Current lab projects

Oat is the fifth or sixth most important cereal grain crop and an important source of soluble dietary fiber, proven in clinical research trials to lower serum cholesterol.  Ironically, its very close relative wild oat (A.fatua) is among the most significant weeds of the temperate zone.  These 42-chromosome species are descended from a series of 14- and 28-chromosome Mediterranean zone grasses having genes for resistance to oat fungal and viral diseases.  We do chromosomal analyses in order to: 1) study chromosome rearrangements in the dynamic oat genome; 2) map genes controlling traits of interest; and 3) characterize species relationships to better conserve these important genetic resources.  The photograph shows an oat root-tip cell from a plant that is nullisomic (missing a pair) for chromosome 7C.

Downy mildew (Peronospora farinosa) is a major pathogen problem encountered in quinoa cultivation.  During seasons that are cool and moist, the pathogen can cause 100% crop loss.  Quinoa varieties display differing degrees of resistance.  The resistance also various according to the isolate that it is inoculated with.  Our project is to validate a resistance screening technique that correlates to other locations and field work.  We will also produce genetic fingerprints using AFLP analysis of the different isolates to facilitate identification for research and
control purposes.

Quinoa is a tetraploid (4x) derived from ancient hybridization between two unknown diploids.  Thus, we would expect that there are at least two copies of every genetic locus.  However, one of the 18S-5.8S-25S ribosomal RNA (aka NOR rDNA) loci has been deleted in quinoa.  We are comparing the sequence of the variable portion of this locus, the intergenic spacer (IGS), among candidate-ancestor 2x wild diploids with 4x quinoa and 4x Mexican huauzontle (C. berlandieri nuttaliae) in an effort to identify the ancestors of these crop species and to study the evolution of this important genetic locus.

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.

Some varieties of quinoa are remarkably well adapted to adverse environmental conditions such as salinity, drought and cold.  As a first step towards understanding the genetic basis for this adaptation, genes are being identified that may play a role.  The quinoa genes are being identified based on their similarity to homologous genes in other plant species such as Arabidopsis thaliana.  For instance, the Salt Overly Sensitive 1 (SOS1) gene of A. thaliana has been shown to play a role in salt sensitivity of the plant.  Students working on this project are hunting for the cloned gene in quinoa cDNA and BAC libraries towards the end of comparing it not only with the A. thaliana homolog but also to identify allelic variants that may confer resistance in quinoa to high salt levels in the soil.

Analysis of DNA sequences of cloned disease resistance genes from a wide range of plant taxa reveal sequence conservation of structural motifs.  We are using degenerate primers of these conserved DNA sequence to clone and sequence quinoa resistance genes.  Genetic mapping of these amplified sequences (Resistant Gene Analogs or RGA) will identify the location of putative disease resistance gene clusters within the genetic map of quinoa.  The identification of resistance genes in quinoa will accelerate the development of disease resistant lines of quinoa, resulting in higher yield.

In contrast to the NOR rDNA loci, 4x quinoa has retained two separate 5S rRNA gene loci.  We are studying the variable non-transcribed spacer, or NTS, of these genes and comparing the sequences to those of 2x potential ancestors and 4x Mexican huauzontle (C. berlandieri nuttaliae) to shed light on phylogenetic relationships among these species.

Triterpenoids are a large class of isoprenoidal natural products present in higher plants.  They exhibit a wide range of both structural diversity and biological activity, and therefore are regarded as important biological compounds.  In Chenopodium quinoa a major seed triterpenoid compound (called saponin) has an anti-nutritional affect on human consumption.  In this project we are cloning the gene that is the first committed step in saponin biosynthesis.

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. 

The Quinoa Seed Analysis Project is directed towards identifying the protein, starch, and mineral content in many varieties of quinoa. This data will be incorporated with the current breeding programs to grow plants that will have exceptional nutrient content.  With quinoa as a staple food source, new contributions and improvements to the crop will literally feed thousands.

Tepary is currently being cultivated as a vegetable in the arid desserts of North and Central America.  Tepary bean provides an exceptional opportunity to employ genetic technology to improve a crop which offers tremendous potential to alleviate malnutrition and hunger in the Developing World.  The goal of this project is to develop a phylogenetic or family tree for tepary.  This is accomplished by isolating repeated DNA sequences within tepary bean.  By comparing small variations in these simple sequence repeats (SSRs) we can create a family tree which illustrates the diversity among the various breeds of tepary.

Tomato spotted wilt virus (TSWV) is large problem in tomato production around the world and can cause complete crop losses in sub-tropic and mild temperate zone areas.  Natural resistance identified in wild relatives of tomato has been identified and introgressed into the cultivated tomato here at BYU.  Our present objectives are to identify and genetically map the genes responsible for TSWV resistance.  Along with develop pathogen derived resistance to the same disease through plant transformation

Over half of the protein consumed worldwide comes from seeds.  Of these harvested crops, the cereal crops such as corn, wheat, and rice are the most important with over 2 billion tons harvested annually.  Although the world relies on these cereals, they are low in protein content, and some important species like maize lack essential amino acids. To better understand these proteins, I am analyzing those of a little studied crop, Pennisetum glaucum (pearl millet).  Because it is a drought-tolerant, ruddy crop with a higher protein content than other cereal crops, many hope to increasingly use it as a feed grain for both animals and humans alike.  We will be quantifying and qualifying these proteins to facilitate its increasing use, and open the door for future genetic improvements.

Endophytic fungi are economically important symbionts of many plant species. Endophytes bestow greater persistence, hardiness, and higher agronomic quality to grasses, in addition to preventing insect pests from eating the leaves. Unfortunately, many of the chemicals they produce are also toxic to livestock. Our endeavor is to develop novel strains of endophytes through natural reproductive processes with the intent of improving them genetically. Specifically we want to enhance their ability to improve the quality of grasses as well as provide greater natural insect resistance without the toxic side effects on livestock.

We are attempting to identify molecular markers for nine unique endophytes.  The endophytes grow in the interstitial spaces in turf grass and produce various compounds that may increase drought resistance, pest tolerance, and/or cause livestock toxicity.  This project involves the isolation of the endophyte cultures onto PDA, DNA extraction, and AFLP markers to compare the endophytes on the molecular level.

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).