Date of Award
Doctor of Philosophy
Max F. Rothschild
Single nucleotide polymorphisms (SNPs) are single base changes in the genome that can differ among populations and among individuals within populations. These genetic markers are widely distributed throughout the genome and relatively easy to genotype on a large scale. Several steps are involved in utilizing SNPs in genomic studies. First, SNPs must be discovered and mapped within the genome. Then, populations can be characterized based on their allele frequencies, and pedigrees can be traced. Whole genome association studies (WGAS) can then be carried out to discover the genetic underpinnings of phenotypes, and the results can be used for such objectives as improving animal production systems. The primary objective of the research reported herein was to assess the usefulness of SNPs in determining the biological bases of important phenotypes in production animals.
The development of a new software package is described for SNP discovery work from expressed sequence tags in Litopenaeus vannamei and related shrimp species. This program predicted 504 SNPs in L. vannamei and had a validation rate of 44% among SNPs genotyped in a specific population. When this same program was used to predict inter- and intraspecies SNPs from nine shrimp species, 4,597 SNPs were predicted, but only 18 of them segregated in multiple species. Consequently, it was concluded that cross-species SNP prediction was not successful for SNP discovery in L. vannamei.
A population of dairy cattle in Kenya was characterized using SNP genotypes from the 50K cattle SNP chip. Just over 10% of the putative relationships were determined to be inaccurate and heavy use of one AI bull indicated that inbreeding could be a problem if not more closely monitored. Finally, breed composition was predicted via comparisons to the HapMap population using the software program, Structure. Most animals were found to be of Holstein or Guernsey descent, with little native African blood.
WGAS were carried out for several traits in pigs. The 60K porcine SNP chip was used to complete genome scans for polydactyly, residual feed intake (RFI), average daily feed intake (ADFI), average daily gain (ADG), backfat, and loin muscle area in Yorkshire swine. Polydactyly was suspected to be a single gene recessive trait with incomplete penetrance, but a causative mutation was not identified. A 25 Mb region on chromosome 8 was implicated based on a long stretch of homozygosity in affected animals. The other traits examined were known to be polygenic, and as such, many regions across the genome were found to be associated with each trait. Both previously known genes, such as MC4R for ADFI and ADG, and novel genes, such as CRAT for RFI, were implicated. Although validation is needed, these results represent potential candidates for marker-assisted selection or drug targets for feed additives to improve animal production.
In conclusion, SNPs are useful for investigating the genetic cause of animal phenotypes, but they do not describe all of the components that are working together to create phenotypes. As sequencing methods become faster and cheaper, the assessment of additional types of mutations will undoubtedly reveal more information about the genetic bases of observed phenotypes. The overall process of data analysis, however, may remain similar for several years to come.
Gorbach, Danielle, "The prediction of single nucleotide polymorphisms and their utilization in mapping traits and determining population structure in production animals" (2011). Graduate Theses and Dissertations. 10336.