Exploration of genetic variance has mostly been limited to additive effects estimated using pedig... more Exploration of genetic variance has mostly been limited to additive effects estimated using pedigree data and non-additive effects have been ignored. This study aimed to evaluate the performance of single nucleotide polymorphisms (SNPs) marker models in the mixed and orthogonal framework including both additive and non-additive effects for estimating variances and genomic prediction in four diabetes-related traits in heterogeneous stock mice. Models have performed differently in detecting SNPs affecting traits. Dominance variances explained over 14.7 and 3.8% of genetic and phenotype variance in a Genomic prediction and variance component estimation method (GVCBLUP) framework. Reliabilities of additive Genomic best linear unbiased prediction model (GBLUP) in different traits ranged from 44.8 to 66.6%, for GVCBLUPs framework including both additive and dominance effects (MAD), and 46.1 to 69% for the model including additive effect (MA). Dominance GBLUP reliabilities ranged from 6 to...
Aim of study: To select the appropriate model for body weight gain (BWG) traits in different ages... more Aim of study: To select the appropriate model for body weight gain (BWG) traits in different ages and estimation of additive and non-additive genetic variances based on the best model, of a crossbred population of quail. Area of study: Zabol, Iran Materials and methods: Four strains of Japanese quail, including Italian Speckled, Tuxedo, Pharaoh, and A&M Texas, were used to create a crossbred population in a partial diallel design over 4 generations. BWG traits were calculated as the average growth performance of the bird in a 5-day period from hatch to 45 days of age. Analyses were performed using the Bayesian method by fitting 24 models including the additive and non-additive genetic effects. The deviance information criteria (DIC) was used for the selection of an appropriate model for each trait. Main results: Based on DIC, the maternal genetic, maternal permanent environmental, dominance and epistasis effects had a significant contribution to the best model for BWG traits before ...
Objective: Transcriptome study of the desired crossbreed and comparing it with the pure parental ... more Objective: Transcriptome study of the desired crossbreed and comparing it with the pure parental population is a method for evaluating and selecting cross with appropriate products, yet disease resistance, high tolerance to environmental stresses, and compatibility with the climate of the breeding tract. RNA-Sequencing (RNA-seq) technology was employed to investigate the effect of crossbreeding by the Montbeliard cattle on the “Sistani cattle” transcriptome. Blood samples were collected from 90 cows (45 pure and 45 crossbreeds). Total RNA was extracted in the Media Teb Gene Laboratory of Iran. The mRNA selection, library preparation, and sequencing were performed at BGI Shenzhen, China on an Illumina HiSeq 2500 sequencer. After assembling the transcripts with the bovine reference genome, Cuffdiff was used to detect differential gene expression in purebred and its crossbred.Results: In total, 45 significantly differentially expressed genes were identified (false discovery rate q< 0...
Twinning is one of the most important economic traits in goat production, which is influenced by ... more Twinning is one of the most important economic traits in goat production, which is influenced by either small or major gene effects. In recent decades, it has been recognized that two members of growth factors originated from oocytes namely GDF9 and BMP15 are essential for follicular development and ovulation. The aim of the current study was to survey the polymorphism of two GDF9 and BMP15 genes and their genotype patterns association with twining rate in Markhoz goat. Blood samples were randomly taken from 50 Markhoz goats and DNA extraction was performed by a salting-out modified method. Polymerase chain reactions (PCR) were employed to amplify a fragment with 862 base pairs from exon 2 of BMP15 gene and 995 base pairs fragment from exon 2 of GDF9 gene. The PCR products after digestion by Hinf1 enzyme were electrophoresed on 3% agarose gel and the animals' genotypes were determined by banding patterns. In the BMP15 gene, the frequencies of B and b alleles were 0.96 and 0.04, ...
The objective of this study was to investigate the effect of birth weight (BW) on future milk pro... more The objective of this study was to investigate the effect of birth weight (BW) on future milk production and reproductive performance in Iranian Holstein cattle. Records of Holstein cows between 1967 and 2010 were obtained from the Animal Breeding Center of Iran. Birth weights within each herd were grouped into five categories based on the standard normal distribution curves (z ≤0.8416, -0.8416 < z ≤ -0.2533, -0.2533 < z ≤ 0.2533, 0.2533 < z ≤ 0.8416, 0.8416 < z). The results indicated that BW significantly affected (P < 0.001) the lactation parameters (e.g. milk yield, protein yield, fat yield), age at first calving (AFC), interval between calving to first insemination (ICFI), calving intervals (CI), calving ease (CE), and first service to conception length (FSTC) during the first three lactation periods. The BW positively affected the lactation performance, but had a negative effect on the reproductive performance. Increase in BW was unexpectedly associated with inc...
Simple Summary: Iranian native breeds have valuable traits that differentiate from their Western ... more Simple Summary: Iranian native breeds have valuable traits that differentiate from their Western 9 counterparts Sistani cattle (Bos indicus), an important native meat type breed in Iran, are well adapted to 10 the tropical region of Sistan (located in east of Iran). In recent years, the crosses between Sistani and foreign 11 breeds such as Holstein, Simmental and Montbeliarde has grown in Zabol province mainly to increase 12 milk production which will compensate the cost of feed will be considered as well as making the most 13 appropriate cross that will adapted to the climate of Sistan region. In this study differences of purebred 14 Sistani and Sistani × Montbeliarde crossbred populations were studied using RNA-seq technology. We 15 found 45 differentially expressed genes between purebreds Sistani and Sistani × Montbeliarde crossbred. 16 Functional analysis of DEGs showed that the immune and inflammatory responses were the most highly17 impacted pathways and functions. These genes...
