A Genome-Wide Association Study of Survival to Unexpected Acute Heat Stress in a F2 Chicken Population
H Asadullahi, R Vaez Torshizi, A Ehsani, A Masoudi
Journal PapersJournal of Agricultural Science and Technology , Volume 23 , Issue 2, 2021 February 1, {Pages 283-292 }
Abstract
Heat stress, or hyperthermia, can have a serious effect on chicken performance in poultry industry in many parts of the world. Both genetics and environment play key role in the performance of a chicken and, therefore, it is important to consider both factors in addressing heat stress. On genetics level, genome-wide association studies have become a popular method for studying heat stress in recent years. A population of 202 F2 chickens was reared for 84 days to find genes and genomic regions affecting growth traits and immune system. But, due to unexpected acute increase in temperature at day 83, 182 birds died (case) and 20 birds remained alive (control). At the age of 70 days, blood sample of all birds was collected to extract their DNA,
Genomic markers play an important role in tracing the flow of genetic causality of observable signals in animals and plants. In farm animals, the participation of male animals in the gene pool of subsequent generations are much higher than female animals and testes are the most important organs of the male reproductive system. This study was conducted to investigate simple sequence repeats (SSR) within the expressed sequence tags (ESTs) in order to classify the Bos taurus testis tissue’s genes for their relationship and specificity with related reproductive domains. A total of 48,549 publicly available EST sequences from cattle testis tissue downloaded from GenBank database, out of which, 10,237 sequences that their library made from test
In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half‐sib families from five hatches derived from reciprocal crosses between an Arian fast‐growing line and an Urmia indigenous slow‐growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12?weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population
Analysis of ovarian tissue transcriptome profile in Shal ewes using RNA-Seq data
Parvin Shariati Gazgazareh, ALI AKBAR MASOUDI, Rasoul Vaez Torshizi, Alireza Ehsani, Zaynab Mousavian
Journal PapersAnimal Production , Volume 22 , Issue 2, 2020 June 21, {Pages 199-209 }
Abstract
The aim of this study was the investigation of gene expression profile in Shal sheep ovarian tissue using RNA sequencing data. For this?purpose, the ovaries of five Shal sheep were isolated after estrous synchronization and their RNA was sequenced using Illumina Hiseq 4000?technology. On average, the data obtained from the sequencing consisted of 26638311 read pairs with 81.08 unique mapping rate. The results?of bioinformatic analyzes revealed the expression of 21085 genes in Shal sheep ovarian tissue, of which 15078 genes had expression mean?above 10. Gene ontology analysis revealed the significant enrichment of 162 GO terms including 41 biological processes, 46 molecular?functions and 75 cellular components. KEGG pathway analysis also ide
Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle
Amir Aliakbari, Alireza Ehsani, Rasoul Vaez Torshizi, Peter L?vendahl, Hadi Esfandyari, Just Jensen, Pernille Sarup
Journal PapersJournal of animal science , 2019 July 5, {Pages }
Abstract
In recent years, metabolomics has been used to clarify the biology underlying biological samples. In the field of animal breeding, investigating the magnitude of genetic control on the metabolomic profiles of animals and their relationships with quantitative traits adds valuable information to animal improvement schemes. In this study, we analyzed metabolomic features (MFs) extracted from the metabolomic profiles of 843 male Holstein calves. The metabolomic profiles were obtained using nuclear magnetic resonance (NMR) spectroscopy. We investigated two alternative methods to control for peak shifts in the NMR spectra, binning and aligning, to determine which approach was the most efficient for assessing genetic variance. Series of u
Immunity-related traits are heritable in chicken, therefore, it is possible to improve the inherent immunity by breeding programs. In this study using the Illumina chicken 60K single nucleotide polymorphisms (SNPs) chip, we performed a set of genome-wide association studies to determine candidate genes and loci responsible for primary and secondary antibody-mediated responses against sheep red blood cell. A F2 population descended from a commercial meat-type breed and an Iranian indigenous chicken was used for this study. Statistical analysis was based on a mixed linear model utilizing genomic relationship matrix to prevent spurious associations. Correction for multiple testing was done by applying 5% and 10% chromosomal false discovery rat
The importance of ascites in the poultry industry warrants a comprehensive systematic review and in-silico modelling to explain responses seen in previous studies in this field. By identifying the genes which are effective and relevant to different indicator traits of ascites in poultry, genes were separated base on chromosomes to determine the most effective chromosome in ascites. Consequently, 12 chromosomes have been discovered as containing effective regions on ascites incidence. Meanwhile, 24 genes including MPPK2, AT1, RhoGTPase, MC4R, CDH6, NOS3, HIF-1A, OSBL6, CCDC141, BMPR2, LEPR, AGTR1, UTS2D, 5HT2B, SST, CHRD, TFRC, CDH13, ACVRL1, ARNT, ACE, ACVRL1, MEF2C, and HTR1A affect ascites according to published studies. The results show
Trend of bias in prediction of genomic estimated breeding values due to selective genotyping in genomic selection schemes in consecutive generations
Seyyed Hasan Hafezian, Jabar Jamali, Mohsen Gholizadeh, Alireza Ehsani
Journal PapersJournal of Livestock Science and Technologies , Volume 7 , Issue 2, 2019 December 1, {Pages 57-63 }
Abstract
