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Article: Novel Polymorphisms in

Azmal, Syed Ali / Bhuiyan, Ali Akbar / Omar, Abdullah Ibne / Ma, Shuai / Sun, Chenghao / Han, Zhongdong / Zhang, Meikuen / Zhao, Shuhong / Li, Shijun

Genes

2019 Volume 10, Issue 5

Abstract: The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked ...

Abstract	The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61-69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (
MeSH term(s)	Alleles ; Animals ; Avian Proteins/genetics ; Chickens/genetics ; Eggs ; Female ; Genome-Wide Association Study ; Genotype ; Guanine Nucleotide Exchange Factors/genetics ; Haplotypes ; Oviposition/genetics ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics
Chemical Substances	Avian Proteins ; Guanine Nucleotide Exchange Factors
Language	English
Publishing date	2019-05-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10050384
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Article ; Online: The construction of recombinant Lactobacillus casei expressing BVDV E2 protein and its immune response in mice.

Bhuyan, Anjuman Ara / Memon, Atta Muhammad / Bhuiyan, Ali Akbar / Zhonghua, Li / Zhang, Bingzhou / Ye, Shiyi / Mengying, Li / He, Qi-Gai

Journal of biotechnology

2018 Volume 270, Page(s) 51–60

Abstract: Bovine viral diarrhea virus (BVDV) is the etiological agent of BVD causes substantial economic losses and endemic in world-wide cattle population. Mucosal immunity plays an important role in protection against BVDV infection and Lactobacillus casei is ... ...

Abstract	Bovine viral diarrhea virus (BVDV) is the etiological agent of BVD causes substantial economic losses and endemic in world-wide cattle population. Mucosal immunity plays an important role in protection against BVDV infection and Lactobacillus casei is believed as an excellent live vaccine vector for expressing foreign genes. In this study, we have constructed a novel recombinant L. casei/pELX1-E2 strain expressing the most immunogenic E2 antigen of BVDV; using growth phage dependent surface expression system pELX1. The expression of E2 protein was verified by SDS-PAGE, Western blotting, and Immunofluorescence microscopic analysis. The immune responses triggered by the E2 producing recombinant L. casei were evaluated in BALB/c mice revealed that oral and intranasal (IN) administration of the recombinant strain was able to induce a significantly higher level of specific anti-E2 mucosal IgA and serum IgG as well as the greater level of cellular response by IFN-γ and IL-12 than those of intramuscular (IM) and control groups of mice. However, IN inoculation was found the most potent route of immunization. The ability of the recombinant strain to induce serum neutralizing antibody against BVDV and reduced viral load after viral challenge indicated better protection of BVDV infection. Therefore, this recombinant L. casei expressing E2 could be a safe and promising mucosal vaccine candidate against BVD.
MeSH term(s)	Administration, Intranasal ; Administration, Oral ; Animals ; Antibodies, Viral/blood ; Diarrhea Viruses, Bovine Viral/genetics ; Diarrhea Viruses, Bovine Viral/immunology ; Diarrhea Viruses, Bovine Viral/metabolism ; Genetic Engineering ; Immunization ; Interferon-gamma/metabolism ; Lactobacillus casei/genetics ; Lactobacillus casei/immunology ; Lactobacillus casei/metabolism ; Mice ; Mice, Inbred BALB C ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/immunology ; Viral Envelope Proteins/metabolism
Chemical Substances	Antibodies, Viral ; IFNG protein, mouse ; Viral Envelope Proteins ; gp53, bovine viral diarrhea virus ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2018-01-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	843647-2
ISSN	1873-4863 ; 0168-1656 ; 1389-0352
ISSN (online)	1873-4863
ISSN	0168-1656 ; 1389-0352
DOI	10.1016/j.jbiotec.2018.01.016
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Article ; Online: A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

Azmal, Syed Ali / Nan, Jiuhong / Bhuiyan, Ali Akbar / Elokil, Abdelmotaleb Ahmed / Ali, Mohammad Ishaque / Adetula, Adeyinka Abiola / Ma, Shuai / Sun, Chenghao / Han, Zhongdong / Yuan, Jingwei / Li, Shijun

Poultry science

2020 Volume 99, Issue 6, Page(s) 2873–2887

Abstract: The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with ... ...

