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.
amir hossein khaltabadi farahani; hossein mohammadi; hossein moradi
Volume 22, Issue 3 , September 2020, , Pages 325-335
Abstract
The aim of this study was to identify the molecular pathways related to litter size in sheep using gene set enrichment analysis. For this purpose, information of high prolificacy sheep breeds including Wadi, Hu, Icelandic, Finnsheep, and Romanov and low prolificacy including Texel and Rahmani ...
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The aim of this study was to identify the molecular pathways related to litter size in sheep using gene set enrichment analysis. For this purpose, information of high prolificacy sheep breeds including Wadi, Hu, Icelandic, Finnsheep, and Romanov and low prolificacy including Texel and Rahmani were used for genome wide association studies and gene set enrichment analysis. Genome-wide association study was conducted using GenABEL package of R program. Gene set enrichment analysis was performed with the goseq R package to identify the biological pathways associated with candidate genes. We identified different sets of candidate genes related to litter size: BMP5, DHCR24, BMPR1B, ESR1, ESR2 andPLCB1 in Wadi and Romanov; SMAD1, SMAD2, INSR and PTGS2 in Finnsheep and Hu; BMP7, NCOA1 and ERBB4 in Icelandic; BMP4, MSRB and SPP1 in Texel; BMP7, EGFR and KCNMA1 in Rahmani. According to pathway analysis, 30 pathways were associated with the litter size trait. Among biological pathways, the TGF-β signaling, Oxytocin signaling, Estrogen signaling, Prolactin signaling, and Insulin signaling pathways have significant association with ovulation rate and litter size trait. Overall, this study supported previous results from GWAS for litter size, also revealed additional regions in the sheep genome associated with litter size in sheep. These findings could potentially be useful for selective breeding for more litter size in sheep.