Relatedness and diversity in Swedish local chicken breeds using mitochondrial DNA D-loop sequences and SNP data

Abstract: Genetic diversity is the variation in genetic information carried by individuals within a species or population. This variability plays a crucial role in enabling species to adapt and survive in changing environments and is essential for evolutionary processes. Additionally, genetic diversity might carry genetic variants that improve resistance to diseases. In this study, a genetic analysis was carried out to investigate the genetic diversity, evolutionary history, and inter-breed relationships of Swedish local chicken populations. The initial 533 base pairs in the hypervariable D-loop region of the mitochondrial DNA was sequenced from 64 individuals representing 13 different breeds, and autosomal SNP data generated from 83 individuals representing eight different breeds was used. The study found that a total of 16 polymorphic sites and 9 distinct genetic sequences (haplotypes) were identified among the 13 Swedish local chicken breeds using the mtDNA data. Clade nomenclature in this study was according to the nomenclature of clades reported in previous studies, where domestic chickens were categorized into nine distinct clades (A to I) based on their association with areas of domestication and geographical dispersal. The majority of the breeds were found to belong to Clade E, while others belong to clades A and B, which suggests that the Swedish local chickens have several maternal lineages that likely originated from the Indian subcontinent, Yunnan province, and the regions of China. The analysis of molecular variance (AMOVA) revealed a higher degree of genetic variation between different chicken populations than within the same population. The nucleotide diversity of the studied breeds was found to range from 0 to 0.0169. An analysis of the mitochondrial DNA D-loop data using a neighbor-joining phylogenetic tree indicated that the Swedish indigenous chicken breeds share a closer evolutionary relationship with haplotypes present in European chicken breeds, rather than those found in Asian breeds. The principal component analysis of the SNP data revealed a closer genetic relationship among five of the Swedish local chicken breeds (Ölandshöna, Öländsk dvärghöna, Skånsk blommehöna, Äsbohöna, Kindahöna), while the other three breeds (Gotlandshöna, Hedemorahöna, and Svarthöna) were observed to be distinct. This research contributes to the understanding of genetic variation in the indigenous populations, and the findings may be applied to develop appropriate breeding and conservation strategies for the Swedish local chicken breeds. For a more comprehensive understanding of genetic diversity, origin, and relationships, it is recommended to perform analyses using both mitochondrial and nuclear DNA.