scholarly journals Mapping QTLs for Breast Muscle Weight in an F2 Intercross between Native Japanese Nagoya and White Plymouth Rock Chicken Breeds

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 754
Author(s):  
Akira Ishikawa ◽  
Bothaina H. Essa ◽  
Sherif M. Nasr ◽  
Sae Suzuki
Keyword(s):  
Muscle Development ◽  
Postnatal Growth ◽  
Breast Muscle ◽  
Chromosome 2 ◽  
Chromosome 4 ◽  
Muscle Weight ◽  
Meat Yield ◽  
Significant Qtls ◽  
Genome Wide ◽  
Chicken Muscle

Nagoya (NAG), a native Japanese chicken breed, has high quality meat but low meat yield, whereas White Plymouth Rock (WPR), a parental breed of commercial broilers, has rapid growth but high body fat. We previously reported three quantitative trait loci (QTLs) for early postnatal growth in 239 F2 chickens between NAG and WPR breeds. In this study, using the same F2 chickens at 4 weeks of age, we performed genome-wide QTL analysis for breast muscle weight, fat weight and serum and liver levels of biochemical parameters. Two significant QTLs for pectoralis minor and/or major weights were revealed on chromosome 2 between 108 Mb and 127 Mb and chromosome 4 between 10 Mb and 68 Mb. However, no QTL for the other traits was detected. The two QTLs explained 7.0–11.1% of the phenotypic variances, and their alleles derived from WPR increased muscle weights. The chromosome 2 QTL may be a novel locus, whereas the chromosome 4 QTL coincided with a known QTL for meat quality. The findings provide information that is beneficial for genetic improvement of meat yield for the lean NAG breed and, furthermore, provide a better understanding of the genetic basis of chicken muscle development.

scholarly journals Betaine and Antioxidants Improve Growth Performance, Breast Muscle Development and Ameliorate Thermoregulatory Responses to Cyclic Heat Exposure in Broiler Chickens

Animals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 162 ◽  
Author(s):  
Majid Shakeri ◽  
Jeremy Cottrell ◽  
Stuart Wilkinson ◽  
Mitchell Ringuet ◽  
John Furness ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Muscle Development ◽  
Average Daily Gain ◽  
Heat Exposure ◽  
Basal Diet ◽  
Breast Muscle ◽  
Broiler Chicks ◽  
Poultry Production ◽  
Feed Conversion ◽  
Muscle Weight

Heat stress (HS) is an environmental stressor challenging poultry production and requires a strategy to cope with it. A total of 288-day-old male broiler chicks were fed with one of the following diets: basal diet, basal with betaine (BET), or with selenium and vitamin E (AOX), or with a combination of BET and AOX, under thermoneutral and cyclic HS. Results showed that HS reduced average daily feed intake (ADFI) (p = 0.01) and average daily gain (ADG) (p < 0.001), and impaired feed conversion ratio (FCR) (p = 0.03) during rearing period (0–42 day). BET increased ADG (p = 0.001) and decreased FCR (p = 0.02), whereas AOX had no effects. Breast muscle weight was decreased by HS (p < 0.001) and increased by BET (p < 0.001). Rectal temperature was increased by HS (p < 0.001) and improved by BET overall. Respiration rate was increased by HS (p < 0.001), but BET decreased it during HS (p = 0.04). Jejunum transepithelial resistance was reduced by HS and had no effect on permeability whereas BET increased jejunum permeability (p = 0.013). Overall, the reductions in ADG of broiler chickens during HS were ameliorated by supplementation with BET, with much of the increase in ADG being breast muscle.

scholarly journals Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

2018 ◽  
Author(s):  
Mohamed Salem ◽  
Rafet Al-Tobasei ◽  
Ali Ali ◽  
Daniela Lourenco ◽  
Guangtu Gao ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Muscle Development ◽  
Genetic Variance ◽  
Cold Water ◽  
Additive Genetic Variance ◽  
Genome Wide Association ◽  
Production Traits ◽  
Significant Qtls ◽  
Snp Chip ◽  
Genome Wide

AbstractDetection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ≥ 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

scholarly journals Recombinant inbred strain and interspecific backcross analysis of molecular markers flanking the murine agouti coat color locus.