The aim of this study was to investigate the trend of bias in genomic estimated breeding values (GEBVs) arising from selective genotyping of the candidate population in an ongoing selection scheme. The bias was calculated as the regression of true breeding values (TBVs) on GEBVs. A simulation study was performed under two scenarios with selection intensities (SI) of 0.798 and 1.755 for three traits with heritability (h 2) of 0.1, 0.25 and 0.4 in 10 consecutive generations. Regression of TBVs on GEBVs was close to one for the first generation when selective genotyping was random, and it continuously receded from one as selection shifted to choose animals with high EBVs from generations 2 to 10. Biasedness became larger with increased SI and
Feed efficiency traits (FETs) are important economic indicators in poultry production. Because feed intake (FI) is a time-dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome-wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lead to an increase in accuracy of selection. Thus, the objectives of this study were to evaluate the accuracy of estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (SNP) genotypes, and to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a total of 312 chickens with p
Genomic loci associated with antibody-mediated immune responses in an F2 chicken population
V Raeesi, A Ehsani, RV Torshizi
Journal Papersanimal , 2018 November 19, {Pages 09-Jan }
Abstract
Immunity-related traits are heritable in chicken, therefore, it is possible to improve the inherent immunity by breeding programs. In this study using the Illumina chicken 60K single nucleotide polymorphisms (SNPs) chip, we performed a set of genome-wide association studies to determine candidate genes and loci responsible for primary and secondary antibody-mediated responses against sheep red blood cell. A F2 population descended from a commercial meat-type breed and an Iranian indigenous chicken was used for this study. Statistical analysis was based on a mixed linear model utilizing genomic relationship matrix to prevent spurious associations. Correction for multiple testing was done by applying 5% and 10% chromosomal false discovery rat
In order to identify loci associated with metabolic traits, a genome-wide association study (GWAS) was carried out in a chicken F2 population derived from a reciprocal cross between Iranian Uromia indigenous chickens and Arian broiler line using Illumina 60K Chicken SNP Beadchip.Six traits including plasma level of triglycerides (TG), cholesterol (Chol), glucose (Glu), total protein (TP), albumin (Alb) and globulin (Glo) were recorded. The association between the identified SNPs and metabolic traits was estimated by general linear model (GLM) and compressed mixed linear model (CMLM).A total of 38 SNPs were identified at the genome-wide significant and suggestive levels, of which five SNPs reached a 5% Bonferroni genome-wide significance (P
Persistence of the semen quality and sperm function is one of the important factors in flock fertility preservation. The aim of this study was to assess the trends of semen and sperm parameters in selected cocks with superior and inferior sperm motility from Iranian native and Arian commercial line. Roosters were grouped into high (HML) and low motility (LML) at the early experiment (27 week). The trends for semen and sperm parameters were monitored during an eight-month period (30–60 weeks). Sperm motility in all groups showed an acceptable range (58–87%). The sperm motility trend of indigenous group was dissimilar to the commercial line. The trend line in the LML group from the indigenous roosters was ascending for the sperm motility,
Persistence of the semen quality and sperm function is one of the important factors in flock fertility preservation. The aim of this study was to assess the trends of semen and sperm parameters in selected cocks with superior and inferior sperm motility from Iranian native and Arian commercial line. Roosters were grouped into high (HML) and low motility (LML) at the early experiment (27 week). The trends for semen and sperm parameters were monitored during an eight-month period (30–60 weeks). Sperm motility in all groups showed an acceptable range (58–87%). The sperm motility trend of indigenous group was dissimilar to the commercial line. The trend line in the LML group from the indigenous roosters was ascending for the sperm motility,
Feed efficiency traits (FETs) are important economic indicators in poultry production. Because feed intake (FI) is a time-dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome-wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lead to an increase in accuracy of selection. Thus, the objectives of this study were to evaluate the accuracy of estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (SNP) genotypes, and to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a total of 312 chickens with p
Using the Illumina 60k SNP chip panel, a genome-wide association study was carried out in order to identify genomic regions underlying lysozyme activity in chicken. Data were collected from an F 2 chicken population originated from reciprocal crosses between Arian broiler line and West Azerbaijan indigenous chicken strains. In this study, the lysozyme activity against Micrococus luteus bacteria, recorded as an indicator for innate immunity. Statistical analysis was based on fixed and mixed linear models to account for population stratifications and avoiding systematic biases generated from sex and hatch. Correction for multiple testing was done by applying a 10% genome-wise false discovery rates as significant threshold. Results showed that
Genomic dissection and prediction of feed intake and residual feed intake traits using a longitudinal model in F2 chickens
H Emamgholi Begli, R Vaez Torshizi, AA Masoudi, A Ehsani, J Jensen
Journal Papers , 2018 January , {Pages }
Abstract
Feed efficiency traits (FETs) are important economic indicators in poultry production. Because feed intake (FI) is a time-dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome-wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lead to an increase in accuracy of selection. Thus, the objectives of this study were to evaluate the accuracy of estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (SNP) genotypes, and to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a total of 312 chickens with p