Date of Award

Fall 2020

Project Type


Program or Major

Biological Sciences

Degree Name

Master of Science

First Advisor

Thomas M Davis

Second Advisor

Matthew MacManes

Third Advisor

Anissa Poleatewich


Quinoa, Chenopodium quinoa Willd., is a potential new high-value crop for Northern New England (NNE) because of its excellent nutritional qualities and its ability to grow in diverse agroecosystems. However, quinoa field trials have not been successful thus far in NNE because of some major issues such as downy mildew disease, severe lodging (bending over), excessive branching, overly long maturation time, and immature grains at harvest. Quinoa is an allotetraploid (2n=4x=36) species of genome composition AABB, and thus has two distinct diploid ancestors. This study reports foundational genetic studies in the BB diploid (2n=2x=18) ancestor, Chenopodium ficifolium, as a potential model system for genetic studies relevant to quinoa gene identification and marker-assisted breeding. The specific objectives of this research were to (1) To make crosses/hybrid between C. ficifolium accessions (2) To evaluate the parental accessions for differences in various traits relevant to quinoa breeding programs and to study the extent of segregation of those traits in F2 generation populations (3) To identify the marker-trait association between the FTL locus marker and any of the segregating traits. C. ficifolium accessions, Portsmouth (P) and Quebec City (QC) were collected from two locations and were reciprocally crossed to generate F1 hybrids, which upon molecular confirmation of hybridity were self-crossed to produce F2 generation populations. Phenotypic data were collected and F2 generation segregation was evident for several agronomically relevant traits, including flowering time, plant height, the number of branches, branch angle, internode distance, and leaf chlorophyll content. The FTL marker locus was used for genotyping the F1 and the F2 population, and both FTL homologs, FTL1 and FTL2, were characterized molecularly by sequencing the PCR amplicons generated from the CrFT345For and CrFT501Rev primer pair. Marker-trait associations were detected in the F2 population between the FTL1 marker and each of three important agronomic traits: flowering time, plant height, and the number of branches. A high positive correlation was also found among the traits flowering time, plant height, and the number of branches. Genomic sequences of P and QC accessions were compared to the quinoa reference genome and 5,218,465 single nucleotide polymorphisms (SNPs) were detected in the P and QC accessions. Polymorphisms were also identified between P and QC accessions for the coding sequence and promoter region of the FTL1 gene that could have some functional significance with the observed trait variance in the F2 population. Although the association of the FTL1 gene to the various traits was identified, this study was not able to confirm a functional role of the FTL1 gene with any of the agronomic traits evaluated. An appropriate growing environment for C. ficifolium was also identified that provided for proper growth and ease of visualization of phenotypic differences between the studied accessions of C. ficifolium. Overall, these results validate and contribute to the development of C. ficifolium as an appropriate diploid model system for studying the genetic and molecular basis for agronomic trait diversity in the related tetraploid crop plant, quinoa.