Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations.
BACKGROUND
Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds.


RESULTS
We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings.


CONCLUSIONS
The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.
Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. anita_op@hotmail.com.
Ana M Perez
AM
O'Brien
Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. daniela.hoeller@aon.at.
Daniela
D
Höller
Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. solomon.boison@students.boku.ac.at.
Solomon A
SA
Boison
Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy. marco.milanesi@unicatt.it.
Marco
M
Milanesi
Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy. lorenzo.bomba@unicatt.it.
Lorenzo
L
Bomba
Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. ytutsunomiya@gmail.com.
Yuri T
YT
Utsunomiya
Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. rcar@fcav.unesp.br.
Roberto
R
Carvalheiro
Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. haroldozoo@hotmail.com.
Haroldo H R
HH
Neves
Empresa Brasileira de Pesquisa Agropecuária - Embrapa Gado de Leite, Juiz de Fora, MG, Brazil. marcos.vb.silva@embrapa.br.
Marcos V B
MV
da Silva
United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA. curt.vantassell@ars.usda.gov.
Curtis P
CP
VanTassell
United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA. tad.sonstegard@ars.usda.gov.
Tad S
TS
Sonstegard
Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. gabor.meszaros@boku.ac.at.
Gábor
G
Mészáros
Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy. paolo.ajmone@unicatt.it.
Paolo
P
Ajmone-Marsan
Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. jfgarcia@fmva.unesp.br.|Universidade Estadual Paulista (UNESP) - Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, SP, Brazil. jfgarcia@fmva.unesp.br.
Fernando
F
Garcia
Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. johann.soelkner@boku.ac.at.
Johann
J
Sölkner
D000818:Animals; D001938:Brazil; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes; D008928:Mitochondria / Q000235:genetics; D020641:Polymorphism, Single Nucleotide