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Article ; Online: Genomic characterization, phylogenetic and expression analysis of foraging gene in Apis mellifera.

Morammazi, Salim / Shokrollahi, Borhan / Hassan, Faiz-Ul

2024 Volume 910, Page(s) 148318

Abstract: The genomic characterization of the foraging gene and its expression analysis are required to better understand the behavior of honey bees (Apis mellifera). The present study performed a genome-wide characterization of the foraging gene, analyzing its ... ...

Abstract	The genomic characterization of the foraging gene and its expression analysis are required to better understand the behavior of honey bees (Apis mellifera). The present study performed a genome-wide characterization of the foraging gene, analyzing its physicochemical properties, phylogenetic features, and expression. An in silico analysis was carried out to characterize the foraging gene and the motifs and conserved domains of the encoded protein to predict its physicochemical properties. Moreover, a phylogenetic analysis of the foraging gene was performed in different species using MEGAX. The relative expression of the foraging gene was determined using qRT-PCR in two groups of forager bee samples (incoming and outgoing bees) during two seasons (five times per day). In addition, the queen effect was evaluated in another experiment. The results revealed that foraging gene expression and bee traffic were influenced by the interaction of season and daytime. The daily foraging traffic and transcription level of the foraging gene were the same in both seasons. The traffic of bees and the transcription abundance of the foraging gene were the highest in the middle and at the end of the day in the first and second seasons, respectively. Furthermore, the mRNA expression of the foraging gene was relatively higher in incoming bees than in outgoing bees. The queen also had a significant effect on the outgoing bees. We conclude that gene-environment interactions affect the foraging behavior of bees through the modulation of the foraging gene transcription.
MeSH term(s)	Bees/genetics ; Animals ; Phylogeny ; Behavior, Animal ; Genomics ; Seasons
Language	English
Publishing date	2024-02-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2024.148318
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Article: Editorial: Interplay of nutrition and genomics: Potential for improving performance and health of poultry.

Hassan, Faiz-Ul / Alagawany, Mahmoud / Jha, Rajesh

Frontiers in physiology

2022 Volume 13, Page(s) 1030995

Language	English
Publishing date	2022-10-03
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2022.1030995
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Article ; Online: Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan

Saif-ur-Rehman, Muhammad / Hassan, Faiz-ul / Reecy, James / Deng, Tingxian

Animal Biotechnology. 2023 Aug. 1, v. 34, no. 4 p.1384-1396

2023

Abstract: The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. ... ...

Abstract	The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1–4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
Keywords	biotechnology ; dairy cattle ; genomics ; genotyping ; homozygosity ; meat ; milk production ; reproduction ; selection pressure ; Pakistan ; Runs of homozygosity ; indigenous cattle ; candidate genes ; QTL
Language	English
Dates of publication	2023-0801
Size	p. 1384-1396.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	2043243-4
ISSN	1532-2378 ; 1049-5398
ISSN (online)	1532-2378
ISSN	1049-5398
DOI	10.1080/10495398.2022.2026369
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Article ; Online: Evaluation of phytochemicals from

Azhar, Jahanzaib / Nadeem, Asif / Javed, Maryam / Ahmad, Hafiz Ishfaq / Hassan, Faiz-Ul / Shah, Faisal Sheraz

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 6, Page(s) 2897–2912

Abstract: Dairy cows undergo immense stress and experience autoimmune reactions during the transition period, majorly due to the generation of ROS in the body. So, pharmacological approaches are needed to manage oxidative stress in the transition cows. Recently, ... ...

Abstract	Dairy cows undergo immense stress and experience autoimmune reactions during the transition period, majorly due to the generation of ROS in the body. So, pharmacological approaches are needed to manage oxidative stress in the transition cows. Recently, the use of phytochemicals as feed additives in cows' nutrition has gained interest in managing various disease conditions. In the current study, we have evaluated the potential effects of phytochemicals derived from methanolic extract of
MeSH term(s)	Female ; Cattle ; Animals ; Kaempferols/pharmacology ; NF-kappa B ; Oxidative Stress ; Phytochemicals/pharmacology ; Plant Extracts/pharmacology ; Antioxidants/pharmacology
Chemical Substances	Kaempferols ; NF-kappa B ; Phytochemicals ; Plant Extracts ; Antioxidants
Language	English
Publishing date	2023-05-08
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2209190
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Article ; Online: Genomic analysis of arginine vasopressin gene in riverine buffalo reveals its potential association with silent estrus behavior

Javed, Maryam / Nadeem, Asif / Hassan, Faiz-ul / Mujahid, Huma / Rehman, Saif-ur-

Mol Biol Rep. 2022 Oct., v. 49, no. 10 p.9315-9324

2022

Abstract: BACKGROUND: Poor estrus expression behavior causes suboptimal reproductive efficiency through poor conception rate. Various signaling pathways are involved in estrus expression but arginine vasopressin (AVP) gene with oxytocin predominantly regulates ... ...

