Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

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Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. / Utsunomiya, Yuri T.; Bomba, Lorenzo; Lucente, Giordana; Colli, Licia; Negrini, Riccardo; Lenstra, Johannes A.; Erhardt, Georg; Garcia, José F.; Ajmone-Marsan, Paolo; Moazami-Goudarzi, K.; Williams, J.; Wiener, P.; Olsaker, I.; Kantanen, J.; Dunner, S.; Cañón, J.; Rodellar, C.; Martín-Burriel, I.; Valentini, A.; Zanotti, M.; Holm, L. E.; Eythorsdottir, E.; Mommens, G.; Polygen, Van Haeringen; Nijman, I. J.; Dolf, G.; Bradley, D. G.

In: BMC Genetics, Vol. 15, 47, 17.04.2014.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Utsunomiya, YT, Bomba, L, Lucente, G, Colli, L, Negrini, R, Lenstra, JA, Erhardt, G, Garcia, JF, Ajmone-Marsan, P, Moazami-Goudarzi, K, Williams, J, Wiener, P, Olsaker, I, Kantanen, J, Dunner, S, Cañón, J, Rodellar, C, Martín-Burriel, I, Valentini, A, Zanotti, M, Holm, LE, Eythorsdottir, E, Mommens, G, Polygen, VH, Nijman, IJ, Dolf, G & Bradley, DG 2014, 'Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle', BMC Genetics, vol. 15, 47. https://doi.org/10.1186/1471-2156-15-47

APA

Utsunomiya, Y. T., Bomba, L., Lucente, G., Colli, L., Negrini, R., Lenstra, J. A., Erhardt, G., Garcia, J. F., Ajmone-Marsan, P., Moazami-Goudarzi, K., Williams, J., Wiener, P., Olsaker, I., Kantanen, J., Dunner, S., Cañón, J., Rodellar, C., Martín-Burriel, I., Valentini, A., ... Bradley, D. G. (2014). Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. BMC Genetics, 15, [47]. https://doi.org/10.1186/1471-2156-15-47

CBE

Utsunomiya YT, Bomba L, Lucente G, Colli L, Negrini R, Lenstra JA, Erhardt G, Garcia JF, Ajmone-Marsan P, Moazami-Goudarzi K, Williams J, Wiener P, Olsaker I, Kantanen J, Dunner S, Cañón J, Rodellar C, Martín-Burriel I, Valentini A, Zanotti M, Holm LE, Eythorsdottir E, Mommens G, Polygen VH, Nijman IJ, Dolf G, Bradley DG. 2014. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. BMC Genetics. 15:Article 47. https://doi.org/10.1186/1471-2156-15-47

MLA

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Utsunomiya, Yuri T. ; Bomba, Lorenzo ; Lucente, Giordana ; Colli, Licia ; Negrini, Riccardo ; Lenstra, Johannes A. ; Erhardt, Georg ; Garcia, José F. ; Ajmone-Marsan, Paolo ; Moazami-Goudarzi, K. ; Williams, J. ; Wiener, P. ; Olsaker, I. ; Kantanen, J. ; Dunner, S. ; Cañón, J. ; Rodellar, C. ; Martín-Burriel, I. ; Valentini, A. ; Zanotti, M. ; Holm, L. E. ; Eythorsdottir, E. ; Mommens, G. ; Polygen, Van Haeringen ; Nijman, I. J. ; Dolf, G. ; Bradley, D. G. / Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. In: BMC Genetics. 2014 ; Vol. 15.

Bibtex

@article{45049df6f71a45c7bd76bc97f44dfe0b,
title = "Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle",
abstract = "Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.",
keywords = "AFLP, Ascertainment bias, Cattle, Genetic differentiation",
author = "Utsunomiya, {Yuri T.} and Lorenzo Bomba and Giordana Lucente and Licia Colli and Riccardo Negrini and Lenstra, {Johannes A.} and Georg Erhardt and Garcia, {Jos{\'e} F.} and Paolo Ajmone-Marsan and K. Moazami-Goudarzi and J. Williams and P. Wiener and I. Olsaker and J. Kantanen and S. Dunner and J. Ca{\~n}{\'o}n and C. Rodellar and I. Mart{\'i}n-Burriel and A. Valentini and M. Zanotti and Holm, {L. E.} and E. Eythorsdottir and G. Mommens and Polygen, {Van Haeringen} and Nijman, {I. J.} and G. Dolf and Bradley, {D. G.}",
year = "2014",
month = apr,
day = "17",
doi = "10.1186/1471-2156-15-47",
language = "English",
volume = "15",
journal = "B M C Genetics",
issn = "1471-2156",
publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

AU - Utsunomiya, Yuri T.

AU - Bomba, Lorenzo

AU - Lucente, Giordana

AU - Colli, Licia

AU - Negrini, Riccardo

AU - Lenstra, Johannes A.

AU - Erhardt, Georg

AU - Garcia, José F.

AU - Ajmone-Marsan, Paolo

AU - Moazami-Goudarzi, K.

AU - Williams, J.

AU - Wiener, P.

AU - Olsaker, I.

AU - Kantanen, J.

AU - Dunner, S.

AU - Cañón, J.

AU - Rodellar, C.

AU - Martín-Burriel, I.

AU - Valentini, A.

AU - Zanotti, M.

AU - Holm, L. E.

AU - Eythorsdottir, E.

AU - Mommens, G.

AU - Polygen, Van Haeringen

AU - Nijman, I. J.

AU - Dolf, G.

AU - Bradley, D. G.

PY - 2014/4/17

Y1 - 2014/4/17

N2 - Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.

AB - Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.

KW - AFLP

KW - Ascertainment bias

KW - Cattle

KW - Genetic differentiation

UR - http://www.scopus.com/inward/record.url?scp=84899922947&partnerID=8YFLogxK

U2 - 10.1186/1471-2156-15-47

DO - 10.1186/1471-2156-15-47

M3 - Journal article

C2 - 24739206

AN - SCOPUS:84899922947

VL - 15

JO - B M C Genetics

JF - B M C Genetics

SN - 1471-2156

M1 - 47

ER -