Notes on Plant and Animal Genomes conference #PAG30 (III)

Monday 16012023

Rajeev Varshney, Murdoch University. Starts by talking about sustainable, climate-smart crops such as legumes and the resources that are changing the way we breed them: marker-assisted breeding, expression atlases, improved reference genomes, and more recently pangomes and superpangenomes. He believes that unadapted germplasm will provide genes for future crops. They are currently exploiting all these tools, for instance to tap on global variability of chickpea (n=3,366). Using the toolbox he and collaborators have mapped 20-50 traits in several legumes and have introgressed selected alelles in elite lines and evaluated them in the field. To streamline genotyping around the world they put together a low-cost high-throughput genotyping project that has benefited dozens of crops. Moreover, they have trained breeders with 15+ meetings around developing countries (52 MSc & PhD students as well). He then goes to show many examples of improved varieties produced in collaboration with local breeders that are now resistant to diseases or tolerate drought much better than checks (see letter at https://www.nature.com/articles/s41587-021-01079-z). What’s the future? Haplotype-based breeding to drive optimal idiotypes, genomic prediction, spatial transcriptomics, machine learning  => fast-forwards breeding (https://www.cell.com/trends/genetics/fulltext/S0168-9525(21)00226-2). He paid homage to green revolution heroes, he’s certainly one of them.

In poster session I discovered a poster by MA Lemay, U Laval, where he does GWAS on a soybean panel and compares the performance of  K-mer based analysis (https://github.com/malemay/katcher , https://github.com/malemay/gwask) to that of GWAS with explicit SV-indels. He finds that K-mer GWAS performs better than SV and comparable to SNP-based GWAS. He actually used https://pubmed.ncbi.nlm.nih.gov/32284578 to perform GWAS on K-mers.

Also read the poster of Merrit Kaipho-Burch, Cornell University,  where she summarized her experiments for the estimation of the effect of TE insertions/deletions on gene expression of maize inbreds and hybrids. The work required correcting for kinship. She concluded that 14% of the tested genes show expression changes, but only 0.9% of TE events had consequences.

Chandler Sutherland, UC Berkeley. Presents her work on plant NLR immune receptors. In A. thaliana they found that there are two classes of NLRs, with low and high amino acid Shannon diversity (https://academic.oup.com/plcell/article/33/4/998/6119334). Can they be identified using epigenomic features? In A. thaliana leaf they find that highly variable (hv) NLRs are more expressed than non-hv (apparently in contradiction with https://www.nature.com/articles/s41467-017-02292-8), and are also less gene-body methylated. They are also closer to TEs and often cluster in the genome.

Dan Sloan talks about mutation rate in plant mitochondria, which apparently are less mutable that other replicons (mt<cp<nucleous), as a result of the action of MutS Homolog 1 (MSH1, https://www.pnas.org/doi/10.1073/pnas.2206973119). Unpublished data suggest that mutation rate is negatively correlated wit the number of copies of the mitochondrial DNA.

Michelle Stitzer, CURRENTLY AT Cornell University. She describes a series of experiments at the Ross-Ibarra lab at UC DAVISto measure the mutation rates (genic, intergenic, TEs) in maize after comparing individuals across generations and even two inbred B73 genomes assembled 4-years apart.

Daniel Koenig, University of California-Riverside. Uses A. thaliana populations to study how variation arises through mutation. His lab looks in particular at CNV of mutator loci and take a reference-free approach with K-mers. They use GWAS and find candidate genes that explain CNV of K-mers, as found a couple of years go in rice (https://www.nature.com/articles/s41467-018-07974-5).

Daniela P. Quiroz, UC Davis. She talks about targeted DNA repair in rice; when repair fails mutations arise. She found that mutation rates were lower in genomic regions marked by H3K4me1, a histone modification found in the gene bodies of actively expressed and evolutionarily conserved genes in plants. This compared to other methylations types in K4 (0, 2, 3). The repair mechanism involves protein domain Tudor (https://www.ebi.ac.uk/interpro/entry/InterPro/IPR002999). This work is published in https://www.biorxiv.org/content/10.1101/2022.05.28.493846v3.