong Won Seo ◽

Hak Kyo Lee ◽

...

Keyword(s):

Text Mining ◽

Genomic Prediction ◽

Causal Variant ◽

Longissimus Dorsi ◽

Nucleotide Polymorphisms ◽

Muscle Area ◽

Eye Muscle ◽

Korean Cattle ◽

Genome Wide ◽

Snp Panels

It was hypothesized that single-nucleotide polymorphisms (SNPs) extracted from text-mined genes could be more tightly related to causal variant for each trait and that differentially weighting of this SNP panel in the GBLUP model could improve the performance of genomic prediction in cattle. Fitting two GRMs constructed by text-mined SNPs and SNPs except text-mined SNPs from 777k SNPs set (exp_777K) as different random effects showed better accuracy than fitting one GRM (Im_777K) for six traits (e.g. backfat thickness: + 0.002, eye muscle area: + 0.014, Warner–Bratzler Shear Force of semimembranosus and longissimus dorsi: + 0.024 and + 0.068, intramuscular fat content of semimembranosus and longissimus dorsi: + 0.008 and + 0.018). These results can suggest that attempts to incorporate text mining into genomic predictions seem valuable, and further study using text mining can be expected to present the significant results.

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Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.17.0154 ◽

2017 ◽

Vol 30 (11) ◽

pp. 1529-1539 ◽

Cited By ~ 7

Author(s):

Yang Cao ◽

Hai-Guo Jin ◽

Hui-Hai Ma ◽

Zhi-Hui Zhao

Keyword(s):

Dna Methylation ◽

Comparative Analysis ◽

Longissimus Dorsi ◽

Longissimus Dorsi Muscle ◽

Dorsi Muscle ◽

Genome Wide

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Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle

Frontiers in Genetics ◽

10.3389/fgene.2021.644091 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kaitlyn R. Daza ◽

Deborah Velez-Irizarry ◽

Sebastian Casiró ◽

Juan P. Steibel ◽

Nancy E. Raney ◽

...

Keyword(s):

Gene Expression ◽

Quantitative Trait Loci ◽

Mirna Expression ◽

Quantitative Trait ◽

Complex Traits ◽

Carcass Composition ◽

Longissimus Dorsi ◽

Expression Quantitative Trait Loci ◽

Genome Wide ◽

Trait Loci

Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry.

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Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Animal Genetics ◽

10.1111/age.13019 ◽

2020 ◽

Author(s):

A. Moscarelli ◽

M. T. Sardina ◽

M. Cassandro ◽

E. Ciani ◽

F. Pilla ◽

...

Keyword(s):

Genome Wide ◽

Brown Cattle

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Comparative genome‐wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs

Animal Genetics ◽

10.1111/age.13029 ◽

2020 ◽

Author(s):

X.‐J. Li ◽

L.‐Q. Liu ◽

H. Dong ◽

J.‐J. Yang ◽

W.‐W. Wang ◽

...

Keyword(s):

Longissimus Dorsi ◽

Methylation Analysis ◽

Comparative Genome ◽

Genome Wide

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Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

BMC Genomics ◽

10.1186/s12864-019-6224-x ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

Author(s):

Jinghang Zhou ◽

Liyuan Liu ◽

Chunpeng James Chen ◽

Menghua Zhang ◽

Xin Lu ◽

...

Keyword(s):

Candidate Genes ◽

Association Studies ◽

Well Being ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Dual Purpose ◽

Genome Wide ◽

Brown Cattle ◽

Dual Purpose Cattle ◽

Resistance Traits

Abstract Background Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995–2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip. Results GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield. Conclusions These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.

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