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 Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0140615 ◽  
Author(s):  
Jingwei Yuan ◽  
Congjiao Sun ◽  
Taocun Dou ◽  
Guoqiang Yi ◽  
LuJiang Qu ◽  
...  
Keyword(s):  
Association Study ◽  
Egg Production ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Production Traits ◽  
Genome Wide

scholarly journals SNPs and GVHD prediction: where to next?

Blood ◽  
2012 ◽  
Vol 119 (22) ◽  
pp. 5066-5068 ◽  
Author(s):  
Anne M. Dickinson
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Candidate Snps ◽  
Cell Transplant ◽  
Nucleotide Polymorphisms ◽  
Hematopoietic Stem ◽  
Novel Approach ◽  
Genome Wide ◽  
Impute Data ◽  
A Genome

The article by Chien at al in this issue of Blood uses a novel approach to assess the role of single nucleotide polymorphisms (SNPs) in acute graft-versus-host disease (GVHD). Using a genome-wide association study (GWAS) employing an Affymetrix GeneChip Genome-Wide Human 500 000 SNP array, they screened 1298 allogeneic hematopoietic stem cell transplant donors and recipients and tested whether the results from 40 previously reported candidate SNPs could be replicated. They also used a novel approach to impute data using IMPUTE software (http://nathgen.stats-ox.ac.uk/impute/impute.html) where the genotyping data were not available.1

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.

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.

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

2020 ◽  
pp. 1-8
Author(s):  
Hamdy Abdel-Shafy ◽  
Mohamed A. A. Awad ◽  
Hussein El-Regalaty ◽  
S. E.-D. El-Assal ◽  
Samy Abou-Bakr
Keyword(s):  
Candidate Genes ◽  
Milk Production ◽  
Genome Wide Association Study ◽  
Potential Candidate ◽  
Production Traits ◽  
Milk Production Traits ◽  
Genome Wide ◽  
Reported Study ◽  
Daily Milk Yield ◽  
Egyptian Buffalo

Abstract The objectives of the current study were to detect putative genomic loci and to identify candidate genes associated with milk production traits in Egyptian buffalo. A total number of 161 479 daily milk yield (DMY) records and 60 318 monthly measures for fat and protein percentages (FP and PP, respectively), along with fat and protein yields (FY and PY, respectively) from 1670 animals were used. Genotyping was performed using Axiom® Buffalo Genotyping 90 K array. Genome-wide association study (GWAS) for each trait was performed using PLINK. After Bonferroni correction, 47 SNPs were associated with one or more milk production traits. These SNPs were distributed over 36 quantitative trait loci (QTL) and located on 20 buffalo chromosomes (BBU). For the 47 SNPs, one was overlapped for three traits (DMY, FY, and PY), six were associated with two traits (one for PP and PY and five for FY and PY) while the rest were associated with only one trait. Out of 36 identified QTL, eleven were overlapped with previously reported loci in buffalo and/or cattle populations. Some of these SNPs are placed within or close to potential candidate genes, for example: TPD52, ZBTB10, RALYL and SNX16 on BBU15, ADGRD1 on BBU17, ESRRG on BBU5 and GRIP1 on BBU4. This is the first reported study between genome-wide markers and milk components in Egyptian buffalo. Our findings provide useful information to explore the genetic mechanisms and relevant genes contributing to the variation in milk production traits. Further confirmation studies with larger population size are necessary to validate the findings and detect the causal genetic variants.

scholarly journals Identification of Candidate Genomic Regions for Chicken Egg Production Traits Based on Genome Wide Association Study

2021 ◽  
Author(s):  
Xiurong Zhao ◽  
Changsheng Nie ◽  
Jinxin Zhang ◽  
Xinghua Li ◽  
Tao Zhu ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Egg Production ◽  
Genome Wide Association Study ◽  
Reproductive Traits ◽  
Genome Wide Association ◽  
Production Traits ◽  
Genome Wide ◽  
Chicken Breeds ◽  
Genomic Regions

Abstract Background: Since the domestication of chicken, various chicken breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic egg yielding differences between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results: We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg production traits or reproductive traits (57 significantly, 91 suggestively). Among them, 18 SNPs overlapped with previously reported quantitative trait loci (QTL), including 13 for egg production and 5 for reproductive traits. Three SNPs were significantly associated with multiple egg production traits, such as egg number, age at first egg, and egg production rate in chickens. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2, KITLG, GHRHR, NCOA1, ITPR1, GAMT, and CAMK4 deserve our attention and further study since they have been reported to be closely related to reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61-48.84Mb on GGA5. In this region, we have repeatedly annotated four genes, in which YY1 and WDR25 have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg production traits. Conclusion: Our study utilized the genomic information from various chicken breeds or populations differed in egg production to understand the molecular genetic mechanisms involved in reproduction traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with reproductive traits, which could help us in developing egg production in chickens.

scholarly journals Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Hehe Liu ◽  
Lei Wang ◽  
Zhanbao Guo ◽  
Qian Xu ◽  
Wenlei Fan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Intake ◽  
Egg Production ◽  
Production Efficiency ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Production Traits ◽  
Pekin Ducks ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks. Results Feed conversation ratio (FCR) was positively correlated with feed intake but negatively correlated with egg-related traits, including egg weight and egg production, both phenotypically and genetically. Estimates of pedigree-based heritability were higher than 0.2 for all traits investigated, except hip-width. Based on whole-genome sequencing data, we conducted genome-wide association studies to identify genomic regions associated with these traits. In total, 11 genomic regions were associated with FCR. No genomic regions were identified as significantly associated with hip-width, total feed intake, average daily feed intake, and total egg production. Analysis of selective sweeps between mallard and Pekin ducks confirmed three of these genomic regions on chromosomes 13, 3 and 6. Within these three regions, variants in candidate genes that were in linkage disequilibrium with the GWAS leader single nucleotide polymorphisms (SNPs) (Chr13:2,196,728, P = 7.05 × 10–14; Chr3:76,991,524, P = 1.06 × 10–12; Chr6:20,356,803, P = 1.14 × 10–10) were detected. Thus, we identified 31 potential candidate genes associated with FCR, among which the strongest candidates are those that are highly expressed in tissues involved in reproduction and nervous system functions of ducks: CNTN4, CRBR, GPR63, KLHL32, FHL5, TRNT1, MANEA, NDUFAF4, and SCD. Conclusions For the first time, we report the identification of genomic regions that are associated with FCR in ducks and our results illustrate the genomic changes that occurred during their domestication and are involved in egg production efficiency.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P &lt; 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

Sign in / Sign up

Export Citation Format

Share Document