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.
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.
Hossein Mohammadi; Amir Hossein khalababdi farahani; Mohammad Hossein Moradi
Volume 24, Issue 2 , July 2022, , Pages 117-126
Abstract
The aim of the present study was to evaluate the genetic architecture, genomic regions and candidate genes associated with body weight gain, feed intake and feed conversion ratio in Japanese quails. For detection the informative genomic windows, genotyping data on 920 quails was used in a single-step ...
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The aim of the present study was to evaluate the genetic architecture, genomic regions and candidate genes associated with body weight gain, feed intake and feed conversion ratio in Japanese quails. For detection the informative genomic windows, genotyping data on 920 quails was used in a single-step genome-wide association study. The BLUPf90 family software was used to perform related analyses. Theresults was calculated based on the proportion of additive genetic variance (agv) explained by genomic region with an average size of 1.5-Mb of adjacent SNPs. Windows with accounting for more than 1% of the agv were used to identify genomic regions and to search for candidate genes. A total of 13 significant windows over 8 chromosomes were explained 23% of the agv for the body weight gain and including SMYD1, ADGRG6 and CFL2 candidate genes. A peak on CJA2 explained the largest proportion of variance. For feed intake, we identified 20 informative windows across 8 chromosomes and including ACSL, PPA2, FGF2 and RBL2 candidate genes. These regions explained 38% of the agv and a peak on CJA4 explained of agv. Also, for the feed conversion ratio, 12 significant windows were identified on 7 chromosomes and explained 23.7% of agv, contained ATRNL1 and PTPN4 candidate genes. Four genomic regions had a pleiotropic effect. Considering the identification of new genome regions and the key role of the mentioned genes related to feed intake, the single step method can be validated for GWAS in feed efficiency traits.
Hossein Mohammadi; Amir Hossein khaltabadi farahani; Mhammad hossein Moradi; Abouzar Najafi
Volume 23, Issue 4 , January 2022, , Pages 481-490
Abstract
Understanding the genetic control of temperament as a complex trait and correlated with economic traits is one of the breeding goals in beef cattle industry. The aim of the current study was genome wide association studies (GWAS) based on Gene set enrichment analysis for detecting the loci associated ...
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Understanding the genetic control of temperament as a complex trait and correlated with economic traits is one of the breeding goals in beef cattle industry. The aim of the current study was genome wide association studies (GWAS) based on Gene set enrichment analysis for detecting the loci associated with temperament traits in Brahman cattle breed. Therefore, 1370 Brahman cattle and phenotype records associated with temperament traits including Exit velocity, Pen Score, and Temperament Score were used. The evaluation of genome-wide association was carried out using PLINK package 1.90. The gene enrichment analysis was performed by the goseq R package for identifying biological pathways of nearby genes in selected candidate regions and finally, GO, Metacyc, KEEG, Reactome and panther databases were applied for bioinformatics analysis. By Gene set enrichment analysis, the biological pathways and candidate genes of neurotransmitter secretion (NRXN3 and CACNG3), Dopamine Neurotransmitter Release Cycle (PPFIA2), regulation of neuron projection development (GRID2), neuron projection (SLC8A1 and KCNQ2), Axonal growth inhibition (RTN4R), Neurotrophin signaling pathway (MAP2K2, MAP3K5 and PSEN1) and Focal adhesion (TLN2) were identified. The detected candidate genes played an important role in differentiation of synapse, neurotransmitters, neurological diseases and disorders, oxidative and environmental stresses, hormone receptors and glucose homeostasis. Considering the confirmation of the previous region of genome wide association and the identification of new genomic regions, the findings of this study can be useful in the genetic selection of higher production cattle through calm animals.
Mir Hossein Najafi; saeed zeinoaldini; Abolfazl Zali; mahdi Ganjkhanlou; Hossein Mohammadi
Volume 23, Issue 1 , March 2021, , Pages 73-82
Abstract
This study was conducted to investigate the effect of reducing dietary ratio of omega-6/omega-3 essential fatty acid (EFA) on dry matter intake, yield and milk composition, ovarian performance and blood concentrations of estradiol and progesterone using 24 multiparous Holstein cows. Experimental treatments ...
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This study was conducted to investigate the effect of reducing dietary ratio of omega-6/omega-3 essential fatty acid (EFA) on dry matter intake, yield and milk composition, ovarian performance and blood concentrations of estradiol and progesterone using 24 multiparous Holstein cows. Experimental treatments including different n-6 to n-3 EFA ratio; namely, 2.5, 4.5, or 6.5 parts of n-6 to 1 part of n-3 EFA. Dry matter intake and milk yield of cows were recorded daily. Also, body condition score and milk composition were recorded and ovarian activity was monitored by transrectal ultrasound scanning. Dry matter intake and milk composition were not affected by treatments. Daily milk yield was significantly higher in low and medium n- 6/n-3 FA ratio diets in comparison to high diet (P<0.05). Cows assigned to high n-6/n-3 FA ratio diet had greater plasma Haptoglobin concentrations compared to other diets (P<0.05). Results indicated that number of large follicles was greater in medium diet than high diet (P<0.05). Progestrone concentration was significantly decrease in high diet treatment (P<0.05). Results of this study indicate that modulating dietary n-6/n-3 FA ratio could lead to a higher milk yield and improve ovarian performance in fresh cows.