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Article ; Online: Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison)

Seyed Milad Vahedi / Siavash Salek Ardestani / Mohammad Hossein Banabazi / K. Fraser Clark

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 13

Abstract: Abstract Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV ... ...

Abstract	Abstract Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case–control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770–98,281 kb and chr1:114,133–120,473) and one on chromosome 6 (chr6:37,953–44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and gene level

SHEIDA VARKOOHI / MOHAMMAD HOSSEIN BANABAZI / MOJGAN GHSEMI-SIAB

Anais da Academia Brasileira de Ciências, Vol 93, Iss

2021 Volume 3

Abstract: Abstract In the current study, allele specific expression analysis was performed in two subspecies cows (Bos taurus and Bos indicus) at SNP and gene levels. RNA-Seq data of 21,078,477 and 20940063 paired end reads from pooling of whole blood samples ( ... ...

Abstract	Abstract In the current study, allele specific expression analysis was performed in two subspecies cows (Bos taurus and Bos indicus) at SNP and gene levels. RNA-Seq data of 21,078,477 and 20940063 paired end reads from pooling of whole blood samples (Leukocyte) from 40 US Holstein (Bos Taurus) and 45 Cholistani cows (Bos indicus) obtained from SRA database in NCBI. Quality control and trimming of row RNA-Seq data were processed by FASTQC and Trimmomatic softwares. The transcriptome was assembled by TopHat2 software in two cow’s population by aligning and mapping the RNA-Seq reads on bovine reference genome. The SNPs were discovered by Samtools software and ASE analysis was performed by Chi-square test. Results showed that 50183 and 137954 SNPs were discovered on the assembled transcriptome of Holstein and Cholistani cow samples, respectively, and 15308 SNPs were common in both breeds. 10158 SNPs from 50183 (20%) in Holstein and 31523 SNPs from 137954 (23%) in Cholistani cows were identified as ASE-SNPs. Reference allele and alternative allele count in Holstein and Cholistani cows were 3041 and 7155, respectively. Among 131 discovered SNPs in 41 genes with different expression in Holstein and Cholistani cows, 31 ASE-SNPs (5 in Holstein; 26 in Cholistani cows) were discovered.
Keywords	SNP discovery ; transcriptome ; Cholistani cows ; Holstein cows ; Science ; Q
Subject code	630
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Academia Brasileira de Ciências
Document type	Article ; Online
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Article ; Online: Identification of genome diversity in different breeds of Iranian native sheep using the whole genome sequencing method

Zeinab Amiri Ghanatsaman / Masoud Asadi Fouzi / Hojjat Asadollahpour nanaei / Mohammad hossein Banabazi

مجله بیوتکنولوژی کشاورزی, Vol 15, Iss 4, Pp 145-

2023 Volume 160

Abstract: Purpose: Iran is considered to be one of the oldest centers of domestication and breeding of livestock and poultry species in the world. Currently, different ecotypes of indigenous sheep are kept in different geographical regions of the country, which ... ...

Abstract	Purpose: Iran is considered to be one of the oldest centers of domestication and breeding of livestock and poultry species in the world. Currently, different ecotypes of indigenous sheep are kept in different geographical regions of the country, which have obvious differences from each other in terms of appearance and production characteristics. So far, there has not been a comprehensive study on the whole genome level to identify the genetic diversity of native Iranian sheep. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protectionMaterials and methodsIn this study, the whole genome sequences of 29 native Iranian sheep were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data has been done by Hiseq2000 and Hiseq X Ten sequencer devices. Quality control of raw data sequences was done by FastQC program. To align the sequence data with the sheep reference genome (Oar v.4.0, https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2), the BWA-MEM algorithm used in the BWA software package was used. Picard program was used to remove PCR duplicates from mapping outputs. The alignment outputs with the reference genome were processed in two stages, including re-alignment of deletions and small insertions and recalibration of the base quality score using the GATK program. The average coverage depth and alignment percentage for alignment output with the reference genome were calculated using depth and flagstat commands used in samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. Nucleotide diversity values and genomic inbreeding coefficient were calculated based on homozygous SNPs for each individual using the het command used in the VCFtools program.ResultsThe average coverage depth of the used data in this study was 18.39 X. The average percentage of alignment of short sequences with the ...
Keywords	iranian native sheep ; whole genome sequencing ; single nucleotide polymorphisms ; Agriculture ; S ; Biotechnology ; TP248.13-248.65
Subject code	630
Language	Persian
Publishing date	2023-11-01T00:00:00Z
Publisher	Shahid Bahonar University of Kerman
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Candidate Chromosomal Regions Responsible for Milk Yield of Cow

Lida Taherkhani / Mohammad Hossein Banabazi / Nasser EmamJomeh-Kashan / Alireza Noshary / Ikhide Imumorin

Animals, Vol 12, Iss 582, p

A GWAS Meta-Analysis

2022 Volume 582

Abstract: Milk yield (MY) is highly heritable and an economically important trait in dairy livestock species. To increase power to detect candidate genomic regions for this trait, we carried out a meta-analysis of genome-wide association studies (GWAS). In the ... ...

