Genome‑wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection

Abstract

Objectives: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens.Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq.Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure.Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and MAPK proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. KEGG pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1-and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through qRT-PCR and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R 2 = 0.92-0.95, p < 0.01).

Population genomics and transcriptomics identify patterns of selection in two Liangshan chicken breeds

“…In tropical desert climates, a comparative genomics study revealed the presence of advantageous alleles in TLR7 and ZC3HAV1 [10], indicating immune adaptation for defense against zoonotic diseases in chickens [11]. The identi cation of heat shock proteins (HSP) through genome-wide analysis resulted in the discovery of a total of 76 HSP genes [12]. As a cornerstone in chicken genomics research, genome resequencing has provided a roadmap for unraveling the genetic code governing adaptability, disease resistance, and production traits.…”