Merino and Merino-derived sheep breeds: a genome-wide intercontinental study.
BACKGROUND
Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset.


RESULTS
Based on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices.


CONCLUSIONS
Our data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.
Dipartimento di Bioscienze, Biotecnologie, Biofarmaceutica, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A 70126, Bari, Italy. elena.ciani@uniba.it.
Elena
E
Ciani
Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX giugno, 74 06121, Perugia, Italy. emiliano.lasagna@unipg.it.
Emiliano
E
Lasagna
Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, 86100, Italy. dandrea@unimol.it.
Mariasilvia
M
D'Andrea
Dipartimento di Bioscienze, Biotecnologie, Biofarmaceutica, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A 70126, Bari, Italy. ingrid.alloggio@agr.uniba.it.
Ingrid
I
Alloggio
Dipartimento di Scienze Agrarie e Ambientali, Universita' di Udine, Via delle Scienze 206, 33100, Udine, Italy. marroni@appliedgenomics.org.|Istituto di Genomica Applicata (IGA), via J Linussio 51, 33100, Udine, Italy. marroni@appliedgenomics.org.
Fabio
F
Marroni
Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX giugno, 74 06121, Perugia, Italy. simo.ceccobelli@tiscali.it.
Simone
S
Ceccobelli
Departamento de Génetica, Universidad de Córdoba, Edificio Méndel C5, Campus Rabanales, 14071, Cordoba, Spain. juanviagr218@gmail.com.
Juan V
JV
Delgado Bermejo
Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX giugno, 74 06121, Perugia, Italy. francesca.sarti@unipg.it.
Francesca M
FM
Sarti
CSIRO Agriculture Flagship, St Lucia, Brisbane, QLD, Australia. James.Kijas@csiro.au.
James
J
Kijas
Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584CM, Utrecht, The Netherlands. J.A.Lenstra@uu.nl.
Johannes A
JA
Lenstra
Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, 86100, Italy. pilla@unimol.it.
Fabio
F
Pilla
D000818:Animals; D001315:Australia; D002681:China; D005060:Europe; D018703:Founder Effect; D051456:Gene Flow; D055106:Genome-Wide Association Study; D009520:New Zealand; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D000068618:Selective Breeding / Q000235:genetics*; D012756:Sheep / Q000145:classification* / Q000235:genetics*