Hossein Mohammadi; mohammad Shamsollahi
Articles in Press, Accepted Manuscript, Available Online from 23 November 2023
Abstract
The aim of the present study genome wide association studies based on Gene set enrichment analysis for identifying the loci associated with related to fleece traits in Cashmere goat using the high-confidence SNPs. For this purpose, the 192 Cashmere goats were performed with fiber length, fiber diameter ...
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The aim of the present study genome wide association studies based on Gene set enrichment analysis for identifying the loci associated with related to fleece traits in Cashmere goat using the high-confidence SNPs. For this purpose, the 192 Cashmere goats were performed with fiber length, fiber diameter and cashmere yield in GEMMA software. Using the biomaRt2 R package the SNP were assigned to genes. Finally, a gene enrichment analysis was performed with the KOBAS platform from online bioinformatics databases. Bioinformatic analysis showed that the identified genomic regions directly and indirectly overlap with genes affecting the production of keratinocytes, epidermal growth and development, hair follicle growth and collagen. According to pathway analysis, 18 pathways from gene ontology and KEGG pathway were associated with the quantity and quality wool trait (P˂0.05). Among those pathways, the Oxytocin signaling pathway, positive regulation of intracellular protein transport and epidermal cell differentiation has an important role in the hair follicle development, keratinocytes differentiation and development of epidermal. Also, the MAPK signaling pathway, cellular response to hormone stimulus and Insulin secretion significant association with quantity wool traits. Using these findings could potentially be useful for genetic selection in the breeding programs and can be used to understand the genetic mechanism controlling this trait. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Using these findings can accelerate the genetic progress in the breeding programs with the aim of producing fine fibers.
Hossein Mohammadi; Amir Hossein Khaltabadi Farahani; Mohammad Hossein Moradi; mohammad shamsollahi
Volume 25, Issue 2 , July 2023, , Pages 133-143
Abstract
Introduction: The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions ...
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Introduction: The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable.
Materials and Methods: In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Results and Discussion: The lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.
Conclusions: our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds.
Mohammad Ebrahim Nooriyan Soroor; Mohammad Ebarhim Nooriyan Soroor; Mohammad Mahdi Moeini
Volume 18, Issue 4 , December 2016, , Pages 729-740
Abstract
Effects of ethanol and acetone extracts of Glycyrrhiza glabra at six levels (0, 50, 100, 200,300 or 500 µl) were evaluated on gas production process, ruminal fermentation and protozoa population in Markhoz goat. The gas production was conducted by alfalfa substrate using compiled randomized design ...
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Effects of ethanol and acetone extracts of Glycyrrhiza glabra at six levels (0, 50, 100, 200,300 or 500 µl) were evaluated on gas production process, ruminal fermentation and protozoa population in Markhoz goat. The gas production was conducted by alfalfa substrate using compiled randomized design with five replications in each treatment. The fermentation parameters, methane, partitioning factor (PF) and volatile fatty acids (VFA) were recorded. The gas production in 24 h was increased in all levels of both extracts (P˂0.01). The methane production decreased in ethanol extract (P˂ 0.05) however, it was increased by acetone extract at level of 300 and 500 µl (P˂0.01). The organic matter degradability was improved by addition of both extracts (P˂0.01). The Ammonia was declined by ethanol extract (P˂ 0.01). The PF and microbial mass production were decreased by inclusion of both extract, however the VFA and metabolizable energy were enhanced at all levels of both extracts (P˂0.01). All subfamily (except Diplodiniinae)and total protozoa population were decreased by both extracts. It can be concluded that ethanol and acetone extracts of Glycyrrhiza glabra has the potential to improve degradability and were decreased methane production and protozoa population of goat rumen.
Ali Khezrian; Mohammad Ebrahim Nooriyan Soroor; Mohammad Mahdi Moeini
Volume 18, Issue 3 , October 2016, , Pages 477-490
Abstract
The aim of this study was to evaluate the effects of Mentha longofolia plant (MLP) and its essential oils (MLE) on ruminal fermentation and protozoa population in goat. The MLP at six levels 0, 25, 35, 55, 75 and 100 mg/30 ml, and the essential oil at six levels 0, 1700,3000,6700,8300 and 10000 mg/L ...
