Bridging the Gap: Using Functional Genomics to Unlock Yield Potential

Sponsored by Corteva Agriscience

About the symposium

On Friday, January 11th, 2019 the first WheatCAP Plant Science Symposium was held on the San Diego State University Campus. As part of the Corteva Plant Sciences Symposia Series, the event included talks from four notable keynote speakers, a panel discussion and six student research talks.

The title of the symposium was Bridging the Gap: Using Functional Genomics to Unlock Yield Potential. The aim of the symposium was to further explore the current and future application of functional genomics techniques in addressing the challenges of yield gaps as well as, yield improvement in cropping systems. Furthermore, this event aimed to provide the next generation of plant scientists, geneticists and breeders the tools to address the existing and emerging challenges related to global food security and production.

We had the privilege of hearing from Corteva spokesperson Dr. Jason Rauscher, Dr. Gina Zastrow-Hayes the Genomics technology leader at Corteva Agriscience, Dr. Ronan O’Malley leader of the Sequencing Technologies Group at the Joint Genome Institute, Dr. Scott Boden a Royal Society research fellow at John Innes Centre and Dr. Scott Jackson professor and director of the Center of Applied Genetic Technologies at the University of Georgia.

Ultimately, the goal of this symposium was to bring together graduate students to encourage networking and the sharing of science. I truly believe these goals were met and at the completion of the event I could not help but feel inspired and motivated to continue in my own attempts to better understand and illuminate the black box of crop yield.

Keynote speakers

Dr. Scott Boden

Project Leader and Royal Society Research Fellow at John Innes Centre

Dr. Scott Boden is currently a project leader at the John Innes Centre in the department of Crop Genetics. Dr. Boden received a Ph.D. in Plant Science from the University of Adelaide, Australia in 2008. Following his Ph.D., Dr. Boden served as a post-doctoral research scientist and Marie Curie International Fellow at the John Inness Centre from 2008-2011. This was followed by an additional post-doctoral position at CSIRO Plant Industry/Agriculture and Food. His research focuses primarily on the genetic regulation of inflorescence architecture and development in wheat as well as the regulation of flowering time and the circadian clock in wheat and barley.

Dr. Ronan O’Malley

Sequencing Technologies Group Lead, DOE Joint Genome Institute

Dr. O’Malley received a BA in Biology/Chemistry and a PhD from the University of Chicago. Dr. O’Malley currently serves as the lead of the Sequencing Technologies group at the United States Department of Energy Joint Genome Institute (JGI). In addition to overseeing community sequencing projects, Dr. O’Malley’s research focuses on the expansion and development of sequence-driven functional genomics methods and technologies. Before joining the JGI in 2016, Dr. O’Malley worked as a staff scientist at the Salk Institute in La Jolla, CA. During his time at the Salk Institute, he worked in the laboratory of Dr. Joseph Ecker to develop functional genomics technologies such as DAP-seq and TDNA-seq.

Dr. Gina Zastrow-Hayes

Genomics Technology Leader at Corteva Agriscience

Dr. Gina Zastrow-Hayes graduated with a degree in Microbiology from the University Wisconsin Madison in 2000 and since has worked in the field of Genomics spanning toxicology, cancer biology, circadian biology and agricultural research programs. She established Genomics and cell based screening facilities at the Scripps Research Florida campus and University of Pennsylvania and joined the Corteva Agriscience Genomics group in 2008 where she has helped expand the use of next generation sequencing technologies for breeding, transgene and gene editing applications. Gina is currently a Technology Leader in the Genomics group and is responsible for a team that manages long and short read sequencing technologies including whole genome sequencing for reference genome production and targeted applications for the gene editing molecular characterization pipeline.

Dr. Scott Jackson

Professor and Director of the Centre of Applied Genetic Technologies at the University of Georgia

Dr. Scott Jackson is currently the Georgia Research Alliance Eminent Scholar and Professor in Plant Functional Genomics at the University of Georgia. He also serves as the Director of the Center for Applied Genetic Technologies. Prior to joining UGA in 2011, he received his master’s and PhD from the University of Wisconsin – Madison and began his professional career at Purdue University. Dr. Jackson’s lab is primarily focused on the development and implementation of genomics tools to solve agricultural and crop improvement issues. Additionally, his research has revealed much about the structural and functional intricacies of several crop genomes, including rice, soybean, and chickpea.

Students’ Session

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. 

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