Date of Graduation

12-2019

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Cell & Molecular Biology (PhD)

Degree Level

Graduate

Department

Cell & Molecular Biology

Advisor/Mentor

Rhoads, Douglas D.

Committee Member

Ivey, D. Mack

Second Committee Member

Du, Yuchun

Third Committee Member

Thallapuranam, Suresh

Keywords

Bio informatics; Genetics; Genome resequencing; Quantitaive trait loci; Quantitative genetics

Abstract

We are using whole genome resequencing to identify chromosomal regions associated with resistance or susceptibility to ascites, a form of pulmonary hypertension syndrome, meat-type chickens. Previous Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping, there are no reliable or potential markers for ascites phenotype. We have completed screening of Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms in ascites resistant and susceptible birds from the relaxed, REL, line derived from a commercial elite broiler line. DNA samples from resistant and susceptible birds were purified, quantified and pooled in two pools of 10 DNAs from each phenotype for both genders. Eight pools (2 pools x 2 phenotypes x 2 genders) were generated. Each pool was submitted for bar-coded library generation, and 2x125 paired end reads on Illumina HiSeq 2500 and with 66X genome coverage. The sequence reads were mapped onto Galgal5 using Bowtie for initial CNV mapping cn.mops (R package). Further mapping to chromosomes were done using NGen and ArrayStar (DNAStar ver 13). So far, we have identified two potential regions for CNVs and 31 regions for SNPs with potential association with ascites phenotype. CPQ gene on chromosome 2 and LRRTM4 gene on chromosome 22 have been validated for containing ascites QTLs. However, their exact role in ascites is yet to be discovered. Further, we screened the regions from REL line in DNAs from an unrelated commercial broiler line using WGR.

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