Investigation of rare alleles in maize using the zea synthetic doubled haploid population

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] The biology of rare alleles is important to our understanding of genotype-to-phenotype relationships. Understanding the role of rare alleles can aid in the selection and development of future breeding lines. Inbreeding and selection of maize over the past 100 years has removed many deleterious alleles, but there are still rare alleles with small effects segregating in maize (Zea mays ssp. mays) germplasm. However, rare alleles have not been extensively studied due to limited resolution and allelic representation issues. Therefore, a new genetic resource, the Zea Synthetic, was created utilizing both teosinte and maize. The Zea Synthetic is a randomly mated synthetic breeding population comprised of the 27 inbred Nested Association Mapping (NAM) founders and 11 geographically diverse teosinte (Zea mays ssp. parviglumis) accessions. Two-thousand doubled haploids (DH) were produced from the Syn-4 (4th)generation of the Zea Synthetic to determine the contributions of allelic variants to fitness throughout the maize genome for both maize and teosinte alleles segregating in a common population. The DH have been genotyped using genotyping-by-sequencing (GBS). GBS data, combined with whole genome sequencing (WGS) of the Zea Synthetic founders, are being used in an identity-by-descent (IBD) analysis to determine which genomic regions were selected against during the DH process. Genotypic and phenotypic data are being combined in association analyses to determine phenotype and genotype relationships.