SNPs Identification in production related genes in strains of white leghorn chicken

Abstract

This is the first comprehensive study aimed to determine Single Nucleotide Polymorphisms (SNPs) in candidate genes (GHR, IGF1, OCX-32 and GDF9) reported to associated with egg production at the age of 64 weeks (EP64) in strains of White Leghorn chicken (Anand Synthetic White Leghorn and Anand Bantamised White Leghorn by sequencing the coding region of respective genes. Both the strains of White Leghorn chicken were categorized into four different groups viz., Anand Synthetic White Leghorn High Production (ASHP), Anand Synthetic White Leghorn Low Production (ASLP), Anand Bantamised White Leghorn High Production (ABHP) and Anand Bantamised White Leghorn Low Production (ABLP) to find out SNPs in coding region of candidate genes and its association with EP64. The genomic DNA was extracted for 96 chickens and then further sequenced with the designed custom amplicon panel on the Illumina MiSeq platform. Raw data collected after sequencing was used for the bio in formatic analysis to confirm its association with EP64. Consequently, over 99% target regions were amplifed and 87 SNPs were available after quality filtering. Only thirty-three variants were novel while majority of the identified variants were catalogued in dbSNP database as known variants. The T21912084G, C21912423A and rs318030570 of OCX-32 and C13415980T of GHR gene was found to have a significant association (p