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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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 journalArticleResearchpeer-review

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