San Diego, CA
Summary of Industry Workshops
Advances in Visualizing Genome Organization – from Haplotypes to Chromosomal Barcoding
James A. Birchler – University of Missouri
Whole chromosome paints have previously been developed for each chromosome of maize that rely on thousands of unique oligonucleotide probes along the length of each chromosome. This set is genotype independent and will label the respective chromosome across all tested maize lines. With the availability of genomic sequences for both B73 and Mo17 inbred lines, the ability to generate probe collections specific to those genotypes is available. Toward this end, Presence/Absence Variation (PAV) and SNPs were used for predicted oligos from one inbred sequence that were absent in the other and vice versa for chromosome 10 from the respective inbreds. The developed oligopaints were effective at distinguishing the two homologues of 10 in a B73/Mo17 hybrid. These haplotype specific probe sets were used to visualize recombination events from progeny of a B73/Mo17 hybrid and in Recombinant Inbred Line populations that fix recombination events from the two parental lines. Ongoing studies are examining the behavior of homologues in meiosis.
Kai Wang – Fujian Agriculture and Forestry University
Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world’s sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, oligo-FISH technology was optimized and a suitable system for sugarcane was established. The creation of oligo-FISH remarkably improves our ability to conduct cytological research on sugarcane, and bring us deep insights into the genomic structure and evolution of sugarcane.
Takayoshi Ishii – Arid Land Research Center, Tottori university
Andreas Houben – Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
We developed a tool to visualize defined genomic sequences in fixed nuclei and chromosomes based on a two-part guide RNA with the recombinant Cas9 endonucleasecomplex. In contrast to classical in situhybridization, RGEN-ISL (RNA-guided endonuclease – in situ labelling) does not require DNA denaturation and therefore permits a better structural chromatin preservation. The application of differentially labelled tracrRNAs allows the multiplexing of RGEN-ISL. We established a combination of RGEN-ISL, immuno-staining and EdU labelling to visualize in situ specific repeats, histone marks and DNA replication sites, respectively. The broad range of adaptability of RGEN-ISL to different temperatures and combinations of methods has the potential to advance the ﬁeld of chromosome biology.
Complete Wheat Exome Analysis – From DNA to Variant Calling
Burkhard Steuernagel – The Sainsbury Laboratory and John Innes Centre
Disease resistance in plants is often conferred by members of a gene family that encode for intracellular receptors. These receptors have a nucleotide binding domain and leucine rich repeats (NLR). Resistance-gene Enrichment Sequencing (RenSeq) targets NLR genes and enables several cost-effective methods to identify such genes. We have designed RenSeq bait libraries for wheat and used them in combination with two complementary approaches. MutRenSeq deploys mutational genomics to target specific resistance genes. AgRenSeq is used for association genetics in a natural diversity panel. Both techniques have been used to identify several novel genes.
Shawn Quinn – Curio Genomics
As part of a collaboration with Daicel Arbor Biosciences the extensible Curio Genomics platform serves as the foundation that enables interpretive and real time analysis of NGS data generated from libraries that are enriched to focus on the high-confidence exon-annotated genome in hexaploid wheat.
In this talk we will demonstrate specific examples of how the platform scales to allow research partners to efficiently ask compound and complex bioinformatic questions of the massive genome of Chinese Spring Wheat samples. We’ll also show how the platform’s unique approach to the storage and processing of wheat genome data empowers researchers to conveniently collaborate with others, perform analyses, compare between samples, change analytical settings, apply different filters, and visualize results – all in real time.
Ute Baumann – The University of Adelaide