Breeding, Markers, and Mapping

C. quinoa Microsatellites:

Microsatellites, AKA simple sequence repeats (SSRs), are found throughout many species genomes. These SSR’s are useful as genetic markers, because they are highly polymorphic and codominant. In this project, after sequencing fragments of the quinoa genome, primers are designed using these DNA sequences. These primers flank the repeat and are used to amplify the SSR. The repeats are then screened to determine polymorphism through gel electrophoresis. Once microsatellite markers are developed, quinoa breeders can implement them to enhance breeding efficiency. The development of these markers provides a foundation for further investigation of the genetics of quinoa.

C. quinoa Linkage Mapping:

One of the first steps to identify genes of agronomic importance is to develop genetic markers and a genetic linkage map. A linkage map allows breeders to pinpoint genes to chromosomal locations and is the first step towards gene cloning. Moreover, the identification of DNA markers linked to genes that influence agronomic characteristics can be used to improve selection via marker-assisted selection. This project will produce a genetic map in quinoa using three recombinant inbred lines (RIL) (F6) populations utilizing primarily microsatellite (SSR) markers. This map will greatly benefit researchers in the quinoa genetics and plant breeding community.

Amaranth SSR Development:

Amaranth is a broadleaf, high-protein seed crop that is similar in many respects to quinoa, though its seed are smaller and it is adapted to warmer climates than quinoa. At least three species of Amaranthus (including caudatus, cruentus, and hypochondriacus) were important crops of the ancient civilizations of the Andes and Mesoamerica. They continue to be locally important crops among subsistence farmers in those areas. Our goal is to develop microsatellite, or simple-sequence repeat (SSR), markers for building genetic maps of these Amaranthus species. One interesting aspect of this effort will be to determine the genetic basis of resistance to herbicides in a group of noxious weedy relatives, including smooth pigweed (A. hybridus), redroot pigweed (A. retroflexus), and waterhemp (A. tuberculatus).