Detection of novel SNPs and mapping of the fatness QTL on pig chromosome 7q1.1-1.4 region

Huang, Wei-Nan; Ma, Zhiyan; Xu, Zaiyan; Xiong, Yuan; Zuo, Bo

doi:10.4238/2011.december.14.2

Cited by 5 publications

(3 citation statements)

References 21 publications

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“…One is apolipoprotein B mRNA-editing enzyme catalytic subunit 2 (APOBEC2), which is expressed in the muscle and affects muscle fiber ratio and body mass in mice (Sato et al, 2010). Another is the MyoD family inhibitor (MDFI) that was proposed as a suggestive candidate gene for a QTL that affects fatness traits in pigs (Huang et al, 2011). Finally, also the interval around the significant marker found on BTA19 included different genes of potential interest.…”

Section: Association Studymentioning

confidence: 99%

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Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel

Macciotta

Gaspa

Bomba

et al. 2015

Journal of Dairy Science

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High-throughput cow genotyping has opened new perspectives for genome-wide association studies (GWAS). Directly recorded phenotypes and several records per animal could be used. In this study, a GWAS on lactation curve traits of 337 Italian Simmental cows genotyped with the Illumina (San Diego, CA) low-density BeadChip (7K) was carried out. Scores of the first 2 principal components extracted from test-day records (7 for each lactation) for milk yield, fat and protein percentages, and somatic cell score were used as phenotypes. The first component described the average level of the lactation curve, whereas the second summarized its shape. Data were analyzed with a mixed linear model that included fixed effects of herd, calving month, calving year, parity, SNP genotype, and random effects of animal and permanent environment. All statistically significant markers (Bonferroni corrected) were associated with the average level component (2 for milk yield, 9 for fat percentage, 6 for protein percentages, and 1 for somatic cell score). No markers were found to be associated with the lactation curve shape. Gene discovery was performed using windows of variable size, according to the linkage disequilibrium level of the specific genomic region. Several suggestive candidate genes were identified, some of which already reported to be associated with dairy traits, such as DGAT1. Others were involved in lipid metabolism, in protein synthesis, in the immune response, in cellular processes, and in early development. The large number of genes flagged in the present study suggests interesting perspectives for the use of low-density genotyped females for GWAS, also for novel phenotypes that are not currently considered as breeding goals.

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Section: Association Studymentioning

confidence: 99%

“…Another interesting gene located close to the significant marker is the lymphocyte cytosolic protein 1 (LCP1), a highly conserved protein of the cattle genome (Lemay et al, 2009). The expression of this gene in the mammary tissue has been found to be associated with infections by Staphylococcus aureus (Huang et al, 2014).…”

Section: Association Studymentioning

confidence: 99%

Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel

Macciotta

Gaspa

Bomba

et al. 2015

Journal of Dairy Science

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“…A significant quantitative trait loci (QTL) for backfat thickness (BFT) has been consistently mapped to sus scrofa chromosomes 7 (SSC7) p1.1-q1.4 in several pig populations [ 23 – 31 ]. Using the F 2 resource population derived from the intercross of Large White boars and Meishan dams, we have identified significant QTLs for carcass and meat quality traits on SSC7 [ 23 , 32 ]. Haplotypes of the porcine PPARD gene are associated with backfat thickness [ 33 ], and PPARD gene also functions in fatty acid metabolism and fat metabolism [ 34 ].…”

Section: Introductionmentioning

confidence: 99%

The Functional SNPs in the 5’ Regulatory Region of the Porcine PPARD Gene Have Significant Association with Fat Deposition Traits

Zhang

Gao

et al. 2015

PLoS ONE

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Peroxisome proliferator-activated receptor delta (PPARD) is a key regulator of lipid metabolism, insulin sensitivity, cell proliferation and differentiation. In this study, we identified two Single Nucleotide Polymorphisms (SNPs, g.1015 A>G and g.1018 T>C) constituting four haplotypes (GT, GC, AC and AT) in the 5’ regulatory region of porcine PPARD gene. Functional analysis of the four haplotypes showed that the transcriptional activity of the PPARD promoter fragment carrying haplotype AC was significantly lower than that of the other haplotypes in 3T3-L1, C2C12 and PK-15 cells, and haplotype AC had the lowest binding capacities to the nuclear extracts. Transcription factor 7-like 2 (TCF7L2) enhanced the transcription activities of promoter fragments of PPARD gene carrying haplotypes GT, GC and AT in C2C12 and 3T3-L1 cells, and increased the protein expression of PPARD gene in C2C12 myoblasts. TCF7L2 differentially bound to the four haplotypes, and the binding capacity of TCF7L2 to haplotype AC was the lowest. There were significant associations between -655A/G and fat deposition traits in three pig populations including the Large White × Meishan F2 pigs, France and American Large White pigs. Pigs with genotype GG had significantly higher expression of PPARD at both mRNA and protein level than those with genotype AG. These results strongly suggested that the SNPs in 5’ regulatory region of PPARD genes had significant impact on pig fat deposition traits.

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Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

Yang,

Wang,

Huang

et al. 2024

Genome Biol

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Background Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. Results We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. Conclusions Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

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Detection of novel SNPs and mapping of the fatness QTL on pig chromosome 7q1.1-1.4 region

Cited by 5 publications

References 21 publications

Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel

Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel

The Functional SNPs in the 5’ Regulatory Region of the Porcine PPARD Gene Have Significant Association with Fat Deposition Traits

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

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