January 24, 2019

Student Breakout Session Speakers

Student Presentations Group 1: The Future of Plant Breeding

2:50 – 3:50 pm in the Union Theatre

Jeff Neyhart – University of Minnesota

A Genome-wide Analysis of Phenotypic Stability in Barley

The resilience of crop production will depend on breeding plant cultivars that are stable in the face of changing climates and extreme weather events. The stability of a cultivar can be analyzed using reaction norms, or the change in phenotype in response to a change in an environmental condition. Ideally, a cultivar will have a favorable trait mean and high stability, but these heritable parameters are often unfavorably correlated. Determining the genetic architecture of the mean and stability of a trait could assist breeding efforts to simultaneously improve both. To better-understand the genetic architectures of mean and stability in barley (Hordeum vulgare L.), we phenotyped a population of 175 genotypes in 35 environments for heading date and grain yield. Genetic correlations between trait means and stability were strong and often unfavorable. Genomewide association analyses for these parameters, performed using 9,279 SNP markers, revealed few marker-trait associations for grain yield but many significant loci for heading date. Markers associated with heading date stability largely coincided with either those associated with the mean, previously detected loci, or known genes. By modeling the reaction norms of individual markers, we could accurately predict phenotypic stability. These results support previous hypotheses that stability may be influenced by the additive environmental reactions of many loci that also influence trait means per se. Breeding across diverse environments may therefore be enhanced by exploiting heritable reaction norms, not necessarily selecting for improved stability.

Laura de Boer – University of California San Diego

Discovery of Expressable Gene Sets of Crop Species by Machine Learning with Omics Data

Determining which predicted gene models produce functional products is an exciting challenge in genome-wide biology. While the number of predicted gene models from plant genomes can exceed 100,000, the plant research community has detected transcript products from only a subset of these genes, and an even smaller subset have detected protein products. Gene homology and expression evidence is often used to curate a high confidence group of genes from full gene model sets, e.g. the filtered versus working gene sets of maize. An open question is whether genes outside of these curated high confidence sets are expressable at the protein level. A random-forest based approach utilizing gene DNA methylation patterns as model features was used to identify the expressable gene sets of two staple food crops. These expressable gene sets were defined with high accuracy for sorghum and two diverse inbred lines of maize, at both the transcript and protein level. While sorghum and the maize inbreds have similar gene content, the expectation is that phenotypic differences between species or inbreds is driven by differences in the proteome. Synteny between grasses was leveraged to identify gene models which are predicted to be uniquely expressible between species and which may explain a portion of the phenotypic diversity between species.

Paola Hurtado – University of California Davis

Non-traditional ways to learn plant breeding

Plant breeding is mainly known as the creative process of getting new plant varieties for human benefit or interests. In wheat, most common breeding goals are the improvement of yield and flour quality needed for obtaining a good bread or dish of spaghetti. However, beyond having a well-performed variety, there is a cyclical system of generation-wise assortative mating and selection process done by a breeder in field. Selection is an artistic process requiring a sharp-eyed person. The selection process is a key part of a breeding program, the skills to be able to accomplish it cannot be acquired by reading, writing or any other traditional scientific path. In fact, this is a knowledge that breeders gain by experience until they get ¨good eyes¨. Those eyes are important for bringing the vision that a breeder needs to guide the breeding program to meet an economic market. However, nobody tells the breeder what a real breeding program looks like, nor the skills needed to develop and pursue a career as a plant breeder. Here, I will share how the opportunity to work closely with a field breeder is an enriching experience that complements my scientific background and inspired my career choice.

