Identification and evaluation of SNPs at the 3’ end of the tva gene segregating among ALSV resistance and susceptible lines of chickens

Avian leukosis and sarcoma virus (ALSV) is an oncogenic retrovirus consisting of six subgroups (A, B, C, D, E, and J). ALSV(A) is the second most common subgroup infecting commercial poultry. Molecular tools to identify the ALSV(A) receptor (tva) positive and negative chickens could be useful to the poultry industry in tracking genetically resistant chickens. Previously, no chicken tva cDNA clones had been found, but using a partial quail tva sequence (L22753), a homologous chicken EST sequence (BM488087) was identified. Primers were designed, and a segment of 1,636 bp of the chicken tva gene was isolated from each of three previously identified tva-positive BAC clones (http://poultry.mph.msu.edu/resources/Resources.htm#bacdata). New primers were then designed, and the sequence was extended at the 3’ end up to 3,155 bp. This region covers a 1,607 bp sequence gap in the draft chicken genome sequence at chr28:819894-821500. Using the original primers, fifteen SNPs were identified among 3 inbred lines of chickens. One of the 15 SNPs was independently found in the BGI SNP database (http://chicken.genomics.org.cn/index.jsp). Eight of the 15 SNPs differed between resistant and susceptible lines of chickens, indicative of significant linkage disequilibrium in this region. A viral tumor induction assay demonstrated that 177 out of 179 inbred and recombinant congenic chickens SNP typed as susceptible developed tumors. One of 17 chickens typed as resistant developed a tumor. New trials are underway to determine if the few outliers are due to inconsistency in the tumor assay or rare recombination between the SNP and the causative tva mutation.