Abstract	Milk yield (MY) is highly heritable and an economically important trait in dairy livestock species. To increase power to detect candidate genomic regions for this trait, we carried out a meta-analysis of genome-wide association studies (GWAS). In the present study, we identified 19 studies in PubMed for the meta-analysis. After review of the studies, 16 studies passed the filters for meta-analysis, and the number of chromosomes, detected markers and their positions, number of animals, and p -values were extracted from these studies and recorded. The final data set based on 16 GWAS studies had 353,698 cows and 3950 markers and was analyzed using METAL software. Our findings revealed 1712 significant ( p -value < 2.5 × 10 −6 ) genomic loci related to MY, with markers associated with MY found on all autosomes and sex chromosomes and the majority of them found on chromosome 14. Furthermore, gene ontology (GO) annotation was used to explore biological functions of the genes associated with MY; therefore, different regions of this chromosome may be suitable as genomic regions for further research into gene expression.
Keywords	candidate SNPs ; dairy cattle ; genome-wide association study ; meta-analysis ; milk yield ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Study of coding genes and SNPs in the brain tissue genome of honeybee related to behavioral traits in Italian and African subspecies using RNA-Seq data analysis

Aliakbar Hasankhani / Hossein Moradi Shahrbabak / Mohammad Moradi Shahrbabak / Abolfazl Bahrami / Gholamali Nehzati paghaleh / Mohammad Hossein Banabazi

مجله بیوتکنولوژی کشاورزی, Vol 14, Iss 2, Pp 171-

2022 Volume 192

Abstract: ObjectiveHoneybees, as pollinating insects, are an important part of nature. Because behavioral traits are so important in honeybees, comparing brain tissue transcriptomes of the two subspecies with aggressive and calm behavioral characteristics makes it ...

Abstract	ObjectiveHoneybees, as pollinating insects, are an important part of nature. Because behavioral traits are so important in honeybees, comparing brain tissue transcriptomes of the two subspecies with aggressive and calm behavioral characteristics makes it possible to understand this behavioral difference genetically. This study aimed to investigate to gene expression profile and identify the key genes in brain tissue in Italian (Apis Mellifera Ligustica) and African (Apis mellifera Scutellata) honeybees concerning behavioral traits. The Italian honeybee has calm behavioral characteristics, while the African is known as an aggressive honeybee.Materials and methodsRNA-Seq data were obtained from the NCBI (GEO) database, and after pre-processing of reads, the brain tissue transcriptomes of both subspecies were aligned and mapped on the honey bee reference genome (v A.mel 4.5), and then data qualification, transcriptome assembly, differential expression analysis, and gene ontology were performed.ResultsDifferential gene expression analysis identified 16,701 genes on the honeybee reference genome, of which 22 genes in brain tissue between the two subspecies had significant differential expression (adj p-value <0 .05 and Log2FC>2). As well, some of these genes were first identified. Gene ontology analysis showed that among these 22 genes, such as ITPR, MRJP, HSP70Ab, MBS, GB45410, and Def1 are directly or indirectly involved in the occurrence of various traits such as defensive, health behavior, reproductive, heat, light, and smell sensitivity. In addition, the SNPs encoding the honeybee brain tissue genome were identified in both subspecies, and 99636 SNPs were identified in the Italian, and 92514 SNPs were identified in the African subspecies.ConclusionsRNA-seq data, due to its high throughput, can provide us with accurate information about the expression of genes in different tissues in various subspecies. In this study, genes involved in honeybee behavioral traits and the SNPs in these genes were identified
Keywords	: behavioral traits ; gene ; honeybee ; snp ; transcriptome ; Agriculture ; S ; Biotechnology ; TP248.13-248.65
Subject code	616
Language	Persian
Publishing date	2022-06-01T00:00:00Z
Publisher	Shahid Bahonar University of Kerman
Document type	Article ; Online
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Article ; Online: Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries

Morteza Bitaraf Sani / Zahra Roudbari / Omid Karimi / Mohammad Hossein Banabazi / Saeid Esmaeilkhanian / Nader Asadzadeh / Javad Zare Harofte / Ali Shafei Naderi / Pamela Anna Burger

Animals, Vol 12, Iss 184, p

2022 Volume 184

Abstract: Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) ...

