Mining of Novel Simple Sequence Repeat (SSR) Markers Derived from Chicken (Gallus gallus) Genome Assembly

Producing food for animals and providing meat and eggs to humans can be done economically through chicken. The creation of novel SSR markers for chicken will be an invaluable tool for evaluating genetic diversity, mapping quantitative trait loci (QTLs), and understanding population structure, and marker-assisted animal breeding applications. On the other hand, the identification of microsatellites is expensive and labor-intensive. The GMATA software was used in the current in silico approach to generate microsatellites with chromosome-anchored SSR markers from the chicken genome assembly. The genome assembly of chicken resulted in the development of 146 054 SSR markers, and marker loci that corresponded to protein coding sequences were determined. Dinucleotide motifs were prevailing (57.92%) in Ross genome. Functional analysis was used to infer the existence of SSR repeats in biologically important classes of proteins, such as kinases, transcription factors, and G protein receptors. These outcome indicated that variability of SSR repeat copies can endow the cell and whole genome and can be realized in KEGG pathways namely involvement of neuroactive ligand-receptor interaction, MAPK signaling pathway, melanogenesis, WNT signaling pathway, and adherens junction. For the first time, the present study developed a whole-genome SSR panel for chicken as part of its research. The considerable quantity of new SSR markers presented in this study serves as a significant asset for molecular genetic studies involving QTL mapping, evaluation of genetic variation, and the use of markers in animal breeding.