Abstract	BACKGROUND: Poor estrus expression behavior causes suboptimal reproductive efficiency through poor conception rate. Various signaling pathways are involved in estrus expression but arginine vasopressin (AVP) gene with oxytocin predominantly regulates estrus behavior. This study aimed to perform genomic characterization and evolutionary dynamics of AVP gene through association testing of the novel polymorphic loci and comparative genomic analysis to explore the potential effect of AVP gene on estrus behavior of Nili-Ravi buffaloes. METHODS AND RESULTS: 198 Nili-Ravi buffaloes were screened for the quest of novel polymorphism in the AVP gene. In exon-1, five polymorphic sites were detected including deletion of two (c.47delA and c.57delA) nucleotides that caused drastic variation in subsequent amino acid sequence due to frame shift including functional short peptide of nine residues. The 3-D structure revealed a loss of transmembrane loop between 16 and 31 residues in Nili-Ravi buffalo AVP protein sequence, suggesting that missing loop apparently reduced the gene functionality in Nili-Ravi buffalo by inhibiting cellular reactions and muting the animal estrus cyclicity. Three polymorphisms detected in AVP gene were significantly associated with silent estrus (P < 0.05). The comparative genomic analysis revealed that AVP gene is present on chromosome 14 having one conserved motif (Neurohypophysial) in buffalo. CONCLUSIONS: This study suggested the potential use of polymorphic sites as promising genetic markers for selection of buffaloes with pronounced estrus expression.
Keywords	amino acid sequences ; arginine vasopressin ; buffaloes ; chromosomes ; conception rate ; estrus ; genes ; genomics ; nucleotides ; oxytocin ; periodicity ; reproductive efficiency ; riparian areas
Language	English
Dates of publication	2022-10
Size	p. 9315-9324.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07776-5
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Article ; Online: Revisiting the Effects of Different Dietary Sources of Selenium on the Health and Performance of Dairy Animals: a Review.

Arshad, Muhammad Adeel / Ebeid, Hossam Mahrous / Hassan, Faiz-Ul

Biological trace element research

2020 Volume 199, Issue 9, Page(s) 3319–3337

Abstract: Selenium (Se) is one of the most important essential trace elements in livestock production. It is a structural component in at least 25 selenoproteins such as the iodothyronine deiodinases and thioredoxin reductases as selenocysteine at critical ... ...

Abstract	Selenium (Se) is one of the most important essential trace elements in livestock production. It is a structural component in at least 25 selenoproteins such as the iodothyronine deiodinases and thioredoxin reductases as selenocysteine at critical positions in the active sites of these enzymes. It is also involved in the synthesis of the thyroid hormone and influences overall body metabolism. Selenium being a component of the glutathione peroxidase enzyme also plays a key role in the antioxidant defense system of animals. Dietary requirements of Se in dairy animals depend on physiological status, endogenous Se content, Se source, and route of administration. Most of the dietary Se is absorbed through the duodenum in ruminants and also some portion through the rumen wall. Inorganic Se salts such as Na-selenate and Na-selenite have shown lower bioavailability than organic and nano-Se. Selenium deficiency has been associated with reproductive disorders such as retained placenta, abortion, early embryonic death, and infertility, together with muscular diseases (like white muscle disease and skeletal and cardiac muscle necrosis). The deficiency of Se can also affect the udder health particularly favoring clinical and subclinical mastitis, along with an increase of milk somatic cell counts in dairy animals. However, excessive Se supplementation (5 to 8 mg/kg DM) can lead to acute toxicity including chronic and acute selenosis. Se is the most vital trace element for the optimum performance of dairy animals. This review focuses to provide insights into the comparative efficacy of different forms of dietary Se (inorganic, organic, and nano-Se) on the health and production of dairy animals and milk Se content.
MeSH term(s)	Animals ; Diet ; Dietary Supplements ; Female ; Glutathione Peroxidase ; Milk ; Pregnancy ; Selenium/pharmacology
Chemical Substances	Glutathione Peroxidase (EC 1.11.1.9) ; Selenium (H6241UJ22B)
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	445336-0
ISSN	1559-0720 ; 0163-4984
ISSN (online)	1559-0720
ISSN	0163-4984
DOI	10.1007/s12011-020-02480-6
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Article ; Online: Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan.