Abstract	The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction-restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.
MeSH term(s)	Animals ; Breeding ; Chickens/genetics ; Chickens/growth & development ; Fertility/genetics ; Genetic Markers ; Genome-Wide Association Study/veterinary ; Polymerase Chain Reaction/veterinary ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide
Chemical Substances	Genetic Markers
Language	English
Publishing date	2020-04-10
Publishing country	England
Document type	Journal Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2019.12.068
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Article: A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken

Poultry science. 2020 June, v. 99, no. 6

2020

Abstract	The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction–restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.
Keywords	breeding ; egg production ; female fertility ; genetic markers ; genome-wide association study ; genotyping ; haplotypes ; laying hens ; loci ; phenotype ; polymerase chain reaction ; reproductive traits ; single nucleotide polymorphism ; spermatozoa
Language	English
Dates of publication	2020-06
Size	p. 2873-2887.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2019.12.068
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transcriptional Profiling of Leucocyte Count Variation from Porcine Peripheral Blood Reveals Differential Gene Expression.

Adetula, Adeyinka Abiola / Liu, Xiangdong / Tran Thi, Thuy Nhien / Bhuiyan, Ali Akbar / Du, Xiaoyong / Zhu, Mengjin / Li, Xinyun / Zhao, Shuhong / Ma, Yunlong / Wang, Haiyan

BioMed research international

2018 Volume 2018, Page(s) 1496536

Abstract: Leucocytes have tremendous health-check importance related to the individual antiviral capacity of pigs and other mammals. However, the molecular mechanism of the immune response of blood leucocytes in pigs is not completely known. This study ... ...

Abstract	Leucocytes have tremendous health-check importance related to the individual antiviral capacity of pigs and other mammals. However, the molecular mechanism of the immune response of blood leucocytes in pigs is not completely known. This study investigated the leucocyte-count variation before and after poly I:C stimulation in a Duroc-Erhualian F2 population. Pigs with increased and decreased differences in leucocyte counts were coded as increased responder (IR) and decreased responder (DR), respectively. Then, we used microarray technology to compare the gene-expression profiles of both groups of pigs. Transcriptomic analysis identified 129 differentially expressed genes (DEGs) in IR pigs and 136 DEGs in DR pigs. Forty-one common DEGs showed that both groups had similar expression patterns of immune responses. These results illustrated a differential expression in both groups. Furthermore, qPCR experiment was performed to verify the differential-expression profile. Functional annotation of the DEGs indicated that both IR and DR pigs were similar in several biological processes, including innate immune response, and also exhibited distinct differences in biological processes, molecular function, and pathways. These results provided insights into the mechanism underlying the antiviral capacity of pigs.
MeSH term(s)	Animals ; Gene Expression Profiling/methods ; Immunity, Innate/genetics ; Leukocyte Count/methods ; Leukocytes/physiology ; Oligonucleotide Array Sequence Analysis/methods ; Swine ; Transcription, Genetic/genetics ; Transcriptome/genetics
Language	English
Publishing date	2018-11-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2018/1496536
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Article ; Online: A Review of CRISPR-Based Genome Editing: Survival, Evolution and Challenges.

Ahmad, Hafiz Ishfaq / Ahmad, Muhammad Jamil / Asif, Akhtar Rasool / Adnan, Muhammad / Iqbal, Muhammad Kashif / Mehmood, Khalid / Muhammad, Sayyed Aun / Bhuiyan, Ali Akbar / Elokil, Abdelmotaleb / Du, Xiaoyong / Zhao, Changzhi / Liu, Xiangdong / Xie, Shengsong

Current issues in molecular biology

2018 Volume 28, Page(s) 47–68

Abstract: Precise nucleic acid editing technologies have facilitated the research of cellular function and the development of novel therapeutics, especially the current programmable nucleases-based editing tools, such as the prokaryotic clustered regularly ... ...

