Genetic control and variation in turkey: molecular insights in selection

The turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat type bird as egg production of this species is very low. Turkey is the second largest contributor to the world’s poultry meat production after chicken. Understanding the etiology and biology underlying production and health traits is very important for the genetic improvement of these traits in the desired direction and to avoid undesired side-effects. The aim of the research described in this thesis was to interrogate the genetics of turkey traits related to meat production and to investigate the genetic diversity of commercial and heritage turkey populations. Different analyses were performed that included the estimation of genetic and (common) environmental variances for growth (body weight as well as growth curve traits), breast meat yield and meat quality traits in turkeys. I describe the construction of a single nucleotide polymorphism (SNP) based linkage map of turkey and its comparison with the physical map of chicken to investigate genome structural differences between these highly important poultry production species. Two inter-, and 57 intra-chromosomal rearrangements between these two species were confirmed or discovered which is a low number in comparison to mammals and lead to the conclusion that turkey and chicken have highly conserved genomic structure. I used the linkage map of turkey together with individual phenotypes to map quantitative trait loci (QTL) in the same population for the traits described above. Results showed quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on the 21 chromosomes. The next step, after the analyses on the reference population was to investigate the genomic variation in turkeys Next generation sequencing was used to investigate genome variation and the discovery of genome-wide signatures of selection in the turkey respectively. Sequencing was performed on 32 individuals from eleven different turkey populations (seven commercial, three heritage and a South Mexican wild population). Analysis of next generation sequencing data resulted in the detection of 5.49 million putative SNPs compared to the reference genome. The average frequency of heterozygous nucleotide positions in individual turkeys was 1.07 Kb-1 which is substantially lower than in chicken and pigs. The SNPs were subsequently used for the analysis of genetic diversity between the different populations. Genetic diversity analysis using pairwise Nei’s genetic distance among all the individuals from the 11 turkey populations showed that all of the commercial lines branched from a single node relative to the heritage varieties and the ancestral turkey population, indicating that commercial lines appear to share a common origin. After assessing genome wide variation and diversity between breeds, the SNP data from ten of the turkey populations (29 individuals) was used to detect selective sweep regions. Across the turkey populations, 54 genomic regions with significant evidence for a selective sweep were detected. These sweeps were distributed over 14 different chromosomes. This study has investigated the genetics i.e. analysis of variances and QTL mapping related to economically important traits in turkey production and the genomic variation of turkey. Furthermore, this study has also created resources e.g. millions of discovered SNPs for subsequent genomic work in the turkey such as to discover variant (s) for both minor and major effects on traits of economic importance, and a high-resolution linkage map can be developed.