Genetics ◽  
1989 ◽  
Vol 122 (3) ◽  
pp. 669-679
Author(s):  
L D Siracusa ◽  
A M Buchberg ◽  
N G Copeland ◽  
N A Jenkins
Keyword(s):  
Molecular Markers ◽  
Inbred Strain ◽  
Mouse Chromosome ◽  
Recombinant Inbred ◽  
Recombinant Inbred Strain ◽  
Interspecific Backcross ◽  
Chromosome 2 ◽  
Chromosome 4 ◽  
Agouti Locus ◽  
Mouse Chromosome 2

Abstract Recombinant inbred strain and interspecific backcross mice were used to create a molecular genetic linkage map of the distal portion of mouse chromosome 2. The orientation and distance of the Ada, Emv-13, Emv-15, Hck-1, Il-1a, Pck-1, Psp, Src-1 and Svp-1 loci from the beta 2-microglobulin locus and the agouti locus were established. Our mapping results have provided the identification of molecular markers both proximal and distal to the agouti locus. The recombinants obtained provide valuable resources for determining the direction of chromosome walking experiments designed to clone sequences at the agouti locus. Comparisons between the mouse and human genome maps suggest that the human homolog of the agouti locus resides on human chromosome 20q. Three loci not present on mouse chromosome 2 were also identified and were provisionally named Psp-2, Hck-2 and Hck-3. The Psp-2 locus maps to mouse chromosome 14. The Hck-2 locus maps near the centromere of mouse chromosome 4 and may identify the Lyn locus. The Hck-3 locus maps near the distal end of mouse chromosome 4 and may identify the Lck locus.

scholarly journals Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness

2006 ◽  
Vol 38 (1) ◽  
pp. 85 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Frédérique Pitel ◽  
Wilfrid Carré ◽  
Behnam Abasht ◽  
Pascale Le Roy ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Breast Muscle ◽  
Muscle Weight ◽  
Trait Loci ◽  
Abdominal Fatness ◽  
Meat Type

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

2009 ◽  
Vol 37 (1) ◽  
pp. 629-636 ◽  
Author(s):  
Haifang Qiu ◽  
Xuewen Xu ◽  
Bing Fan ◽  
Max F. Rothschild ◽  
Yerle Martin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Development ◽  
Chromosome 2

scholarly journals Comprehensive Proteomic Characterization of the Pectoralis Major at Three Chronological Ages in Beijing-You Chicken

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Zhang ◽  
Jing Cao ◽  
Ailian Geng ◽  
Haihong Wang ◽  
Qin Chu ◽  
...  
Keyword(s):  
Meat Quality ◽  
Muscle Development ◽  
Expression Profiles ◽  
Pectoralis Major ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
Chronological Age ◽  
Chicken Breast ◽  
Group 13 ◽  
Oocyte Meiosis

Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the chronological age of 90, 120, and 150 days. Each chronological age contained 3 pooling samples or 15 birds (five birds per pooling sample). A total of 1,413 proteins were identified in chicken breast muscle with FDR &lt; 1% and 197 of them were differentially expressed (fold change ≥1.2 or ≤0.83 and p &lt; 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. In summary, these results provided some candidate protein-coding genes for further functional validation and contribute to a comprehensive understanding of muscle development and age-dependent meat quality regulation by proteins in chickens.

scholarly journals Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

2020 ◽  
Author(s):  
Catherine Stein ◽  
Penelope Bencheck ◽  
Jacquelaine Bartlett ◽  
Robert P Igo ◽  
Rafal S Sobota ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Sub Saharan Africa ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Chromosome 5 ◽  
Epigenetic Marks ◽  
Genome Wide ◽  
A Genome ◽  
Immunodeficiency Virus ◽  
Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

scholarly journals Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

2021 ◽  
Vol 9 ◽  
Author(s):  
Weihua Tian ◽  
Zhang Wang ◽  
Dandan Wang ◽  
Yihao Zhi ◽  
Jiajia Dong ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Intramuscular Fat ◽  
Breast Muscle ◽  
Chromatin Interaction ◽  
Chicken Breast ◽  
Meat Production ◽  
Skeletal Muscle Development ◽  
Significant Difference ◽  
Imf Content

Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.

scholarly journals Copy Number Variation in SOX6 Contributes to Chicken Muscle Development

Genes ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 42 ◽  
Author(s):  
Shudai Lin ◽  
Xiran Lin ◽  
Zihao Zhang ◽  
Mingya Jiang ◽  
Yousheng Rao ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Muscle Development ◽  
Chicken Muscle ◽  
Number Variation

scholarly journals Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data

2020 ◽  
Vol 42 (4) ◽  
pp. 393-403
Author(s):  
Donghe Li ◽  
Hahn Kang ◽  
Sanghun Lee ◽  
Sungho Won
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Longitudinal Data ◽  
Density Lipoprotein ◽  
Phenotypic Traits ◽  
Chromosome 2 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Longitudinal Changes ◽  
Genome Wide ◽  
A Genome

Abstract Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

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