scholarly journals Associations of IGF2 and DRD2 polymorphisms with laying traits in Muscovy duck

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4083 ◽  
Author(s):  
Qiao Ye ◽  
Jiguo Xu ◽  
Xinfeng Gao ◽  
Hongjia Ouyang ◽  
Wei Luo ◽  
...  
Keyword(s):  
Growth Factor ◽  
Egg Production ◽  
Follicular Development ◽  
Egg Laying ◽  
Muscovy Duck ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Muscovy Ducks

Insulin-like growth factor 2 (IGF2) and dopamine receptor 2 (DRD2) play important roles in ovarian follicular development. In this study, we analyzed tissue-specific expression of the Muscovy duck IGF2 and DRD2 genes and cloned those genes transcripts. Polymorphisms in these genes were tightly linked with egg production traits and both genes were highly expressed in the ovary. Moreover, we identified five single nucleotide polymorphisms (SNPs) for IGF1 and 28 for DRD2. Mutations A-1864G and C-1704G of IGF2 were positively correlated with increased egg laying at 59 weeks (E59W) (P < 0.05). The C+7T and C+364G mutations of DRD2 were highly and significantly associated with first-egg age (FEA) and egg numbers at 300 days (E300D) (P < 0.01). Moreover, C+3301G and C+3545G of DRD2 were highly significantly associated with FEA, E59W and E300D (P < 0.01). Other mutations were positively associated with FEA or E300D or E59W (P < 0.05). These data suggest specific roles for IGF1 and DRD2 polymorphisms in egg production in Muscovy ducks.

New polymorphisms of PAPPA and PAPPA2 genes and their associations with egg production traits in Chinese Dagu chickens

2017 ◽  
Author(s):  
D. Liu ◽  
X. L. Niu ◽  
T. L. Tyasi ◽  
N. Qin ◽  
H. Zhu ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Egg Production ◽  
Protein A ◽  
Follicular Development ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide ◽  
Egg Weight ◽  
Conformation Polymorphism

Pregnancy-associated plasma protein A, pappalysin1 (PAPPA) and pappalysin2 (PAPPA2) genes were implicated in regulation of hen ovarian follicular development and growth. Four novel single nucleotide polymorphisms (SNPs) were identified using PCR-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing. Among them, A/G transition at position 172864 and T/C mutation at position 172952 in 3‘-untranslated region (UTR) of PAPPA named SNP A172864G and T172952C, respectively. A/G transition at position 77421 and T/C at position 77455 in 3‘-UTR of PAPPA2 gene named as SNP A77421G and T77455C, respectively. For SNP A172864G and T172952C (PAPPA), 360 Dagu hens were classified as AA, AB and BB genotypes based on PCR-SSCP patterns, and BB genotype correlated significantly (P less than 0.05) with higher hen-housed egg production (HHEP) at 30 and 57 weeks (wks) of age and higher egg weight (EW) at 43 wks of age. Consequently, these SNPs identified will be potential genetic markers to improve egg productivity in chicken breeding.

scholarly journals Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 384 ◽  
Author(s):  
Syed Ali Azmal ◽  
Ali Akbar Bhuiyan ◽  
Abdullah Ibne Omar ◽  
Shuai Ma ◽  
Chenghao Sun ◽  
...  
Keyword(s):  
Association Analysis ◽  
Egg Production ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Egg Laying ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Nucleotide Exchange ◽  
Genome Wide

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.

scholarly journals The Association Between Novel Polymorphisms of Gremlin Genes and Egg-Laying Performance Traits in Chinese Village Dagu Hens

2018 ◽  
Vol 18 (2) ◽  
pp. 361-373 ◽  
Author(s):  
Thobela Louis Tyasi ◽  
Ning Qin ◽  
Dehui Liu ◽  
Xiaotian Niu ◽  
Hongyan Zhu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Egg Production ◽  
Single Strand Conformation Polymorphism ◽  
Synonymous Substitution ◽  
Egg Laying ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Coding Region ◽  
Laying Performance ◽  
Performance Traits

Abstract Gremlin (GREM1, GREM2) genes are the known bone morphogenetic proteins (BMPs) inhibitors, but their genetic diversity in animal species remains unknown. The current study was conducted to investigate single nucleotide polymorphisms (SNPs) in chicken GREM1 and GREM2 genes, and their association with egg production traits using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and deoxyribonucleic acid (DNA) sequencing. The results discovered novel SNPs and, among these variations, C/T transition at position 436 in exon 1 of the GREM1 gene leads to synonymous substitution of amino acids, and T/C transition at position 690 in the coding region of the GREM2 gene leads to a non-synonymous substitution of amino acids (valine acid 114-to-alanine acid). Association analysis established that at the age of 43, 57 and 66 wks, hen-house egg production (HHEP) was more highly significantly associated (P<0.05) with the AA genotype in the GREM1 gene. In the GREM2 gene, the TC genotype was remarkably linked with higher HHEP at the age of 30, 57 and 66 wks. Our results provide evidence that the GREM1 and GREM2 genes have potential effects on HHEP in chickens. SNPs determined in this work may be utilised as favourable potential DNA markers for improving of egg-laying performance traits.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

Sign in / Sign up

Export Citation Format

Share Document