scholarly journals Using targeted re-sequencing for identification of candidate genes and SNPs for a QTL affecting the pH value of chicken muscle

2015 ◽  
Author(s):  
Xidan Li ◽  
Xiaodong Liu ◽  
Javad Nadaf ◽  
Elisabeth Le Bihan-Duval ◽  
Cécile Berri ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Ph Value ◽  
Sequence Data ◽  
Chromosome 1 ◽  
Chicken Breast ◽  
Candidate Snps ◽  
Post Mortem ◽  
Synonymous Snps ◽  
Chicken Muscle ◽  
Genetic Mechanisms

Using targeted genetical genomics, a QTL affecting the initial post-mortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) was recently fine-mapped. Thirteen genes were present in the QTL region of about 1 Mb. In this study, ten birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for re-sequencing. After enrichment for 1 Mb around the QTL region, > 200 x coverage for the QTL region in each of the ten birds was obtained. We used custom tools to identify putative causal mutations in the mapped QTL region from next generation sequence data. Four non-synonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B and E1BTD2). These were defined to be most likely candidate SNPs to explain the QTL effect. Moreover, 29 consensus SNPs were detected within gene-related regions (UTR regions and splicing sites) for the QQ birds and 26 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial post-mortem pH value of chicken muscle.

scholarly journals Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

PheGee@Home

2012 ◽  
pp. 1885-1903
Author(s):  
Bertil Schmidt ◽  
Chen Chen ◽  
Weiguo Liu ◽  
Wayne P. Mitchell
Keyword(s):  
Comparative Genomics ◽  
Environmental Factors ◽  
Candidate Genes ◽  
Sequence Data ◽  
Computer Architectures ◽  
Graphics Hardware ◽  
Microbial Genomes ◽  
Genetically Determined ◽  
Physical Manifestation ◽  
Grid Based

In this chapter we present PheGee@Home, a grid-based comparative genomics tool that nominates candidate genes responsible for a given phenotype. A phenotype is the physical manifestation of the interplay of genetic, epigenetic and environmental factors. Our tool is designed to facilitate the discovery and prioritization of candidate genes controlling or contributing to the genetically determined portion of a specified phenotype. However, in order to make reliable nominations of candidate genes from sequence data, several genome-size sequence datasets are required. This makes the approach impractical on traditional computer architectures leading to prohibitively long runtimes. Therefore, we use a computational architecture based on a desktop grid environment and commodity graphics hardware to significantly accelerate PheGee. We validate this approach by showing the deployment and evaluation on a grid testbed for the comparison of microbial genomes.

scholarly journals PSVI-1 Improvement of gut morphology and meat quality of broiler chickens by encapsulated citral and cinnamaldehyde

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 195-195
Author(s):  
Chongwu Yang ◽  
Janghan Choi ◽  
Marion Mogire ◽  
Argenis Rodas-González ◽  
Moussa S Diarra ◽  
...  
Keyword(s):  
Growth Performance ◽  
Meat Quality ◽  
Ph Value ◽  
Basal Diet ◽  
Positive Control ◽  
Negative Control ◽  
Intestinal Morphology ◽  
Post Mortem ◽  
Gut Morphology

Abstract This study investigated the effects of encapsulated citral (CIT) and cinnamaldehyde (CIN) on growth performance, intestinal morphology and meat quality in broilers. A total of 320 0-day-age male broilers (Cobb 500) were allocated 32 pens with 8 pens per treatment. The treatments included: 1) Corn-wheat-SBM basal diet (negative control); 2) basal diet with 30 ppm avilamycin premix (positive control); 3) basal diet with 50 ppm encapsulated CIT and CIN (CCL); 4) basal diet with 100 ppm encapsulated CIT and CIN (CCH). There were no significant differences between treatments in growth performance (P > 0.05) at each feeding stage. Additionally, birds had similar relative organ weights of heart, liver, spleen and bursa (P > 0.05). The higher ratios of villus height to crypt depth (VCR; P ≤ 0.05) were detected in broilers fed either CCL or CCH, with an average being 14.67 and 15.13 in the duodenum, and 15.13 and 13.58 in the jejunum, respectively. Regarding meat quality, a higher pH value (pH = 6.21) in the breast was observed in 24-h post mortem chickens fed CCL (P ≤ 0.05). No significant differences of pH were detected in the breast in 96-h post mortem birds. The breast color (redness, yellowness, and lightness) in either 24-h or 96-h post mortem chickens was not significantly different among treatments (P > 0.05). No change in purge loss (%) was observed in the breast after 48 h. The severity of white striping (WS) or woody meat (WB) was higher in the positive control (WS = 0.58; WB = 0.15) than in other treatments (P ≤ 0.05). In conclusion, dietary treatment with encapsulated CIT and CIN improved gut morphology and meat quality of broilers by increasing VCR in the small intestine and reducing the severity of WS/WB in the breast, respectively, without affecting growth performance.

Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens

Genome ◽  
2020 ◽  
Vol 63 (3) ◽  
pp. 133-143 ◽  
Author(s):  
Jun Guo ◽  
Liang Qu ◽  
Tao-Cun Dou ◽  
Man-Man Shen ◽  
Yu-Ping Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linear Mixed Model ◽  
Bone Size ◽  
Chromosome 1 ◽  
Meat Production ◽  
Phenotypic Variance ◽  
Femur Length ◽  
Genome Wide ◽  
Length And Area ◽  
Tibia Length

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

scholarly journals The amino acid sequence of the peptide containing the thiol group of creatine kinase from normal and dystrophic chicken breast muscle. Comparison of some of the immunological properties of the antibodies developed in rabbits against these enzymes

1974 ◽  
Vol 143 (1) ◽  
pp. 171-179 ◽  
Author(s):  
Buddha P. Roy
Keyword(s):  
Creatine Kinase ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Thiol Group ◽  
Chicken Breast ◽  
Thiol Groups ◽  
Dystrophic Muscle ◽  
Muscle Enzymes ◽  
Chicken Muscle ◽  
Dystrophic Chicken

The major14C-labelled peptides from creatine kinase from normal and dystrophic chicken muscle obtained by carboxymethylating the reactive thiol groups with iodo[2-14C]acetic acid and digestion with trypsin were purified by ion-exchange chromatography on Dowex-50 (X2) and by paper electrophoresis. The chromatographic characteristics of the14C-labelled peptides, their electrophoretic mobilities at pH6.5, and their amino acid compositions were identical for the two enzymes. The sequence of amino acids around the essential thiol groups of creatine kinase from normal and dystrophic chicken muscle was shown to be Ile-Leu-Thr-CmCys-Pro-Ser-Asn-Leu-Gly-Thr-Gly-Leu-Arg (CmCys, carboxymethylcysteine). This sequence is almost identical with that for the creatine kinases in human and ox muscle and bovine brain and is very similar to that of arginine kinase from lobster muscle. Antibodies to the enzymes were raised in rabbits and their reaction with the creatine kinase from normal and dystrophic muscles in interfacial, immunodiffusion and immunoelectrophoretic experiments was studied. The cross-reaction between normal muscle creatine kinase and antisera against the dystrophic muscle enzyme (or vice versa) observed by immunodiffusion and by immunoelectrophoretic experiments further suggests that the enzymes from normal and dystrophic chicken muscle are similar in structure. The results of the present study, the identical amino acid sequence of the peptides containing the reactive thiol group from both the normal and dystrophic chicken muscle enzymes and the immunological similarities of the two enzymes are in accord with the similarity of the two enzymes observed by Roy et al. (1970).

scholarly journals Genetic profiling of chromosome 1 in breast cancer: mapping of regions of gains and losses and identification of candidate genes on 1q

2006 ◽  
Vol 95 (10) ◽  
pp. 1439-1447 ◽  
Author(s):  
B Orsetti ◽  
M Nugoli ◽  
N Cervera ◽  
L Lasorsa ◽  
P Chuchana ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Candidate Genes ◽  
Chromosome 1 ◽  
Genetic Profiling ◽  
Gains And Losses

TRANSCRIPT ANNOTATION PRIORITIZATION AND SCREENING SYSTEM (TrAPSS) FOR MUTATION SCREENING

2007 ◽  
Vol 05 (06) ◽  
pp. 1155-1172 ◽  
Author(s):  
BRIAN M. O'LEARY ◽  
STEVEN G. DAVIS ◽  
MICHAEL F. SMITH ◽  
BARTLEY BROWN ◽  
MATHEW B. KEMP ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Information Management ◽  
Sequence Data ◽  
Mutation Screening ◽  
Disease Genes ◽  
Screening System ◽  
Genomic Context ◽  
Significant Information ◽  
Algorithmic Technique ◽  
Protein Functional Domains

