مجله علوم دامی ایران
سال پنجاه و سوم شماره 3 (پاییز 1401)

Single-step genomic prediction models became the prevailing tool in genetic evaluations of livestock due to high genomic performance, high genotyping costs for some animals, and utilizing both genotyped and un-genotyped animals. The objective of the current study was to investigate the effect of genetic relationships between the training and validation populations on the performance of single and multi-step GBLUP and BayesB, which in this regard the importance of un-genotyped individuals in generations after genomic selection and their roles on the necessity of reusing genomic selection in binary threshold traits was investigated. For this purpose, genomic populations were simulated to reflect the different number of QTL (33 and 534) with two different distributions of QTL (normal and gamma) on 29 chromosomes. Four statistical models (GBLUP, SS-GBLUP, BayesB and SS-BayesB) were implemented to analyze the simulated data. According to the results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for multi-step models than for single-step models. Multi-step and single-step BayesB methods showed an obvious advantage over GBLUP and SSGBLUP when the trait is controlled by fewer QTLs. For the normal QTL effects distribution, BayesB methods (especially multi-step BayesB) obtained the lower accuracy than that of if more QTLs affecting the trait. Generally, since the increasing generation distance is a major challenge in the genomic selection of threshold traits, therefore the use of single-step methods makes possible reuse of genomic selection during the early generations of selection unnecessary. However, using single-step BayesB methods and its advantages in genomic evaluation depends on the identification of trait genetic architecture.

Coat color is one of the important economic traits in sheep and it can be used for breed identification and characterization as well. The aim of the present study was to perform genome wide association study (GWAS) and pathway analysis based on gene set enrichment analysis for identifying the loci associated with coat color in Lori-Bakhtiari sheep breed. The GWAS was carried out using PLINK v. 1.90. The gene enrichment analysis was performed by goseq R package in R v.3.6.1 with the aim of identifying functional clusters and biological pathways of the genes in selected candidate regions and finally, for bioinformatics analysis we used online databases and softwares of GO, Metacyc, KEEG, Reactome and panther. In this study significant SNP markers were identified on chromosomes 1, 2, 6, 9, 10, and 16 that overlapped with EDNRB, PDGFRA, TCF25, and TYRP1 genes. According to pathway analysis, four GO pathways were associated with the coat color trait (P˂0.05). Among these pathways, regulation of protein tyrosine kinase activity, regulation of protein kinase A signaling and activation of protein kinase activity biological pathways, were previously reported to have an important role on the melanocyte development and coat pigmentation. Considering that the genomic regions identified in the current study have been confirmed to be associated with coat color in sheep and other species in previous reports, as well as the identification of some novel putative regions, the identified candidate genes in our study could be further studied and eventually used in genetic selection for coat color in sheep.

This study aimed to compare the effects of combined buffer and sodium bicarbonate on growth performance and ruminal parameters of Holstein young bulls with an average weight of 330.8±43.1 kg and an age of 240 days, fed with a high-concentrate diet. The experiment was conducted for 90 days with 10 days of habituation in a completely randomized design with three dietary treatments and 10 replications, and a forage: concentrate ratio of 20 to 80%. Experimental diets included a control diet (without buffer), a basal diet with 1% sodium bicarbonate, and a basal diet with 1% mixed buffer. Daily feed intake, monthly weight gain, and digestibility were measured. The experimental diets did not affect feed intake, weight changes, and digestibility. The best feed conversion ratio for bulls was in treatment of diet containing the mixed buffer supplement (P<0.05). Daily weight gain was higher in bulls fed with the combined buffer than that of the control group (P<0.05). Rumen ammonia nitrogen was higher in the control group than the bulls receiving mixed buffer (P<0.05). The pH of rumen fluid was lowest in the control group, two hours after feeding (P<0.05). The present study results showed that the mixed buffer had a better performance in controlling the rumen acidity of bulls fed with high concentrate diets compared to sodium bicarbonate, especially in terms of improving feed conversion ratio, and it seems to be necessary to add it to such diets.

The aim of this study was to evaluate the effects of CLA supplementation in diets with different levels of forage NDF on performance, serum metabolites and liver functionality in Holstein fresh cows. Forty Cows were blocked based on their body condition score at calving and 305-d mature-equivalent milk yield, and randomly allocated to 1 of 4 experimental diets from calving to 21 days in milk (DIM). Treatments were used in a 2×2 factorial arrangement with 2 levels of fNDF and 2 doses of CLA supplement; Treatments were formulated to contain 18.0 or 23.0% fNDF without or with CLA supplement for diets 18fNDF-CLA, 18fNDF+CLA, 23fNDF-CLA and 23fNDF+ CLA. There was no effect of fNDF by CLA interaction on investigated items. Dry matter intake increased up to 1.5 kg with 18fNDF diet compared to 23FNDF (P<0.01), while the addition of CLA reduced the dry matter intake to 1.15 kg/d compared to diets without CLA supplementation (P<0.01). Cows fed 23fNDF diet lost more body weight than those fed 18fNDF. Milk yield was higher for cows fed 18fNDF than 23fNDF (P<0.01). Cows fed diets containing CLA produced more milk, lower milk fat percentage, and higher lactose content. (P<0.05). Serum glucose was higher in cows fed CLA-containing diets (P<0.01). Cows fed 18fNDF had lower serum concentrations of NEFA and BHBA compared to those fed 23fNDF (P<0.05), but CLA supplementation did not affect serum NEFA and BHBA (P>0.05). (P<0.05). In general, the reduction of forage NDF in the diet of fresh cows led to improved feed intake and production performance. Addition of CLA to the diet of fresh cows led to glucose savings by reducing fat synthesis, increasing lactose content and milk production.

This research aimed to investigate the reasons for the difference of gene expression between two subspecies of Holstein and Cholistani cattle and the importance of mitochondrial genes of these two breeds, the genes under study were COX1, COX2, COX3, ND1and ND2, which are involved in essential processes such as energy metabolism, resistance to biological and non-biological stresses, as well as disease resistance. In this study, RNA-Seq data were used, including 40 samples from the University of Wisconsin Dairy Cattle Center (Bos taurus) and 45 Cholistani cows (Bos indicus) of Gujaratpir farm in Bahawalpur, Punjab, Pakistan. IGB software was used to investigate the level of transcriptome coverage and genetic differences, which included polymorphic, deletion and addition and binding regions. MEGA6 and DnaSPV.5 softwares were also used to determine the location of polymorphic areas as well as to calculate the percentage of different types of transitional and transversional replacements of nucleotides and to align sequences. The results showed that the COX1 gene, with a length of 1542 bp, had the highest level of transcriptome coverage in the mitochondrial genome and the lowest level of transcriptome coverage was related to the ND1 gene. Among mitochondrial genes, the COX1 gene showed the highest deletions and additions, which were higher in Holstein than Cholistani breeds. The number of polymorphic regions in the COX1 locus (19 areas) was higher than other genes. The results also showed that the percentage of transitional substitution is higher than transversional substitution which is the reason for the stability of changes during different generations. Therefore, possible reasons for differences in mtDNA gene expression may be due to differences in deletion and addition processes, transcriptome coverage, and polymorphic regions.