Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits

	Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits
	Mahdabi, E; Esmailizadeh, A; Han, JL; Wang, MS
	2025
发表期刊	VET MED SCI
卷号	11 期号:1
摘要	Runs of homozygosity (ROH) are contiguous stretches of identical genomic regions inherited from both parents. Assessment of ROH in livestock species contributes significantly to our understanding of genetic health, population genetic structure, selective pressure and conservation efforts. In this study, whole genome re-sequencing data from 140 birds of 10 Iranian indigenous chicken ecotypes, 3 commercial chicken breeds and 1 red junglefowl (RJF) population were used to investigate their population genetic structure, ROH characteristics (length and frequency) and genomic inbreeding coefficients (FROH). Additionally, we examined ROH islands for selection footprints in the indigenous chicken populations. Our results revealed distinct genetic backgrounds, among which the White Leghorn breed exhibited the greatest genetic distance from other populations, while the gamecock populations formed a separate cluster. We observed significant differences in ROH characteristics, in which the commercial breeds showed a higher number of ROH compared to indigenous chickens and red junglefowls. Short ROH ranging from 0.1 to 1 Mb were dominant among the populations. The Arian line had the highest mean length of ROH, while the White Leghorn breed showed the highest number of ROH. Among indigenous chickens, the Lari-Afghani ecotype exhibited the highest FROH, but the Sari inherited the richest genetic diversity. Interestingly, GGA16 carried no ROH in the red junglefowls, whereas GGA22 had the highest FROH across all populations, except in the Isfahan ecotype. We also identified ROH islands associated with genetic adaptations in indigenous ecotypes. These islands harboured immune-related genes contributing to disease resistance (TLR2, TICAM1, IL22RA1, NOS2, CCL20 and IFNLR1), heat tolerance and oxidative stress response (NFKB1, HSF4, OSGIN1 and BDNF), and muscle development, lipid metabolism and reproduction (MEOX2, CEBPB, CDS2 and GnRH-I). Overall, this study highlights the genetic potential of indigenous chickens to survive and adapt to their respective environments.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14461
专题	科研部门_进化与生物多样性基因组学（王明山）
推荐引用方式 GB/T 7714	Mahdabi, E,Esmailizadeh, A,Han, JL,et al. Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits[J]. VET MED SCI,2025,11(1).
APA	Mahdabi, E,Esmailizadeh, A,Han, JL,&Wang, MS.(2025).Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits.VET MED SCI,11(1).
MLA	Mahdabi, E,et al."Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits".VET MED SCI 11.1(2025).

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
WMS2025040801.pdf（1304KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文