Assiri, Abdulwahab
(2025)
The genetic adaptation of indigenous chickens to harsh environments.
PhD thesis, University of Nottingham.
Abstract
Indigenous chicken populations are recognized for their strong local adaptation, limited productivity, and substantial genetic diversity. Unfortunately, this diversity is under threat, highlighting the urgent need for conservation strategies to safeguard these breeds. These birds are typically resilient to diseases and are well-adapted to the demands of smallholder farmers in harsh and resource-limited environments. As such, they play a crucial role in promoting food security, particularly in low- and medium-income countries.
Understanding the genetics of environmental adaptations is key to improving breeding programs and guiding conservation efforts, both crucial in mitigating the effects of climate change on agriculture and livestock diversity. Indigenous chickens of the Arabian Peninsula have uniquely adapted to desert ecologies and scavenging conditions. However, their genetic adaptation mechanisms remain poorly understood. Here, genome analyses, including signatures of positive selection and copy number variation analyses, were applied to identify genetic responses to key environmental stressors and compare them with populations from different environmental conditions.
Following a brief literature review in Chapter 1 (Setting the Scene), the thesis comprises three results chapters. Chapter 2 explore the diversity and population structure of thirteen indigenous and two commercial chicken populations from diverse climatic zones, representing both cold and warm ecological conditions. About 24.9 million SNPs were characterized in the populations of which 38.26% were novel. Our results clearly demonstrate the clustering of all populations according to their geographic region of origin, with minimal genetic differentiation within the populations. Admixture analysis shows evidence of shared ancestry among all Arabian Peninsula indigenous populations. Our findings suggest that the Arabian Peninsula populations represent a distinct gene pool with a significant genomic diversity compared to other geographic regions.
In Chapter 3, populations were ranked accordingly to their region of origin. Signatures of positive selection for each population and pair population (warm and cold locations) were investigated using ZHp, iHS, ZFST and XP-EHH methods. Strong candidate selected regions identified overlapping genes that have highly relevant functions for adaptation to thermotolerance. These are involved in energy balance and metabolism (SUGCT, HECW1, and MMADHC), cells apoptosis (APP, SRBD1, NTN1, PUF60, SLC26A8, DAP, and SUGCT), angiogenesis (RYR2, and LDB2), skin protection to solar radiation (FZD10, BCO2, WNT5B, COL6A2 and SIRT1), and immunity (CD300LG, KIAA1549L, and IL22RA1) as well as growth (NELL1, LBFABP, and MYOM3).
In Chapter 4, using whole-genome sequences, we examine deletion and duplication variants in twelve chicken populations adapted to harsh environments. After applying a hard filtering threshold for each population, 1,391 unique deletions and duplications were identified. Among these, 442 CNVRs overlapped across at least two populations, comprising 372 deletions, 68 duplications, and 3 mixed deletion-duplication events. Through gene annotation and gene ontology analyses of the identified CNVRs, specific genes and biological processes related to nervous system function (TAFA5, HMX2, LYSMD2, FADS6, NSF, ABHD14A, SEMA3B, and SEMA3F), growth (LBFABP, MYOM3, SNX29, XKR4, CPPED1, LDB2, GK2, HAO2, RHOA, ECM2, SLC25A30, AAMDC, and TCEB3), and immunity (CD300LG, KIAA1549L, and IL22RA1) were identified. Five genes (LDB2, CD300LG, KIAA1549L, IL22RA1, and MYOM3) were detected in both the signature of selection and copy number variation chapters.
In summary, our study provides new insights into the genetic diversity and population structure of indigenous chickens from the Arabian Peninsula. We identified several key candidate genes likely under selection for adaptation, particularly linked to thermotolerance in response to the harsh desert environment. Additionally, numerous critical copy number variation regions (CNVRs) associated with thermotolerance adaptation were uncovered. These results will help guide the development of targeted breeding programs and poultry management strategies aimed at reducing heat stress improving disease resistance and enhancing overall productivity.
To the best of our knowledge, this is the first comprehensive analysis utilizing whole-genome resequencing to identify diverse adaptive candidate genes in indigenous chickens from the Arabian Peninsula. This work represents a significant advancement in promoting breeding programs aimed at the sustainable conservation of the genetic resources of these chicken populations.
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