Study of extended homozygous chromosome regions in Italian partridge breed of chickens

Selection and accompanying inbreeding are the basis for breeding chicken breeds. With the advent of modern molecular methods for assessing inbreeding, it has become possible to identify genes and their functions in the homozygous regions (ROH) of chicken chromosomes. In this study, a genome-wide analysis of homozygous regions of chromosomes in Italian partridge chickens was carried out using an SNP chip Illumina Chicken 60KSNPiSelectBeadChipchip. An average of 177 ± 5 ROH-sequences per chicken were identified in the chicken chromosomes, and the average inbreeding coefficient was 0.30 ± 0.01. It was determined that the chicken genome is dominated by short ROH-sequences of 0.25–2 Mbp. ROH-sequences longer than 8 Mbp indicating recent inbreeding account for no more than 2.2%. It was found that, in general, ROH-sequences are more densely distributed in chicken microchromosomes, with the exception of chromosome 16, which does not have ROH-sequences. This fact is due to the heterozygosity of the alleles of the genes responsible for immunity, located in microchromosome 16. ROH-islands were found in the chicken chromosomes 1, 5, and 14. The genes in ROH-islands are responsible for feather pecking in chickens ( DMD gene), immune status ( TAB3 , EIF2S3 genes), body weight ( IL1RAPL1 gene), pH of meat ( EIF2S3 , APOO , KLHL15 genes), egg production ( APOO gene), feed uptake ( SAT1 gene), aggressiveness of roosters ( SLITRK6 gene), transport of intracellular components in developing neurons and protection of heterochromatin in the cell nuclei of neurons ( NDE1 gene), adaptation of chickens to tropical living conditions ( CDIN1 gene). Thus, ROH analysis allowed us to identify genes potentially selectable as a result of breeding Italian partridge breed chickens.