Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection

Abstract

The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and FROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (FST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and FROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population.

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

“…The ErRo was in a homozygous state but with the alternate allele with respect to the other breeds (i.e., Brzl, BrCI, NeIt, CoEu) as shown in Supplementary Materials, Table S4 . Comparing the results of this study with the ROHs mapped in a commercial turkey hybrid, this region does not appear to be in a homozygous state in the commercial selected, fast-growing, heavy turkey line as reported by Strillacci et al [ 11 ]. The intense selection for body weight in commercial turkeys determined a reduction in reproductive performance, as reported by Nestor et al, who discussed the genetics of growth and reproduction using the performance measured in over 40 generations of selection for 16-week body weight in turkey [ 37 ].…”

“…Heritage turkey breeds were recently studied and, even if still limited, some indication about their genomic variability and diversity is nowadays available [ 4 , 5 , 6 , 7 , 8 , 9 ]. Recent studies were performed on run of homozygosity (ROH): Marras et al characterized ROH-rich regions in a commercial turkey hybrid, and Strillacci et al discussed the difference in ROH between the autochthonous Mexican and commercial hybrid turkeys [ 10 , 11 ].…”

Copy Number Variants in Four Italian Turkey Breeds

“…The genetic variability in turkey populations has been recently studied mainly using Single Nucleotide Polymorphisms (SNPs) as markers [ 12 , 13 , 14 , 15 ] and by the analysis of mtDNA D-loop sequences [ 16 ]. Copy number variants (CNVs) in turkeys species are still poorly studied [ 17 , 18 , 19 ].…”

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

“…Therefore, this region potentially contributes to the distinctive characteristics of Maremmana related to growth, carcass, and meat traits. The region on BTA06 also showed nine genes ( CHRNA9 , LIAS , N4BP2 , PDS5A , RBM47 , RHOH , SMIM14 , UBE2K , and UGDH ) that overlaps with a ROH island in fast-growing meat commercial hybrid Turkey ( Strillacci et al, 2020 ). Notably, CHRNA9 gene is also associated with meat quality traits in pigs ( Velez-Irizarry et al, 2019 ).…”