Weigend, A. | bioRxiv Science

bioRxiv2020

Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations

Migration of populations from their founder population is expected to cause a reduction in genetic diversity and facilitates population differentiation between the populations and their founder population as predicted by the theory of genetic isolation by distance. Consistent with that, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be well explained by their geographic expansion from the founders, which is correlated to the genetic differentiation. To investigate this in the chicken, we have estimated the relationship between the genetic diversity in 172 domesticated chicken populations and their genetic distances to wild populations. We have found a strong inverse relationship whereby 87.5% of the variation in the overall genetic diversity of domesticated chicken can be explained by the genetic distance to the wild populations. We also investigated if different types of SNPs and genes present similar patterns of genetic diversity as the overall genome. Among different SNP classes, the non-synonymous ones were the most deviating from the overall genome. However, the genetic distances to wild populations still explained more variation in domesticated chicken diversity in all SNP classes ranging from 81.7 to 88.7%. The genetic diversity seemed to change at a faster rate within the chicken in genes that are associated with transmembrane transport, protein transport and protein metabolic processes, and lipid metabolic processes. In general, such genes are flexible to be manipulated according to the population needs. On the other hand, genes which the genetic diversity hardly changes despite the genetic distance to the wild populations are associated with major functions e.g. brain development. Therefore, changes in the genes may be detrimental to the chickens. These results contribute to the knowledge of different evolutionary patterns of different functional genomic regions in the chicken. Author summaryThe chicken was first domesticated about 6000 B.C. in Asia from the jungle fowl. Following domestication, chickens were taken to different parts of the world mainly by humans. Evolutionary forces such as selection and genetic drift have shaped diversification within the chicken species. In addition, new breeds or strains have been developed from crossbreeding programs facilitated by man. These events, together with other breeding practices, have led to genomic alterations causing genetic differentiation between the domesticated chickens and their ancestral/wild population as well as manipulation of the genetic diversity within the domesticated chickens. We investigated the relationship between 172 domesticated chicken populations from different selection, breeding and management backgrounds and their genetic distance to the wild type chickens. We found that the genetic diversity within the populations decreases with the increasing genetic distances to the wild types. Human manipulation of chicken genetic diversity has more effect on the genetic differentiation than simple geographic separations (through migrations) do. We further found that some genes associated with vital functions show evolutionary constraints or persistent selection across the populations and do not comply with this relationship i.e. the genetic diversity within the populations is constant despite the change in the genetic distance to the wild types.

genetics↗

bioRxiv2019

How Array Design Affects SNP Ascertainment Bias

Single nucleotide polymorphisms (SNPs), genotyped with SNP arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown with main influencing factors being the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.

genomics↗