Lawal, Raman Akinyanju
(2018)
Signatures of selection and introgression in the genus Gallus.
PhD thesis, University of Nottingham.
Abstract
Here I investigate, using autosomal whole-genome sequence data, the signature of positive selection and/or introgression in the indigenous domestic village chickens from three countries (Ethiopia, Saudi Arabia, Sri Lanka), three fancy birds, three junglefowl species (red junglefowl Gallus gallus, grey junglefowl G. sonneratii, Ceylon Junglefowl G. lafayettii) and the Javan red junglefowl G. g. bankiva. All the new sequencing data were obtained from Illumina HiSeq 2000/2500 DNA sequencers with an individual bird depth of genome coverage ranging from 10 X to 30 X. The analyses in this thesis have been completed using the reference genome Galgal 4.0.
For the detection of signatures of positive selection, this analysis excluded the three fancy birds and the grey junglefowl due to small sample size. Using the pool heterozygosity and SweeD composite likelihood selection signature methods, I identified two candidate selected regions shared between all the three indigenous domestic village chicken populations and the red junglefowl (chapter 2). These regions contain genes that are associated with the development of the central nervous system and adaptation to hypoxic environments. Five candidate regions were shared among the three indigenous village chicken populations, and they represent candidate domestication regions. Unique regions in each domestic chicken population were also identified. Functional genes have not been assigned to most of these regions but in those where the genes have been annotated, the gene function may be related to production and reproductive traits as well as adaptation to cold/hot temperatures and hypoxia.
In chapter 3, I analysed only the Ceylon and green junglefowl whole genome sequences for the detection of candidate signatures of positive selection using both the pool heterozygosity and Tajima’s D. In both species, I identified candidate selected regions that contained genes which may be linked to adaptation to different environmental challenges e.g disease resistance, stress, thermoregulation and hypoxia. In the genome of green junglefowl, candidate selected regions associated with skeletal formation and ovarian follicle development were significantly detected.
In chapter 4, I identified introgressed candidate regions from the grey and Ceylon junglefowls in domestic chicken (including the three indigenous chicken populations and fancy birds) using the ABBA – BABA four taxon method. Our result shows that, domestic chickens shared 75.8% of their genome with the red junglefowl, 4% with the grey junglefowl and 1.1% with the Ceylon junglefowl. I observed introgression in both directions, namely from the grey/Ceylon junglefowls into domestic chickens and vice versa. While from the grey junglefowl, introgression was present in all the domestic chicken populations as well as interestingly in the red junglefowl, for the Ceylon junglefowl, introgression was more restricted to the domestic chicken from Sri Lanka. From the ABBA – BABA analysis between the grey junglefowl and the domestic chicken, I also identified a single candidate introgressed region from the green junglefowl G. varius in two domestic birds from Sri Lanka. Future study should therefore consider investigating the genome-wide analysis of introgression from the green junglefowl into the domestic chicken.
In chapter 5, I ended our introgression study by investigating if a distantly related subspecies of red junglefowl, the Javan red junglefowl Gallus gallus bankiva, has contributed to the gene pool of the domestic chicken. Alongside the three indigenous domestic chicken populations, I included the genome sequences of three domestic chickens sampled from the Java island of Indonesia. Our result shows a significant 10.6% genome admixture between the domestic chicken and the Javan red junglefowl.
Overall, our results indicate that the genetic make-up of the domestic chicken is rather complex with multiple species and subspecies influences. These introgression events have contributed to the genetic diversity of these domesticates. Our results also support the geographic difference of introgression and indicate that these introgression events may have contributed to the adaptive traits of the domestic chicken. However, this requires further investigation.
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