Exploring genetic diversity in natural and domestic populations through next generation sequencing

• Main Author: Rafati, Nima
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi 2017
• Subjects: Ecological adaptation; seasonal reproduction; Atlantic herring; domestication; speciation; rabbit; skeletal atavism; Shetland ponies; NGS; SMRT sequencing; genome; transcriptome; assembly; structural variation; genetic diversity; HCE; TSHR; SHOX; CRLF2; Genetics; Genetik; North Atlantic
• Online Access: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-315032

Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies. The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role. The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which ...