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  1. AU="Kaisa, Kaiho"
  2. AU="Pierangeli, Giulia"
  3. AU=Manolagas Stavros C
  4. AU="Cilia, Roberto"
  5. AU="Mistry, Sejal N"

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  1. Article ; Online: Characterization of BoLA class II DQA and DQB by PCR-RFLP, cloning, and sequencing reveals sequence diversity in crossbred cattle

    Parasar, Parveen / Bhushan, Bharat / Panigrahi, Manjit / Kumar, Harshit / Kaisa, Kaiho / Dutt, Triveni

    Animal Biotechnology. 2023 Aug. 1, v. 34, no. 4 p.955-965

    2023  

    Abstract: The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, ... ...

    Abstract The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64–80, 110–200, and 207–264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3–25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5–14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes.
    Keywords amino acids ; biotechnology ; cattle ; crossbreds ; exons ; nucleotides ; phylogeny ; restriction endonucleases ; sequence diversity ; Polymorphism ; diversity ; sequence ; restriction enzymes ; PCR-RFLP
    Language English
    Dates of publication 2023-0801
    Size p. 955-965.
    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 10.1080/10495398.2021.2006205
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  2. Article ; Online: Molecular and phylogenetic analysis of MHC class I exons 7–8 in a variety of cattle and buffalo breeds

    Patra, Biswanath / Panigrahi, Manjit / Kumar, Harshit / Kaisa, Kaiho / Dutt, Triveni / Bhushan, Bharat

    Animal Biotechnology. 2023 Aug. 1, v. 34, no. 4 p.1655-1661

    2023  

    Abstract: The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was ... ...

    Abstract The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. Alul restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7–8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7–8 is highly polymorphic in buffalo as compared to cattle.
    Keywords Holstein ; Jersey ; Sahiwal ; biotechnology ; buffaloes ; cattle ; crossbreds ; exons ; phylogeny ; sequence analysis ; stop codon ; MHC ; BoLa-A polymorphism ; buffalo ; exon
    Language English
    Dates of publication 2023-0801
    Size p. 1655-1661.
    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 10.1080/10495398.2021.1999969
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Characterization of BoLA class II

    Parasar, Parveen / Bhushan, Bharat / Panigrahi, Manjit / Kumar, Harshit / Kaisa, Kaiho / Dutt, Triveni

    Animal biotechnology

    2021  Volume 34, Issue 4, Page(s) 955–965

    Abstract: The BoLA class ... ...

    Abstract The BoLA class II
    MeSH term(s) Cattle/genetics ; Animals ; Polymorphism, Restriction Fragment Length ; Phylogeny ; Amino Acid Sequence ; Polymerase Chain Reaction/veterinary ; Cloning, Molecular ; Nucleotides ; Alleles
    Chemical Substances Nucleotides
    Language English
    Publishing date 2021-11-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2043243-4
    ISSN 1532-2378 ; 1049-5398
    ISSN (online) 1532-2378
    ISSN 1049-5398
    DOI 10.1080/10495398.2021.2006205
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Molecular and phylogenetic analysis of MHC class I exons 7-8 in a variety of cattle and buffalo breeds.

    Patra, Biswanath / Panigrahi, Manjit / Kumar, Harshit / Kaisa, Kaiho / Dutt, Triveni / Bhushan, Bharat

    Animal biotechnology

    2021  Volume 34, Issue 4, Page(s) 1655–1661

    Abstract: The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7-8 of the MHC class I gene was ... ...

    Abstract The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7-8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle.
    MeSH term(s) Cattle/genetics ; Animals ; Buffaloes/genetics ; Phylogeny ; Genes, MHC Class I ; Exons/genetics ; Nucleotides ; Alleles
    Chemical Substances Nucleotides
    Language English
    Publishing date 2021-11-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2043243-4
    ISSN 1532-2378 ; 1049-5398
    ISSN (online) 1532-2378
    ISSN 1049-5398
    DOI 10.1080/10495398.2021.1999969
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Selection of breed-specific SNPs in three Indian sheep breeds using ovine 50 K array

    Kumar, Harshit / Panigrahi, Manjit / Rajawat, Divya / Panwar, Anuradha / Nayak, Sonali Sonejita / Kaisa, Kaiho / Bhushan, Bharat / Dutt, Triveni

    Small ruminant research. 2021 Dec., v. 205

    2021  

    Abstract: Recently DNA-based genetic purity determination tools have gained popularity, especially, in small ruminants like sheep. The objective of the present study was to select breed-specific SNPs for the three commercially important sheep breeds of India, i.e., ...

