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

BMC Genomics

Research Article

Julie A Long¹  Le Ann Blomberg¹  John WM Bastiaansen²  Martien AM Groenen²  Richard PMA Crooijmans²  Muhammad L Aslam²  Hendrik-Jan Megens²  Martin G Elferink²  Tad S Sonstegard³  Steven G Schroeder³  Curtis P Van Tassell³  Robert C Fleischer⁴ 

[1] Animal Biosciences and Biotechnology Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture, 20705, Beltsville, MD, USA;Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD, Wageningen, The Netherlands;Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, United States Department of Agriculture, 20705, Beltsville, MD, USA;Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, 20013, Washington, DC, USA;

关键词: Chicken Genome;    Allelic State;    Heritage Variety;    Putative SNPs;    Small Effective Population Size;   

DOI  :  10.1186/1471-2164-13-391

 received in 2012-03-26, accepted in 2012-08-09,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsAlignment 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.ConclusionThe 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.

【 授权许可】

CC BY   
© Aslam et al.; licensee BioMed Central Ltd. 2012