Research article

BMC Genomics

, 13:391

Open Access This content is freely available online to anyone, anywhere at any time.

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)

  • Muhammad L AslamAffiliated withAnimal Breeding and Genomics Centre, Wageningen University Email author 
  • , John WM BastiaansenAffiliated withAnimal Breeding and Genomics Centre, Wageningen University
  • , Martin G ElferinkAffiliated withAnimal Breeding and Genomics Centre, Wageningen University
  • , Hendrik-Jan MegensAffiliated withAnimal Breeding and Genomics Centre, Wageningen University
  • , Richard PMA CrooijmansAffiliated withAnimal Breeding and Genomics Centre, Wageningen University
  • , Le Ann BlombergAffiliated withAnimal Biosciences and Biotechnology Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture
  • , Robert C FleischerAffiliated withCenter for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute
  • , Curtis P Van TassellAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture
  • , Tad S SonstegardAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture
    • , Steven G SchroederAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture
    • , Martien AM GroenenAffiliated withAnimal Breeding and Genomics Centre, Wageningen University
    • , Julie A LongAffiliated withAnimal Biosciences and Biotechnology Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture

Abstract

Background

The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome.

Results

Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles.

Conclusion

The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.