    Abstract Recently DNA-based genetic purity determination tools have gained popularity, especially, in small ruminants like sheep. The objective of the present study was to select breed-specific SNPs for the three commercially important sheep breeds of India, i.e., Changthangi, Deccani, and Garole. Sheep genotype data (Ovine 50 K SNP array) from 344 individuals of eight sheep breeds (Garole, Deccani, Changthangi, Tibetan, Australian Merino, Dorset Horn, Rambouillet, and Irish Suffolk) were used as a reference population. Here, we used pre-selection statistics and the minor allele frequency–linkage disequilibrium (MAF-LD) method to analyze the reference population dataset. SNPs selection and breed assignment was executed with a panel of 768 markers for eight breeds near intermediate gene frequencies. We identified 95, 89, and 92 breed-specific SNPs for Changthangi, Deccani, and Garole, respectively. These informative SNPs were found to be associated with essential candidate genes associated with production and disease resistance. This methodology may be implemented in practice to identify individuals as being purebred or not.
    Keywords Merino ; Rambouillet ; alleles ; data collection ; disease resistance ; genotype ; purebreds ; research ; sheep ; single nucleotide polymorphism arrays ; statistics ; India
    Language English
    Dates of publication 2021-12
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 286928-7
    ISSN 0921-4488
    ISSN 0921-4488
    DOI 10.1016/j.smallrumres.2021.106545
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    In stock of ZB MED Bonn / Germany

    Z 4801: Show issues

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  6. Article: Trajectory of livestock genomics in South Asia: A comprehensive review

    Panigrahi, Manjit / Kumar, Harshit / Saravanan, K.A. / Rajawat, Divya / Sonejita Nayak, Sonali / Ghildiyal, Kanika / Kaisa, Kaiho / Parida, Subhashree / Bhushan, Bharat / Dutt, Triveni

    Gene. 2022 Nov. 15, v. 843

    2022  

    Abstract: Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of ... ...

    Abstract Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
    Keywords cattle ; genes ; genetic variation ; genomics ; humans ; livelihood ; livestock and meat industry ; marker-assisted selection ; mithuns ; poultry ; yaks ; South Asia
    Language English
    Dates of publication 2022-1115
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2022.146808
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    In stock of ZB MED Bonn / Germany

    Z 79/715: Show issues

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  7. Article ; Online: Trajectory of livestock genomics in South Asia: A comprehensive review.

    Panigrahi, Manjit / Kumar, Harshit / Saravanan, K A / Rajawat, Divya / Sonejita Nayak, Sonali / Ghildiyal, Kanika / Kaisa, Kaiho / Parida, Subhashree / Bhushan, Bharat / Dutt, Triveni

    Gene

    2022  Volume 843, Page(s) 146808

    Abstract: Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of ... ...

    Abstract Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
    MeSH term(s) Animals ; Asia ; Cattle/genetics ; Genome ; Genome-Wide Association Study ; Genomics ; Goats/genetics ; Horses/genetics ; Humans ; Livestock/genetics ; Sheep/genetics ; Swine
    Language English
    Publishing date 2022-08-13
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2022.146808
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1357: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data.

    Kumar, Harshit / Panigrahi, Manjit / Panwar, Anuradha / Rajawat, Divya / Nayak, Sonali Sonejita / Saravanan, K A / Kaisa, Kaiho / Parida, Subhashree / Bhushan, Bharat / Dutt, Triveni

    Journal of computational biology : a journal of computational molecular cell biology

    2022  Volume 29, Issue 9, Page(s) 943–960

    Abstract: Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele ... ...

    Abstract Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
    MeSH term(s) Genetics, Population ; Genomics/methods ; Machine Learning ; Metagenomics ; Selection, Genetic
    Language English
    Publishing date 2022-05-30
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2021.0447
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