干旱区生态环境知识资源中心(Arid): Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

Arid

DOI	10.1186/s12864-022-08434-7
	Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens
	Nanaei, Hojjat Asadollahpour; Kharrati-Koopaee, Hamed; Esmailizadeh, Ali
通讯作者	Nanaei, HA ; Esmailizadeh, A
来源期刊	BMC GENOMICS
ISSN	1471-2164
出版年	2022
卷号	23 期号:1
英文摘要	Background: Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes.To detect genomic signatures of adaptation, we applied nucleotide diversity (en) and F s r statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits. Results: By generating whole-genome data, we assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (similar to 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits. Conclusions: The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.
英文关键词	Adaptation Population genomics Iranian indigenous chickens Heat shock protein Whole-genome sequence
类型	Article
语种	英语
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000772072400002
WOS关键词	SINGLE-NUCLEOTIDE POLYMORPHISM ; WHOLE-GENOME ASSOCIATION ; MESSENGER-RNA ; GALLUS-GALLUS ; STRESS ; EXPRESSION ; BREEDS ; HSP70 ; HEAT-SHOCK-PROTEIN-70 ; TEMPERATURE
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/391999
推荐引用方式 GB/T 7714	Nanaei, Hojjat Asadollahpour,Kharrati-Koopaee, Hamed,Esmailizadeh, Ali. Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens[J],2022,23(1).
APA	Nanaei, Hojjat Asadollahpour,Kharrati-Koopaee, Hamed,&Esmailizadeh, Ali.(2022).Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens.BMC GENOMICS,23(1).
MLA	Nanaei, Hojjat Asadollahpour,et al."Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens".BMC GENOMICS 23.1(2022).