A practical approach to detect ancestral haplotypes in livestock populations

E Sanchez-Molano, D Tsiokos, D Chatziplis, H Jorjani, L Degano, C Diaz, A Rossoni, H Schwarzenbacher, F Seefried, L Varona, D Vicario, EL Nicolazzi, G Banos

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    Abstract

    Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.
    Original languageEnglish
    JournalBMC Genetics
    Volume17
    Issue number91
    Early online date24 Jun 2016
    DOIs
    Publication statusFirst published - 24 Jun 2016

    Fingerprint

    haplotypes
    livestock
    Simmental
    population dynamics
    chromosomes
    genomics
    Brown Swiss
    cattle
    conservation programs
    breeding
    linkage disequilibrium
    dairy protein
    lipid content
    breeds
    genome
    color
    animals

    Bibliographical note

    1028465

    Keywords

    • Ancestral haplotypes
    • Cattle
    • Population dynamics
    • Selection strategies

    Cite this

    Sanchez-Molano, E., Tsiokos, D., Chatziplis, D., Jorjani, H., Degano, L., Diaz, C., ... Banos, G. (2016). A practical approach to detect ancestral haplotypes in livestock populations. BMC Genetics, 17(91). https://doi.org/10.1186/s12863-016-0405-2
    Sanchez-Molano, E ; Tsiokos, D ; Chatziplis, D ; Jorjani, H ; Degano, L ; Diaz, C ; Rossoni, A ; Schwarzenbacher, H ; Seefried, F ; Varona, L ; Vicario, D ; Nicolazzi, EL ; Banos, G. / A practical approach to detect ancestral haplotypes in livestock populations. In: BMC Genetics. 2016 ; Vol. 17, No. 91.
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    abstract = "Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.",
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    Sanchez-Molano, E, Tsiokos, D, Chatziplis, D, Jorjani, H, Degano, L, Diaz, C, Rossoni, A, Schwarzenbacher, H, Seefried, F, Varona, L, Vicario, D, Nicolazzi, EL & Banos, G 2016, 'A practical approach to detect ancestral haplotypes in livestock populations', BMC Genetics, vol. 17, no. 91. https://doi.org/10.1186/s12863-016-0405-2

    A practical approach to detect ancestral haplotypes in livestock populations. / Sanchez-Molano, E; Tsiokos, D; Chatziplis, D; Jorjani, H; Degano, L; Diaz, C; Rossoni, A; Schwarzenbacher, H; Seefried, F; Varona, L; Vicario, D; Nicolazzi, EL; Banos, G.

    In: BMC Genetics, Vol. 17, No. 91, 24.06.2016.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A practical approach to detect ancestral haplotypes in livestock populations

    AU - Sanchez-Molano, E

    AU - Tsiokos, D

    AU - Chatziplis, D

    AU - Jorjani, H

    AU - Degano, L

    AU - Diaz, C

    AU - Rossoni, A

    AU - Schwarzenbacher, H

    AU - Seefried, F

    AU - Varona, L

    AU - Vicario, D

    AU - Nicolazzi, EL

    AU - Banos, G

    N1 - 1028465

    PY - 2016/6/24

    Y1 - 2016/6/24

    N2 - Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.

    AB - Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.

    KW - Ancestral haplotypes

    KW - Cattle

    KW - Population dynamics

    KW - Selection strategies

    U2 - 10.1186/s12863-016-0405-2

    DO - 10.1186/s12863-016-0405-2

    M3 - Article

    VL - 17

    JO - BMC Genetics

    JF - BMC Genetics

    SN - 1471-2156

    IS - 91

    ER -

    Sanchez-Molano E, Tsiokos D, Chatziplis D, Jorjani H, Degano L, Diaz C et al. A practical approach to detect ancestral haplotypes in livestock populations. BMC Genetics. 2016 Jun 24;17(91). https://doi.org/10.1186/s12863-016-0405-2