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New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus)

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Abstract

Cattle (Bos taurus) and goat (Capra hircus) belong to the Bovidae family, and they share a common ancestor 19.7–21.5 Ma ago (MYA). The Bovidae family apparently experienced a rapid species radiation in the middle Miocene. The present day cattle and goat possess the same diploid chromosome number (2n = 60) and structurally similar autosomes, except that a small subcentromeric portion of cattle chromosome nine has been translocated to goat chromosome 14. In this study, we adopted a new strategy that involves the use of bioinformatics approach to detect unknown cryptic chromosome divergences between cattle and goat using and subsequent validation using the fluorescence in situ hybridization (FISH) of bacterial artificial chromosome clones. We identified two hypothetical discrepancies between the cattle and goat genome assemblies: an inversion in the goat chromosome 13 and a transposition in the goat chromosome 6. The FISH technique allowed clear validation of the existence of a new 7.4 Mb chromosomal inversion in the goat chromosome 13. Regarding the transposition in the goat chromosome six, FISH analyses revealed that the cattle and goat genomes shared the same organization, with the assembly of the goat genome being the correct one. Moreover, we defined, for the first time, the size and orientation of the translocated fragment involved in the evolutionary translocation between cattle chromosomes 9 and goat chromosome 14. Our results suggest that bioinformatics represents an efficient method for detecting cryptic chromosome divergences among species.

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Abbreviations

MYA:

Million years ago

FISH:

Fluorescent in situ hybridization

CHI:

Capra hircus

BTA:

Bos taurus

Mb:

Megabase

BAC:

Bacteria artificial chromosome

INRA:

Institut nationale de la recherche agronomique

Kb:

Kilobase

CNV:

Copy number variation

EBP:

Evolutionary break point

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Acknowledgments

We are grateful to the animal owner for providing blood samples.

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Authors and Affiliations

  1. Department of Agricultural and Environmental Sciences, Milan University, Via Celoria 2, 20133, Milan, Italy

    Lisa De Lorenzi, Luca Malagutti & Pietro Parma

  2. Department of System Biology, Vic University, Carrer de la Laura 13, 08500, Vic, Spain

    Jordi Planas

  3. Department of Molecular Medicine, Pavia University, Via Forlanini 14, 27100, Pavia, Italy

    Elena Rossi

Authors
  1. Lisa De Lorenzi
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  2. Jordi Planas
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  3. Elena Rossi
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  4. Luca Malagutti
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  5. Pietro Parma
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Corresponding author

Correspondence to Pietro Parma.

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Responsible Editor: Fengtang Yang

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De Lorenzi, L., Planas, J., Rossi, E. et al. New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus). Chromosome Res 23, 225–235 (2015). https://doi.org/10.1007/s10577-014-9462-4

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  • DOI: https://doi.org/10.1007/s10577-014-9462-4

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