Abstract	Precise nucleic acid editing technologies have facilitated the research of cellular function and the development of novel therapeutics, especially the current programmable nucleases-based editing tools, such as the prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases (Cas). As CRISPR-based therapies are advancing toward human clinical trials, it is important to understand how natural genetic variation in the human population may affect the results of these trials and even patient safety. The development of "base-editing" technique allows the direct, stable transformation of target DNA base into an alternative in a programmable way, without DNA double strand cleavage or a donor template. Genome-editing techniques hold promises for the treatment of genetic disease at the DNA level by blocking the sequences associated with disease from producing disease-causing proteins. Currently, scientists can select the gene they want to modify, use the Cas9 as a "molecular cutter" to cut it out, and transform it into a more desirable version. In this review, we focus on the recent advances of CRISPR/Cas system by outlining the evolutionary and biotechnological implications of current strategies for improving the specificity and accuracy of these genome-editing technologies.
MeSH term(s)	Biotechnology/trends ; CRISPR-Cas Systems/genetics ; Gene Editing/methods ; Gene Editing/trends ; Genetic Diseases, Inborn/genetics ; Genetic Diseases, Inborn/therapy ; Humans
Language	English
Publishing date	2018-02-11
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.21775/cimb.028.047
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Article ; Online: De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs.

Ni, Pan / Bhuiyan, Ali Akbar / Chen, Jian-Hai / Li, Jingjin / Zhang, Cheng / Zhao, Shuhong / Du, Xiaoyong / Li, Hua / Yu, Hui / Liu, Xiangdong / Li, Kui

Genetica

2018 Volume 146, Issue 3, Page(s) 277–285

Abstract: Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild ... ...

Abstract	Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.
MeSH term(s)	Animals ; Animals, Wild ; Bayes Theorem ; Computational Biology/methods ; Evolution, Molecular ; Genetic Variation ; Genome, Mitochondrial ; Genomics/methods ; Phylogeny ; Selection, Genetic ; Sus scrofa ; Swine/classification ; Swine/genetics
Language	English
Publishing date	2018-05-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2165-9
ISSN	1573-6857 ; 0016-6707
ISSN (online)	1573-6857
ISSN	0016-6707
DOI	10.1007/s10709-018-0018-y
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Article ; Online: Exploring the Genetic Resistance to Gastrointestinal Nematodes Infection in Goat Using RNA-Sequencing.

Bhuiyan, Ali Akbar / Li, Jingjin / Wu, Zhenyang / Ni, Pan / Adetula, Adeyinka Abiola / Wang, Haiyan / Zhang, Cheng / Tang, Xiaohui / Bhuyan, Anjuman Ara / Zhao, Shuhong / Du, Xiaoyong

International journal of molecular sciences

2017 Volume 18, Issue 4

Abstract: Gastrointestinal nematodes (GINs) are one of the most economically important parasites of small ruminants and a major animal health concern in many regions of the world. However, the molecular mechanisms of the host response to GIN infections in goat are ...

Abstract	Gastrointestinal nematodes (GINs) are one of the most economically important parasites of small ruminants and a major animal health concern in many regions of the world. However, the molecular mechanisms of the host response to GIN infections in goat are still little known. In this study, two genetically distinct goat populations, one relatively resistant and the other susceptible to GIN infections, were identified in
MeSH term(s)	Animals ; Cluster Analysis ; Disease Resistance/genetics ; Gastrointestinal Diseases/genetics ; Gastrointestinal Diseases/parasitology ; Gastrointestinal Diseases/veterinary ; Gene Expression Profiling/methods ; Gene Ontology ; Goat Diseases/genetics ; Goat Diseases/parasitology ; Goats ; Haemonchiasis/genetics ; Haemonchiasis/parasitology ; Haemonchiasis/veterinary ; Haemonchus/growth & development ; Haemonchus/physiology ; Host-Parasite Interactions ; Molecular Sequence Annotation ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, RNA/methods ; Signal Transduction/genetics
Language	English
Publishing date	2017-04-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms18040751
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