Student Presentations Group 2: Mapping and Cloning

2:50 – 3:50 pm in the Green Room

Ian McNish – University of Minnesota

Genome-wide association of quantitative resistance to oat crown rust

Crown rust is the most important disease of cultivated oats. Crown rust is primarily controlled by using fungicides and genetically resistant oat cultivars. Genetic resistance is more desirable. Unfortunately, crown rust is notoriously difficult to control using single, large effect size, resistance genes because the pathogen population quickly evolves to defeat these genes. Developing quantitatively resistant oat cultivars, where the progression of disease is reduced, is an alternative genetic resistance strategy that has been more durable. Quantitative resistance can be a difficult trait to improve because quantitative resistance is phenotypically negatively correlated with heading date. Unfortunately, late maturing cultivars are undesirable in the northern United States because farmers prefer to finish the oat harvest safely before the corn harvest begins. Ideally, we would like to identify crown rust resistance loci not associated with heading date to use in marker assisted selection. Traditional univariate genome wide association is not capable of distinguishing between loci controlling a trait of interest and loci controlling traits correlated to the trait of interest. It is possible that genetic loci that control resistance could be distinguished from loci that control heading date by comparing univariate analyses of the two traits, univariate analysis of crown rust severity using heading date as a covariate. Our results indicate that loci on linkage groups 1, 15, and 24 are associated with quantitative oat crown rust resistance. These loci are distinct from loci associated with heading date and are not impacted by including heading date as a covariate in the GWAS model.

Gazala Ameen – North Dakota State University

The hijacking of barley wall associated kinases by Bipolaris sorokiniana to cause spot blotch disease

Plants have sophisticated layers of immunity receptors that sense the pathogen or host derived cues triggering transcriptional reprogramming to initiate defense responses which mostly result in programmed cell death (PCD). This PCD mediated resistance subdues the biotrophic pathogens, but can be hijacked by necrotrophs to colonize the resulting dead host cells. We show that barley wall associated kinase (WAK) genes, underlying the rcs5 QTL, function as immunity receptors that are hijacked by the necrotrophic fungal pathogen Bipolaris sorokiniana elicitors to cause spot blotch disease. The rcs5 genetic interval was delimited to ~0.23 cM, representing an ~234 kb genomic region that contained four WAK genes, designated HvWak2, Sbs1, Sbs2 (susceptibility to Bipolaris sorokiniana 1&2), and HvWak5. Post-transcriptional gene silencing of Sbs1&2 in the susceptible barley lines Steptoe and Harrington resulted in resistance, thus, the WAKs function as dominant susceptibility genes. Transcript analysis of Sbs1&2 showed nearly undetectable expression in resistant and susceptible lines prior to pathogen challenge, however, upregulation of both genes specifically occurred in susceptible lines post inoculation. Allele analysis of Sbs1&2 from eight resistant and two susceptible barley lines identified sequence polymorphisms associated with disease phenotypes in the promoter regions indicating that differential transcriptional regulation by virulent isolates contribute to WAK mediated susceptibility. Virulent isolate apoplastic wash fluids induced Sbs1 suggesting regulation by an apoplastic-secreted effector. Thus, the Sbs1&2 genes underlying the rcs5 QTL are the first susceptibility/resistance genes identified that confer resistance against spot blotch, a disease that threatens barley and wheat production worldwide.

Burcu Alptekin – Montana State University

Genome-wide Characterization of Autophagy-Related Genes Revealed Their Importance for Better Crop Performance in Bread Wheat

Autophagy is an important molecular mechanism in which the cellular material is degraded and recycled for purposes such as disposal of toxic materials, misfolded proteins or satisfying immediate energy need. Autophagy is essential for many aspects of cellular life such as development, stress response, and survival, thus; the autophagic pathway is well conserved between different organisms in a range from yeast to plants. In plants, the contribution of autophagy has been shown for several aspects of plant life such as plant development, reproduction, biotic and, abiotic stress resistance. In addition, the involvement of autophagy in monocarpic senescence indicates that it might be a key mechanism affecting the grain-end-quality for cereals such as wheat and barley. Considering the vital role of autophagy for plants, gaining deep information about its pathway and autophagy-related genes is highly important. In this study, autophagy-related genes are identified from the hexaploid wheat genome and a total of 44 coding regions transcribing for 18 isoforms of ATG genes were detected. The promoter regions of ATG genes showed special motifs for transcription factor families such as NAC, WRKY, ERF. In silico expression analysis of ATG genes revealed the potential contribution of autophagy process in grain development, salt and drought stress in bread wheat. Further investigation of detected genes may facilitate the path of crop improvement for cereals and may pave the way for better yielding varieties under stress conditions.