“Unveiling the genetic symphony: Diversity and expression of chicken IFITM genes in Aseel and Kadaknath breeds”

In this investigation, single nucleotide variants (SNVs) within the chicken interferon-inducible transmembrane protein (<i>chIFITM</i>) genes were explored in Aseel and Kadaknath breeds. Comparative analysis with the GRCg6a reference genome revealed 9 and 16 SNVs in the <i>chIFITM</i> locus for Aseel and Kadaknath breeds, respectively. When referencing the Genome Reference Consortium GRCg7b, Kadaknath exhibited 10 variants, contrasting with none in Aseel. Notably, 17, 8, 2, and 5 SNVs were identified in <i>chIFITM1</i>, <i>chIFITM2</i>, <i>chIFITM3</i>, and <i>chIFITM5</i> genes, with <i>chIFITM1</i> showing the highest polymorphism in Kadaknath, featuring 10 intronic variants, including three SNVs (rs16457112, rs16457111, and rs313341707) common to both breeds. Two synonymous exonic variants (g.1817767C > A and g.1819102C > T) were also noted in chIFITM1. Although <i>chIFITM</i> protein sequences were generally conserved, genetic variations clustered predominantly in UTR and intronic regions. Examination of immune response dynamics in live embryos uncovered notable variations in <i>chIFITM</i> gene expression across diverse organs and chicken breeds. Specifically, <i>chIFITM1</i> mRNA was abundant in cecal tonsils for both breeds and bursa of Aseel (7.61 folds), but it was absent in the heart and lung tissues of both breeds. Conversely, <i>chIFITM3</i> consistently exhibited heightened expression, particularly in bursa of Aseel (10.23 folds). Whereas mRNA of the <i>chIFITM2</i> gene was found to be abundant in the heart of Kadaknath (11.03 folds) and lung of both breeds. Furthermore, the expression pattern of <i>chIFITM5</i> diverged between the two breeds, the heart of Kadaknath chickens showed highest (10.45 folds). The study discovered that breed-specific genetic variants within these genes present a potential pathway for selection and breeding to improve disease resistance in chicken. The observed genetic variation among chicken populations highlights the critical importance of these variants in reinforcing virus resistance, exhibiting applicability across a wide range of breeds.