When searching for disease-causing mutations with polymerase chain reaction (PCR)-based methods, candidate genes are usually screened in their entirety, exon by exon. Genomic resources (i.e. www.ncbi.nih.gov, www.ensembl.org, and genome.ucsc.edu) largely support this paradigm for mutation screening by making it easy to view and access sequence data associated with genes in their genomic context. However, the administrative burden of conducting mutation screening in potentially hundreds of genes and thousands of exons in thousands of patients is significant, even with the use of public genome resources. For example, the manual design of oligonucleotide primers for all exons of the 10 Leber's congenital amaurosis (LCA) genes (149 exons) represents a significant information management challenge. The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to accelerate mutation screening by (1) providing a gene-based local cache of candidate disease genes in a genomic context, (2) automating tasks associated with optimizing candidate disease gene screening and information management, and (3) providing the implementation of an algorithmic technique to utilize large amounts of heterogeneous genome annotation (e.g. conserved protein functional domains) so as to prioritize candidate genes.

Post-Mortem Changes in Protein Extractability in Beef, Pork, and Chicken Muscle

1967 ◽  
Vol 32 (2) ◽  
pp. 208-209 ◽  
Author(s):  
ELAINE NELSON McINTOSH
Keyword(s):  
Post Mortem ◽  
Chicken Muscle ◽  
Protein Extractability

scholarly journals Molecular Cloning of MSRG-11 Gene Related to Apoptosis of Mouse Spermatogenic Cells

2005 ◽  
Vol 37 (3) ◽  
pp. 159-166 ◽  
Author(s):  
Yun Deng ◽  
Dong-Song Nie ◽  
Jian Wang ◽  
Xiao-Jun Tan ◽  
Zhao-Yan Nie ◽  
...  
Keyword(s):  
Cell Apoptosis ◽  
Sequence Data ◽  
Critical Role ◽  
Chromosome 1 ◽  
Amino Acid Residues ◽  
Spermatogenic Cells ◽  
Iq Motif ◽  
Calmodulin Binding ◽  
New Gene ◽  
Theoretical Molecular Mass

Abstract Beginning with a new contig of the expressed sequence tags (Mm.63892) obtained by comparing testis libraries with other tissue and cell line libraries using the digital differential display program, we cloned a new gene which is related to the apoptosis of mouse spermatogenic cells using the Genscan program and polymerase chain reaction (PCR) technology. The sequence data have been submitted to the GenBank database under accession number AY747687. The full cDNA length is 1074 bp, and the gene with 7 exons and 6 introns is located in mouse chromosome 1 H5. The protein is recognized as a new member of calmodulin (CaM) binding protein family because the sequence contains three short calmodulin-binding motifs containing conserved Ile and Gln residues (IQ motif) and is considered to play a critical role in interactions of IQ motif-containing proteins with CaM proteins. The putative protein encoded by this gene has 192 amino acid residues with a theoretical molecular mass of 23.7 kDa and a calculated isoelectric point of 9.71. The sequence shares no significant homology with any known protein in databases. RT-PCR and Northern blot analyses revealed that 1.3 kb MSRG-11 transcript was strongly expressed in adult mouse testis but weakly expressed in the spleen and thymus. The MSRG-11 gene was expressed at various levels, faintly at two weeks postpartum and strongly from three weeks postpartum in adult testes. The green fluorescence produced by pEGFP-C2/MSRG-11 was detected in the cytoplasm of COS7 cells 24 h post-transfection. The pcDNA3.1(–)/MSRG-11 plasmid was constructed and introduced into COS7 cells using Lipofectamine 2000 transfection reagent (Invitrogen, Carlsbad, USA). MSRG-11 can accelerate COS7 cell apoptosis, which suggests that this gene may play an important role in the development of mouse testes and is a candidate gene of testis-specific apoptosis. Based on these observations, it was considered that we cloned a new gene which probably accelerates spermatogenetic cell apoptosis in mouse.

Sign in / Sign up

Export Citation Format

Share Document