Exploration of genetic variance has mostly been limited to additive effects estimated using pedig... more Exploration of genetic variance has mostly been limited to additive effects estimated using pedigree data and non-additive effects have been ignored. This study aimed to evaluate the performance of single nucleotide polymorphisms (SNPs) marker models in the mixed and orthogonal framework including both additive and non-additive effects for estimating variances and genomic prediction in four diabetes-related traits in heterogeneous stock mice. Models have performed differently in detecting SNPs affecting traits. Dominance variances explained over 14.7 and 3.8% of genetic and phenotype variance in a Genomic prediction and variance component estimation method (GVCBLUP) framework. Reliabilities of additive Genomic best linear unbiased prediction model (GBLUP) in different traits ranged from 44.8 to 66.6%, for GVCBLUPs framework including both additive and dominance effects (MAD), and 46.1 to 69% for the model including additive effect (MA). Dominance GBLUP reliabilities ranged from 6 to...
Aim of study: To select the appropriate model for body weight gain (BWG) traits in different ages... more Aim of study: To select the appropriate model for body weight gain (BWG) traits in different ages and estimation of additive and non-additive genetic variances based on the best model, of a crossbred population of quail. Area of study: Zabol, Iran Materials and methods: Four strains of Japanese quail, including Italian Speckled, Tuxedo, Pharaoh, and A&M Texas, were used to create a crossbred population in a partial diallel design over 4 generations. BWG traits were calculated as the average growth performance of the bird in a 5-day period from hatch to 45 days of age. Analyses were performed using the Bayesian method by fitting 24 models including the additive and non-additive genetic effects. The deviance information criteria (DIC) was used for the selection of an appropriate model for each trait. Main results: Based on DIC, the maternal genetic, maternal permanent environmental, dominance and epistasis effects had a significant contribution to the best model for BWG traits before ...
Objective: Transcriptome study of the desired crossbreed and comparing it with the pure parental ... more Objective: Transcriptome study of the desired crossbreed and comparing it with the pure parental population is a method for evaluating and selecting cross with appropriate products, yet disease resistance, high tolerance to environmental stresses, and compatibility with the climate of the breeding tract. RNA-Sequencing (RNA-seq) technology was employed to investigate the effect of crossbreeding by the Montbeliard cattle on the “Sistani cattle” transcriptome. Blood samples were collected from 90 cows (45 pure and 45 crossbreeds). Total RNA was extracted in the Media Teb Gene Laboratory of Iran. The mRNA selection, library preparation, and sequencing were performed at BGI Shenzhen, China on an Illumina HiSeq 2500 sequencer. After assembling the transcripts with the bovine reference genome, Cuffdiff was used to detect differential gene expression in purebred and its crossbred.Results: In total, 45 significantly differentially expressed genes were identified (false discovery rate q< 0...
Twinning is one of the most important economic traits in goat production, which is influenced by ... more Twinning is one of the most important economic traits in goat production, which is influenced by either small or major gene effects. In recent decades, it has been recognized that two members of growth factors originated from oocytes namely GDF9 and BMP15 are essential for follicular development and ovulation. The aim of the current study was to survey the polymorphism of two GDF9 and BMP15 genes and their genotype patterns association with twining rate in Markhoz goat. Blood samples were randomly taken from 50 Markhoz goats and DNA extraction was performed by a salting-out modified method. Polymerase chain reactions (PCR) were employed to amplify a fragment with 862 base pairs from exon 2 of BMP15 gene and 995 base pairs fragment from exon 2 of GDF9 gene. The PCR products after digestion by Hinf1 enzyme were electrophoresed on 3% agarose gel and the animals' genotypes were determined by banding patterns. In the BMP15 gene, the frequencies of B and b alleles were 0.96 and 0.04, ...
The objective of this study was to investigate the effect of birth weight (BW) on future milk pro... more The objective of this study was to investigate the effect of birth weight (BW) on future milk production and reproductive performance in Iranian Holstein cattle. Records of Holstein cows between 1967 and 2010 were obtained from the Animal Breeding Center of Iran. Birth weights within each herd were grouped into five categories based on the standard normal distribution curves (z ≤0.8416, -0.8416 < z ≤ -0.2533, -0.2533 < z ≤ 0.2533, 0.2533 < z ≤ 0.8416, 0.8416 < z). The results indicated that BW significantly affected (P < 0.001) the lactation parameters (e.g. milk yield, protein yield, fat yield), age at first calving (AFC), interval between calving to first insemination (ICFI), calving intervals (CI), calving ease (CE), and first service to conception length (FSTC) during the first three lactation periods. The BW positively affected the lactation performance, but had a negative effect on the reproductive performance. Increase in BW was unexpectedly associated with inc...
Simple Summary: Iranian native breeds have valuable traits that differentiate from their Western ... more Simple Summary: Iranian native breeds have valuable traits that differentiate from their Western 9 counterparts Sistani cattle (Bos indicus), an important native meat type breed in Iran, are well adapted to 10 the tropical region of Sistan (located in east of Iran). In recent years, the crosses between Sistani and foreign 11 breeds such as Holstein, Simmental and Montbeliarde has grown in Zabol province mainly to increase 12 milk production which will compensate the cost of feed will be considered as well as making the most 13 appropriate cross that will adapted to the climate of Sistan region. In this study differences of purebred 14 Sistani and Sistani × Montbeliarde crossbred populations were studied using RNA-seq technology. We 15 found 45 differentially expressed genes between purebreds Sistani and Sistani × Montbeliarde crossbred. 16 Functional analysis of DEGs showed that the immune and inflammatory responses were the most highly17 impacted pathways and functions. These genes...
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