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The aim of this study was to evaluate the effects of Mentha longofolia plant (MLP) and its essential oils (MLE) on ruminal fermentation and protozoa population in goat. The MLP at six levels 0, 25, 35, 55, 75 and 100 mg/30 ml, and the essential oil at six levels 0, 1700,3000,6700,8300 and 10000 mg/L plus monensin (as positive control, 50 mg and dissolved in ethanol) added to rumen fluid respectively. The in vitro gas production was conducted by compiled randomized design with five replications for each treatment. The gas production was decreased at levels of 75 and 100 mg of MLP (p˂0.001). Organic matter degradability was reduced (p˂0.001) at 75 and 100 mg levels respectively of MLP compared to control. Ammonia nitrogen concentration was decreased (p˂0.001) at all levels of MLP compared with control and monensin treatments. However, partition factor was increased (p˂0.001) only at 100 mg of MLP. The efficiency of microbial protein production was increased (p˂0.001). The metabolisable energy and net energy lactation were decreased (p˂0.001) by inclusion MLP at two level of 75 and 100 mg as total volatile fatty acids reduced, compared with control treatment. The total protozoa and subfamily of Entodinninea were declined (p˂0.001) at all levels of MLP compared with control and positive control treatments. The parameters of methane production, ammonia N and protozoa population were reduced (p˂0.001) by all levels of MLE. The efficiency of microbial protein production was enhanced (p˂0.001).Results suggest that the methane gas production, ammonia N and protozoa populations were reduced in both MLP and MLE and improved partition factor and microbial protein production.
Alireza Hasani Bafarani; Seyed Ziaoddin Mirhoseini; Farid Heidari
Volume 16, Issue 1 , May 2014, , Pages 43-51
Abstract
The Spermatogonial Stem Cells (SSCs) are founder of spermatogenesis and they are the only stem cells that can transmit genetic materials to offspring’s. This research was conducted to achieving a reliable origin of SSCs from the goat testicular tissues according to a four steps procedure; a) Collection ...
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The Spermatogonial Stem Cells (SSCs) are founder of spermatogenesis and they are the only stem cells that can transmit genetic materials to offspring’s. This research was conducted to achieving a reliable origin of SSCs from the goat testicular tissues according to a four steps procedure; a) Collection and preparing testicular tissues, b) Two enzymatic digestions, c) Using mesh and cell suspension and d) Culture the isolated SSCs on goat embryonic fibroblasts. ِDistinct markers of pluripotency such as NANOG, SOX2and OCT4 were expressed in the isolated SSCs and also in these cells, nonspecific alkaline phosphatase test was positive. These cells used for co-culturing with GEF for several passages without differentiation or changing the shape. It was also found out that by using DMSO, these cells can be held in -70°C for one month. The result showed that the used procedure was efficient and the cells not only can express distinct markers of pluripotency but also can be culture and proliferate for long period of time without differentiations.
Mahnaz Salehi; Raziyeh Hezareh Moghadam
Volume 13, Issue 1 , September 2011, , Pages 17-22
Abstract
To study the fleece characteristics of native goats in Sistan and Balouchestan province, fiber sample was taken from 270 females between one to three years old from Khash, Saravan and Iranshahr cities. The differences between age groups for all fleece parameters except fleece weight were not significant. ...
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To study the fleece characteristics of native goats in Sistan and Balouchestan province, fiber sample was taken from 270 females between one to three years old from Khash, Saravan and Iranshahr cities. The differences between age groups for all fleece parameters except fleece weight were not significant. The fleece weight of two and three years old goats were 263.4 (± 7.7) and 315 (± 7.8) gr, respectively and were more than the fleece weight of yearling goats 323 (± 7.7) gr. The results of cashmere in Khash goats was highest (26.3 ± 1%), and the goats of Iran-shahr had the finest cashmere of (12.5± 0.3 micron).