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; Hossein Moradi Shahrebabak; mohammad shamsollahi
Volume 25, Issue 3 , October 2023, , Pages 241-254
Abstract
Introduction: Identifying of genes with large effects on economically important traits, has been one of the important goal to sheep breeding. Over recent years, advances in DNA-based marker technology have made it possible to identify genomic regions or quantitative trait loci (QTLs) underlying complex ...
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Introduction: Identifying of genes with large effects on economically important traits, has been one of the important goal to sheep breeding. Over recent years, advances in DNA-based marker technology have made it possible to identify genomic regions or quantitative trait loci (QTLs) underlying complex traits, such as fleece traits, in sheep. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the loci associated with wool traits in native Zandi sheep using the 50K arrays.
Material and Methods: A total of 300 Iranian Zandi sheep used in this study came from the Zandi sheep breeding station. Wool sampling coincided with the maximum wool growth prior to the shearing of wool. In order to facilitate sampling, sheep were restrained in a lateral position and true wool from the left mid-side site was cut from a 5×5 cm2 close to the skin using regular scissors. Each sample was separately packaged and labeled with ear tag number of the sheep. We measured and recorded four wool production traits: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (CVFD), and the proportion of fiber that are equal or more than 30 µm (PR), kemp percentage (KEMP%) and outer coat fiber (OCF) were measured. Genomic DNA extraction from sheep blood was performed by the applying a modified salting out protocol and genotyping of the Sheep SNPChip 50 K SNP Bead from Illumina Inc. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories, and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with wool traits using GEMMA software. Using the biomaRt2 R package, the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 50 kb up- and downstream of the gene and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in GeneCards databases.
Result and Discussion: The result from genomic control showed weak population stratification with for woot traits among Zandi sheep population. We identified different sets of candidate genes related to wool traits including: CEP290, PRKCZ, TMTC3, RHPN2, TNFSF4, NLGN1, SPHKAP, PLCE1, FAT1 and PIK3R4 in Zandi sheep. Some of the found genes, are consistent with some of the previous studies related to reproductive traits. According to pathway analysis, 21 pathways from gene ontology and biological pathways were associated with the wool traits (P˂0.05). Some of the genes were found are consistent with some prior studies and to be involved biological pathways related to hair follicle development, keratinocytes differentiation, synthesizes an enzyme of threonine kinases, development of epidermal and Wnt signaling pathway.
Conclusion: In total, this study supported previous results from GWAS of wool traits, also revealed additional regions in the sheep genome associated with these economically important traits. 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.
Kamel Amozadeh Araee; Taghi Ghoorchi; Abdolhakim Toghdory
Volume 25, Issue 3 , October 2023, , Pages 267-279
Abstract
Introduction: Minerals affect wool production in sheep by affecting feed intake, altering rumen function and affecting the flow of nutrients from the rumen or by directly disrupting the animal's metabolism. Wool has the highest concentration of sulfur, which indicates the higher need of wool-producing ...
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Introduction: Minerals affect wool production in sheep by affecting feed intake, altering rumen function and affecting the flow of nutrients from the rumen or by directly disrupting the animal's metabolism. Wool has the highest concentration of sulfur, which indicates the higher need of wool-producing sheep for sulfur than other breeds. The purpose of this study was to investigate the effect of different levels of bentonite sulfur on yield, wool quality, blood minerals, liver enzymes and thyroid hormones of ewes.Materials and Methods: An experiment was conducted to evaluate the use of different levels of bentonite sulfur in sheep. For this purpose, 18 Dalagh ewes (average weight 38 ± 3.5 kg) were kept individually for 42 days with three treatments and 6 repetitions. Experimental treatments included: 1) control (without bentonite sulfur), 2) treatment containing 0.15 percent of bentonite sulfur and 3) treatment containing 0.3 percent of bentonite sulfur(based on dry matter). At first, to ensure the health of all the ewes, they are subjected to a thorough and thorough examination. The bentonite sulfur used in this research contanied 90% sulfur and 10% bentonite. The diets used in this experiment were prepared and adjusted according to the tables of NRC and were given to the ewes in the morning and evening. Ewes were weighed at the beginning and the end of the period after 16 hours of starvation using a digital scale. In order to determine the quality of sheep's wool, in the initial test, the ewes were arranged uniformly on the 41st day of the experiment, and samples were taken from the left side of the ewes in a 10 x 10 cm format according to the common and standard instructions using a manual wool picker. For determination of blood parameters, on the last day of the experiment, three hours after morning feeding, blood samples were taken from the jugular vein of the ewes.Results and discussion: The results obtained from this research showed that with the increase in the level of bentonite sulfur in the diet, the length of fibers, efficiency, strength, kemp and the coefficient of variation of fiber diameter increased (P<0.05). Also, increasing the level of bentonite sulfur increased the concentration of serum sulfur and triiodothyronine hormone (P<0.05). Bentonite sulfur supplementation had no significant effect on final weight, daily weight gain, dry matter intake and feed conversion ratio of ewes. Also, different levels of bentonite sulfur had no significant effect on Non-Medullated fibers, Medullated fibers, average diameter and fiber crude protein. copper gallate, calcium, selenium, phosphorus and serum molybdenum. Addition of bentonite sulfur had no significant effect on serum concentrations of copper, calcium, selenium, phosphorus, molybdenum as well as the concentration of liver enzymes of experimental ewes. Conclusion: The results of this study indicated that the use of bentonite sulfur up to the level of 0.3% of dry matter, could improve the strength and efficiency of wool fibers and it can be used in feeding ewes without having negative effects on their health and performance.