Abstract	Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via JAK-STAT , and cytokine activity. EFCAB5 , MTIF2 , MYO3A , TBX15 , IFNL3 , PREX1 , and TMOD3 genes are candidates for improving growth in camel breeding programs.
Keywords	growth ; biological theme ; gene ontology ; dromedaries ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	612
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Multi-Omics Integration and Network Analysis Reveal Potential Hub Genes and Genetic Mechanisms Regulating Bovine Mastitis

Masoumeh Naserkheil / Farzad Ghafouri / Sonia Zakizadeh / Nasrollah Pirany / Zeinab Manzari / Sholeh Ghorbani / Mohammad Hossein Banabazi / Mohammad Reza Bakhtiarizadeh / Md. Amdadul Huq / Mi Na Park / Herman W. Barkema / Deukmin Lee / Kwan-Sik Min

Current Issues in Molecular Biology, Vol 44, Iss 23, Pp 309-

2022 Volume 328

Abstract: Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate genes and identify ... ...

Abstract	Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate genes and identify biomarkers and the molecular mechanisms underlying mastitis in dairy cattle. Hence, the present study aimed to explore the genetic basis of bovine mastitis by integrating microarray and RNA-Seq data containing healthy and mastitic samples in comparative transcriptome analysis with the results of published genome-wide association studies (GWAS) using a literature mining approach. The integration of different information sources resulted in the identification of 33 common and relevant genes associated with bovine mastitis. Among these, seven genes— CXCR1 , HCK , IL1RN , MMP9 , S100A9 , GRO1 , and SOCS3 —were identified as the hub genes (highly connected genes) for mastitis susceptibility and resistance, and were subjected to protein-protein interaction (PPI) network and gene regulatory network construction. Gene ontology annotation and enrichment analysis revealed 23, 7, and 4 GO terms related to mastitis in the biological process, molecular function, and cellular component categories, respectively. Moreover, the main metabolic-signalling pathways responsible for the regulation of immune or inflammatory responses were significantly enriched in cytokine–cytokine-receptor interaction, the IL-17 signaling pathway, viral protein interaction with cytokines and cytokine receptors, and the chemokine signaling pathway. Consequently, the identification of these genes, pathways, and their respective functions could contribute to a better understanding of the genetics and mechanisms regulating mastitis and can be considered a starting point for future studies on bovine mastitis.
Keywords	mastitis ; transcriptome sequencing ; hub genes ; multi-omics data ; regulatory networks ; bovine ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

Siavash Salek Ardestani / Mehdi Aminafshar / Mohammad Bagher Zandi Baghche Maryam / Mohammad Hossein Banabazi / Mehdi Sargolzaei / Younes Miar

Animals, Vol 10, Iss 1, p

2019 Volume 53

Abstract: Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic ... ...

Abstract	Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.
Keywords	horse ; musculoskeletal ; non-sport ; signature of selection ; sport ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic prediction for growth using a low-density SNP panel in dromedary camels

Morteza Bitaraf Sani / Javad Zare Harofte / Mohammad Hossein Banabazi / Saeid Esmaeilkhanian / Ali Shafei Naderi / Nader Salim / Abbas Teimoori / Ahmad Bitaraf / Mohammad Zadehrahmani / Pamela Anna Burger / Vincenzo Landi / Mohammad Silawi / Afsaneh Taghipour Sheshdeh / Mohammad Ali Faghihi

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 14

Abstract: Abstract For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel ... ...

Abstract	Abstract For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genetic Variation Within and Between Five Iranian Sheep Populations Using Microsatellites Markers

Saeid Esmaeilkhanian / Mohammad Hossein Banabazi

Pakistan Journal of Biological Sciences, Vol 9, Iss 13, Pp 2488-

2006 Volume 2492

Abstract: Genetic variation within and between five Iranian sheep populations; Sanjabi (SAN), Kordi Kordistan (KKO), Kordi Khorasan (KKH), Mehraban (MEH) and Moghani (MOG) was assessed using 6 microsatellite markers (McMA2, McMA26, MAF64, OarAE64, OarCP26 and ... ...

Abstract	Genetic variation within and between five Iranian sheep populations; Sanjabi (SAN), Kordi Kordistan (KKO), Kordi Khorasan (KKH), Mehraban (MEH) and Moghani (MOG) was assessed using 6 microsatellite markers (McMA2, McMA26, MAF64, OarAE64, OarCP26 and OarFCB304). There are significant deviation from Hardy-Weinberg equilibrium in all population-locus combinations except the locus McMA2 in the MOG population (p<0.005). The lowest D A genetic distance (0.234) was obtained between KKH and KKO and the highest (0.388) between SAN and MOG. D based on D A distances, neighbor-joining revealed one cluster containing KKO, KKH and SAN and another cluster with MEH and MOG. The average expected heterozygosity within populations ranged from 0.744 to 0.847 for KKH and MEH, respectively. The estimated time of divergence for two Kordi populations (KKO and KKH) was 445 years that has accordance with historical evidence. This study showed that microsatellite loci can be an useful tool for evaluating variation evolutionary relationships among local sheep populations.
Keywords	Iranian sheep ; microsatellite genetic variation ; heterozygosity ; polymorphism ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	590
Language	English
Publishing date	2006-01-01T00:00:00Z
Publisher	Asian Network for Scientific Information
Document type	Article ; Online
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