Rachman, Mifta
(2023)
GENOME DIVERSITY AND ENVIRONMENTAL ADAPTATION OF NIGERIAN INDIGENOUS CHICKEN.
PhD thesis, University of Nottingham.
Abstract
Indigenous breeds develop their genomic characteristics by adapting to local environments over a long period of time. Most of them have abilities to survive in harsh environments or tolerate particular diseases but are not productive in commercial terms. Moreover, climate changes, particularly those that contribute to weather extremes like a long dry season, excessive humidity, and high precipitation, may result in reduced performance and reproduction and could compromise the organism’s immune function. Their adaptive characteristics could be in response to natural selection and artificial selection for production traits that over time may leave selection signatures in the genome. The goal of this study is to analyse genome sequence data of Nigerian indigenous chickens from diverse ecotypes to assess their genetic diversity and to identify selection signatures that may be involved in their adaptation to tropical environments.
The study started by unravelling genomic diversity, which is presented in Chapter 2. I analysed Whole-Genome Sequencing (WGS) data from 120 Nigerian indigenous chickens from 14 populations and detected ~17 million SNP variants after applying some filtration steps. About 24% of these SNPs are novel from the catalogue present in public databases. Genomic sequence data generated under this study have been submitted to the European Nucleotide Archive (ENA) under the Accession: PRJEB39536 (publicly released in 2023) for wider research use.
In Chapter 2, several analyses were performed on autosomal SNP data to assess genetic diversity within and among the Nigerian indigenous chicken populations, including assessing nucleotide diversity and inbreeding co-efficients of individual populations, investigating population structure and ancestry based on Principal Component Analysis (PCA), pairwise population differentiation (FST and Mantel test), genetic admixture, and assessing linkage disequilibrium decay (LD decay). The result at the autosomal genome level indicates high genomic diversity but a low population structure across the Nigerian indigenous chicken populations.
In Chapter 3, I conducted a selection signature analysis from the same individuals genotyped in Chapter 2. The aim here was to identify candidate genomic regions related to climatic heat stress and rainfall pattern based on temperature and precipitation data from the WorldClim database. Eighty-seven samples from 12 regions, which were not significantly different in terms of average annual temperature, were analysed together to unravel the adaptation for heat stress using a pooled heterozygosity (Hp) method, whereas two extreme groups based on precipitation data (high and low) - with ten samples per group - were analysed using an FST approach to identify genomic regions of differential selection. The result of Hp analysis uncovered seventeen candidate genes for heat stress adaptation that are either overlapping or residing close to the putative selection signature regions. These genes have either direct involvement in thermal or heat tolerance or have other stress-response related functions such as important roles in the oxidoreductase pathway (oxidative stress), hypoxia and angiogenesis, immune system, and thermogenesis, e.g., HSF1, CDC37, SFTPB, HIF3A, and ILF3 genes. Meanwhile, thirty-three genes were found overlapping the candidate regions from the FST analysis between high versus low precipitation groups and many of them are related to immune response (e.g., DGKB, REL, EGFR) while the rest were involved in heat stress and oxidative stress (AHSA2) and reproductive performance (e.g., LRP8, GRM3).
In Chapter 4 I investigated the same WGS dataset in a different way; this time the analyses were done based on Nigeria’s agro-ecological zones which were considered distinct ecotypes. Eight ecotypes from the northern part to the southern part of Nigeria. were classified as: Sudan savanna, Northern Guinea savanna, Southern Guinea savanna, Derived savanna, Mid-Altitude, Rainforest, Freshwater swamp, and Mangrove Swamp. The first two ecotypes were living under warm-arid conditions, the next two ecotypes were from warm semi-arid regions, while the last three ecotypes were living in a warm-humid zone. Only the Mid-Altitude ecotype was located in a cool region. Analyses of the selective sweeps within ecotypes (using the Hp approach) and among ecotypes (using the FST approach) found several genes (differently) linked to oxidative stress and immune response. Besides, heat response-related genes dominated in the chicken ecotypes living in warm-arid, warm semi-arid, and warm-humid zones, while cold response, hypoxia response and osmotic stress contributed to the adaptation in cool and warm-humid zones, respectively.
To sum up, my project identified a number of important candidates for adaptation to be under selection in Nigerian indigenous chickens, especially in relation to thermotolerance and immune response as a consequence of living under tropical conditions. Furthermore, this study, for the first time, has performed high coverage WGS on a large number of Nigerian indigenous chickens from diverse ecotypes and has unravelled significant genomic diversity in them. The results of this study offer valuable insight into the genetic diversity of Nigerian indigenous chickens and their population structure, which will guide their improvement by helping design specific breeding programs as well as poultry management strategies to minimise heat stress and enhance disease resistance and productive performance. Put together, the findings of this thesis introduce the fact that Nigerian indigenous chickens are a group of unique birds whose genetic resources could be employed for the genetic improvement of livestock productivity. I hope that our results will be the baseline for further investigation into the genomic landscape of the Nigerian chicken.
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