Saif-Ur-Rehman, Muhammad / Hassan, Faiz-Ul / Reecy, James / Deng, Tingxian

Animal biotechnology

2022 Volume 34, Issue 4, Page(s) 1384–1396

Abstract: The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds ( ...

Abstract	The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (
MeSH term(s)	Cattle/genetics ; Animals ; Pakistan ; Polymorphism, Single Nucleotide/genetics ; Homozygote ; Inbreeding ; Genome/genetics ; Genotype
Language	English
Publishing date	2022-01-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2043243-4
ISSN	1532-2378 ; 1049-5398
ISSN (online)	1532-2378
ISSN	1049-5398
DOI	10.1080/10495398.2022.2026369
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Article ; Online: Genetic variants of

Asim, Muhammad / Saif-Ur Rehman, Muhammad / Hassan, Faiz-Ul / Awan, Faisal Saeed

Animal biotechnology

2022 Volume 34, Issue 7, Page(s) 2951–2962

Abstract: Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes ( ...

Abstract	Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes (
MeSH term(s)	Female ; Cattle/genetics ; Animals ; Buffaloes/genetics ; Caseins/genetics ; Caseins/metabolism ; Milk/chemistry ; Milk Proteins/genetics ; Polymorphism, Single Nucleotide/genetics ; Lactation/genetics
Chemical Substances	Caseins ; Milk Proteins
Language	English
Publishing date	2022-09-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2043243-4
ISSN	1532-2378 ; 1049-5398
ISSN (online)	1532-2378
ISSN	1049-5398
DOI	10.1080/10495398.2022.2126365
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Article ; Online: Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo.

Liu, Shen-He / Ma, Xiao-Ya / Hassan, Faiz-Ul / Gao, Teng-Yun / Deng, Ting-Xian

Journal of dairy science

2022 Volume 105, Issue 5, Page(s) 4324–4334

Abstract: Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, ...

Abstract	Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (F
MeSH term(s)	Animals ; Buffaloes/genetics ; Cattle ; Diarrhea/veterinary ; Genotype ; Homozygote ; Inbreeding ; Italy ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	242499-x
ISSN	1525-3198 ; 0022-0302
ISSN (online)	1525-3198
ISSN	0022-0302
DOI	10.3168/jds.2021-21543
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Article ; Online: Genomic analysis of arginine vasopressin gene in riverine buffalo reveals its potential association with silent estrus behavior.

Javed, Maryam / Nadeem, Asif / Hassan, Faiz-Ul / Mujahid, Huma / Rehman, Saif Ur

Molecular biology reports

2022 Volume 49, Issue 10, Page(s) 9315–9324

Abstract: Background: Poor estrus expression behavior causes suboptimal reproductive efficiency through poor conception rate. Various signaling pathways are involved in estrus expression but arginine vasopressin (AVP) gene with oxytocin predominantly regulates ... ...

Abstract	Background: Poor estrus expression behavior causes suboptimal reproductive efficiency through poor conception rate. Various signaling pathways are involved in estrus expression but arginine vasopressin (AVP) gene with oxytocin predominantly regulates estrus behavior. This study aimed to perform genomic characterization and evolutionary dynamics of AVP gene through association testing of the novel polymorphic loci and comparative genomic analysis to explore the potential effect of AVP gene on estrus behavior of Nili-Ravi buffaloes. Methods and results: 198 Nili-Ravi buffaloes were screened for the quest of novel polymorphism in the AVP gene. In exon-1, five polymorphic sites were detected including deletion of two (c.47delA and c.57delA) nucleotides that caused drastic variation in subsequent amino acid sequence due to frame shift including functional short peptide of nine residues. The 3-D structure revealed a loss of transmembrane loop between 16 and 31 residues in Nili-Ravi buffalo AVP protein sequence, suggesting that missing loop apparently reduced the gene functionality in Nili-Ravi buffalo by inhibiting cellular reactions and muting the animal estrus cyclicity. Three polymorphisms detected in AVP gene were significantly associated with silent estrus (P < 0.05). The comparative genomic analysis revealed that AVP gene is present on chromosome 14 having one conserved motif (Neurohypophysial) in buffalo. Conclusions: This study suggested the potential use of polymorphic sites as promising genetic markers for selection of buffaloes with pronounced estrus expression.
MeSH term(s)	Animals ; Arginine Vasopressin/genetics ; Buffaloes/genetics ; Estrus/genetics ; Female ; Genetic Markers ; Genomics ; Nucleotides ; Oxytocin/genetics
Chemical Substances	Genetic Markers ; Nucleotides ; Arginine Vasopressin (113-79-1) ; Oxytocin (50-56-6)
Language	English
Publishing date	2022-07-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07776-5
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