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  1. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 810: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  2. Article: 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

    American Dairy Science Association Journal of dairy science. 2022 Feb. 07,

    2022  

    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 (FROH) ranged from 0.0201 to 0.0371. Pearson correlations between FROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.
    Keywords buffaloes ; cattle ; dairy science ; genetic improvement ; genome-wide association study ; genomics ; homozygosity ; milk ; protein-protein interactions ; quantitative traits
    Language English
    Dates of publication 2022-0207
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 242499-x
    ISSN 1525-3198 ; 0022-0302
    ISSN (online) 1525-3198
    ISSN 0022-0302
    DOI 10.3168/jds.2021-21543
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  3. Article: Transcriptome-Wide m6A Analysis Provides Novel Insights Into Testicular Development and Spermatogenesis in Xia-Nan Cattle.

    Liu, Shen-He / Ma, Xiao-Ya / Yue, Ting-Ting / Wang, Zi-Chen / Qi, Kun-Long / Li, Ji-Chao / Lin, Feng / Rushdi, Hossam E / Gao, Yu-Yang / Fu, Tong / Li, Ming / Gao, Teng-Yun / Yang, Li-Guo / Han, Xue-Lei / Deng, Ting-Xian

    Frontiers in cell and developmental biology

    2021  Volume 9, Page(s) 791221

    Abstract: Testis is the primary organ of the male reproductive tract in mammals that plays a substantial role in spermatogenesis. Improvement of our knowledge regarding the molecular mechanisms in testicular development and spermatogenesis will be reflected in ... ...

    Abstract Testis is the primary organ of the male reproductive tract in mammals that plays a substantial role in spermatogenesis. Improvement of our knowledge regarding the molecular mechanisms in testicular development and spermatogenesis will be reflected in producing spermatozoa of superior fertility. Evidence showed that N6-Methyladenosine (m6A) plays a dynamic role in post-transcription gene expression regulation and is strongly associated with production traits. However, the role of m6A in bovine testis has not been investigated yet. In this study, we conducted MeRIP-Seq analysis to explore the expression profiles of the m6A and its potential mechanism underlying spermatogenesis in nine bovine testes at three developmental stages (prepuberty, puberty and postpuberty). The experimental animals with triplicate in each stage were chosen based on their semen volume and sperm motility except for the prepuberty bulls and used for testes collection. By applying MeRIP-Seq analysis, a total of 8,774 m6A peaks and 6,206 m6A genes among the studied groups were identified. All the detected peaks were found to be mainly enriched in the coding region and 3'- untranslated regions. The cross-analysis of m6A and mRNA expression exhibited 502 genes with concomitant changes in the mRNA expression and m6A modification. Notably, 30 candidate genes were located in the largest network of protein-protein interactions. Interestingly, four key node genes (
    Language English
    Publishing date 2021-12-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2021.791221
    Database MEDical Literature Analysis and Retrieval System OnLINE

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