Behzad Rajabi Marand; Hossein Moradi Shahrbabak; Mostafa Sadeghi; Rostam AbdolahiArpanahi
Volume 21, Issue 4 , January 2020, , Pages 419-430
Abstract
The aim of current study was to evaluate the accuracy of genomic breeding values (GEBV) for two important economical traits of milk yield and somatic cell score using SNP markers and LD-based haplotype blocks (haploblocks) by two statistical methods of GBULP and Bayes B. The data set consisted ...
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The aim of current study was to evaluate the accuracy of genomic breeding values (GEBV) for two important economical traits of milk yield and somatic cell score using SNP markers and LD-based haplotype blocks (haploblocks) by two statistical methods of GBULP and Bayes B. The data set consisted of 1654 bulls genotyped with different marker densities. When SNPs were used, the accuracy of breeding values obtained by Bayes B was better than GBLUP. In other words, for milk yield and somatic cell score traits, the prediction accuracy of GBLUP was 0.54 and 0.44 and by Bayes B was 0.58 and 0.44,respectively. For milk yield, the prediction accuracy of using haploblocks in both statistical methods was higher than the prediction accuracy using SNPs, while for the somatic cell score, this increase was more pronounced when GBLUP was used. However, when Bayes B was used this superiority was only obtained when the r2 statistic used to build the haploblocks was higher than 0.2. The results showed that the optimum level of r2 for building haploblocks depends on the trait type and its heritability. As a result, using r2 statistic more than 0.2 for building haploblocks can increase the accuracy of breeding valuesfoe both traits compared to SNP markers.
Abdollah Rezagholivand Lahrud; Mohammad Moradi Shahre Babak; Hossein Moradi Shahrbabak; Morteza Sattaei Mokhtari
Volume 20, Issue 4 , February 2019, , Pages 499-511
Abstract
The objective of the present study was the genetic evaluation of retained placenta (RP), metritis (MET), number of inseminations to conception (INS), and days open (DO) in Holstein cows using standard (SMMs) and recursive (RMMs) mixed models. Data on 50230 first-lactation Holstein dairy cattle, collected ...
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The objective of the present study was the genetic evaluation of retained placenta (RP), metritis (MET), number of inseminations to conception (INS), and days open (DO) in Holstein cows using standard (SMMs) and recursive (RMMs) mixed models. Data on 50230 first-lactation Holstein dairy cattle, collected during 2008 to 2017 in 17 large dairy herds were used. The data was analyzed using four-variate animal Threshold-Gaussian models under SMMs and RMMs. The existence of causal effects from RP on MET, INS and DO, from MET on INS and DO and from INS to DO were considered in RMMs. The causal effects of RP and MET on INS were 0.19 and 0.09 services, respectively; and those on DO were 4.74 and 5.38 days, respectively. Also, causal effect of INS on DO was obtained as 33 days. The considered causal relationships except that of RP on MET, phenotypic and residual correlations among the disorders and fertility traits were statistically significant and different under two models. Posterior means of heritability for RP, MET, INS and DO were 0.15, 0.17, 0.07 and 0.09 under SMMs, respectively; and 0.16, 0.17, 0.07 and 0.1 under RMMs, respectively. The difference between the corresponding heritability estimates under SMMs and RMMs were not statistically significant. Therefore; RMMs may be an alternative for SMMs in genetic evaluation of studied traits in first -lactation Holstein cows.
hamid marzbani; Hossein Moradi Shahrbabak; Mohammad Moradi Shahre Babak
Volume 20, Issue 1 , May 2018, , Pages 29-41
Abstract
This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 Sarabi cow using SNP-chip 40k of Illumina company. After genotyping and quality control, 27386 SNP markers on autosomal chromosomes remained for analyzing. The LD was measured by r2 and ...
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This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 Sarabi cow using SNP-chip 40k of Illumina company. After genotyping and quality control, 27386 SNP markers on autosomal chromosomes remained for analyzing. The LD was measured by r2 and D' statistics. In this study the average of r2 and D' for range less than of 2.5 kb were maximum with 0.505 and 0.927, respectively. The average of r2 and D' were minimum with 0.064 and 0.486, respectively in range of 2-5 Mb. 582 haplotype blocks were observed in the genome of Sarabi cow. 6.73% SNP from all of the SNPs were covered and 0.83% (21.43 Mb) of the autosomal genome were covered by the blocks haplotype. Population effective size was estimated about 40 that refer to four generations ago. The low number of haplotype block and also low LD level in Sarabi cow population showed high variation. In refer to the result and the number of haplotype blocks in this breed, applying the haplotype blocks could be improve results and high precision on genomic selection study so it was recommended that in study of genomic selection applying the haplotype blocks really useful than single SNP study
H. Moradi Shahrbabak; A. Asadi; P. Azizi; S. Elahian
Volume 14, Issue 2 , January 2012, , Pages 43-50
Abstract
Expression of the Growth Hormone receptor (GHR) gene which is located on the sixteenth chromosome of sheep and its binding with GH is essential for growth and fat metabolism. In this study, blood samples were collected from the jugular vein from 88 sheep of Kermani breed.DNA was extracted from blood ...
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Expression of the Growth Hormone receptor (GHR) gene which is located on the sixteenth chromosome of sheep and its binding with GH is essential for growth and fat metabolism. In this study, blood samples were collected from the jugular vein from 88 sheep of Kermani breed.DNA was extracted from blood sample using the modified salting out method for amplification of 155 bp fragment containing a part of exon 10 of GHR genes. Single Strand Conformation Polymorphism (SSCP) was used for genotyping. The vertical electrophoresis of PCR products was performed on 12 percent polyacrylamide gel, at 300 V, for 17 h at 4 ˚C. The silver-staining of gels, resulted identification of six genotypic patterns: 1, 2, 3, 4, 5 and 6 with frequencies of 9.09, 4.54, 13.63, 9.09, 35.22 and 28.40 percent, respectively. Analysis of variance was performed using SAS software and association of different patterns was not significant with growth traits.