Plant genomic applications – PPP2019

EDIT: This post was written at the symposium as it happened. It has now been edited to correct some errors made while working rapidly, fix links, and add tweets from other people at the symposium.

If you think I’ve been out of my depth with some of the talks, then strap in. Usually, I cover genomics papers very slowly.

Ana Caicedo opened by looking at weed rice, or red rice. It’s a competitor with cultivated rice, and reduces yields. Possible progenitors of weedy rice could be the wild pre-domesticated rice, or domesticated rice stains. What Caicedo has found is weedy rice is an example of recurrent evolution. It keeps coming back from domesticated rice with relatively few genetic changes required for the emergence of weediness traits. It’s an example of de-domestication.

The plants we call weedy rice converge on similar traits. Caicedo concentrated on seed shattering. It’s a useful weedy trait. It’s something that is bred out of domesticated rice. The reemergence of shattering is not a reversion of a domesticated allele. They have evolved it in novel ways.

Shattering in rice depends on the formation of an abscission zone. It’s where the grain detaches when it falls off. All weedy rice forms an abscission zone. The ancestral state differes among weedy rice groups. Even with an abscission zone, cultivated rice does not shatter and weedy rice does.

Caicedo and colleagues are crossing weeds with ancestral crops and seeing what happens. They can track QTLs, and find they don’t match between crosses, so it looks like different genes are triggering shattering. They also found different genes were expressed, supporting their findings.

This means that shattering is something that rice finds very easy to re-evolve. As weed‐adaptive alleles originate through multiple mechanisms, it’s going to be a difficult problem to fight.

Talk by Richard Buggs

Following that was Richard Buggs on genomics for future trees. “Just as we need more trees in the world, we’re losing trees.”

How do we get more trees? Buggs looks at wheat domestication and compares that with tree breeding. “Tree breeding is in the Neolithic.” This is a well-known problem with generation times difficult for experimentation. Ash needs 10 years to reproduce and 30 years to grow to harvest for timber. Where ash does have an advantage is that its genome is just one-eighteenth the size of wheat.

There were three experiments he talked about, all in press. One was a GWAS, with DNA from ill trees. He could not get DNA from dead trees, so the most susceptible weren’t in the survey, but he got trees that were as bad as they could practically be. It looked like they had found genes that helped fight ash dieback. Using the genome, they tried to predict the health of a tree from its DNA. With just 200 SNPs, they got to 90% accuracy.

He has also looked at the phylogenomics of convergence in relation to emerald ash borer. Asian trees are much better at killing the larvae of the beetle. Studying the genes and mapping that on to the susceptibility of the ash trees. They found three branches that led to resistance to emerald ash borer. That gave hope of finding convergent evolution that leads to insect resistance in developing chemical defences. Fifteen genes were candidates for detection and signalling for defence responses.

Finally, there are Genome-Environment Association studies. He’d been working with James Borrell on birch for this. They tried to look for correlations between SNPs and environments. If matches can be found, it opens the possibility of moving seed around to help with local adaptation.

Talk by Andrew Groover

Andrew Groover came up next to talk about trait variation in Populus. Genetic variation is the foundation of adaptation of a species, which matters if your climate is changing. Most commercially-important traits are quantitative. Groover said that most ecologically-important variation is quantitative too.

While you can interrogate the genetic data, there’s still a gap in going to genes to phenotype. Groover pointed out that some of this is because you need to consider how genes interact with each other. Copy number variation can increase variation, by changing the targets of genes. Adding or deleting copies, (a bit like partial polyploidy – I think) can add variation for study into a population. This could explain a lot of variation in phenology, but less so in biomass.

Populus leaves have extraordinary variation. In some desert species this can change with the season to ensure fitness for an environment. Looking at gene dosage in leaves is a way of identifying the genes that are responsible for certain phenotypes.

Groover close looking at water transport in wood, where not only the amount of wood but also the morphology of the water‐conducting cells are modified in response to environmental conditions. However, there is also a strong inherited element too.

Talk by Katherine Denby

Katherine Denby has been working on the genetic improvement of leafy vegetables. Along with the usual problems of under and over nutrition, Denby highlighted the problem of lack of micronutrients, like Vitamin A.

She opened with lettuce as a problem. There are a couple of fungal pathogens that typically cause losses of 10%, but it can be much higher. The fungi can develop fungicide resistance quite quickly. They’re a difficult target as there’s no single gene resistance against the pathogens.

The team tried network direct screening to identify key genes. This uses transcriptome time series data. The study looked at the very earliest responses to see how the plant responded. Denby’s team also looked at gene expression in the pathogen too, to see how it reacted to defences. They found overexpression of network hub genes provides disease resistance in lettuce.

They have also looked at lettuce diversity for sources of genes. The wild relatives seem to have better resistance to Botrytis. While you can identify patterns in QTLs, you can’t immediately move to genes.

https://twitter.com/plantspplplanet/status/1169608415435530241

Another project Denby has is working on African leafy vegetables, in particular Amaranthus. There are around 60 species, but this is under debate. They’re rich in vitamins and minerals, and grow in most parts of southern Africa. They’re hardy, C4 plants, with drought tolerance and popular as a source for a relish. But as people move to the cities, they give up eating it.

Denby is trying to find ways of improving Amaranth and encourage smallholders to grow the plant rather than just gather it. She’s started by looking at Amaranth diversity and looking at water use efficiency, and nutritional water use efficiency. This means the plants keep their nutritional value when in drought conditions. It is also necessary for the plant to taste pleasant.

Talk by Zoë Migicovsky

The last speaker was Zoë Migicovsky on the genomics of apple domestication.

Malus domestica is thought to have been domesticated from M. sieversii, though there are significant genetic differences, due to introgression from other species like European crab apple. Looking at the genes, the crab apple has a stronger influence on cider apples over eating apples.

She has been looking into colour. Earlier this year reseachers found an association between a retrotransposon and red colour. She has found selection in the same region of the genome.

Another study was on firm against soft apples, it’s hard to tell, but there might have been some selection for firmer apples. Allelic diversity of NAC18.1 is a major determinant of fruit firmness and harvest date in apple.

Apples are clonally propagated. By taking cuttings an grafting there’s very little to no genetic variation in apple cultivars. Variation does happen on branches in buds, and these can be selected for. Even though they look different, they’re nearly genetically identical.

Somewhat surprising is that nine of the top ten apples are fairly closely related. Migicovsky presented a diagram of apple cultivars connected by their first degree relatives. You can get between most of the popular cultivars in just one or two steps. The outlier is Honeycrisp, an apple that hasn’t taken off in Europe yet. If you want a diverse apple, go for Honeycrisp.

There’s a lot of work to be done. There’s a thousand accessions in the Nova Scotia apple collection. You can follow Zoë Migicovsky on Twitter at @zoemig.

Further reading

Atwell, S., Corwin, J. A., Soltis, N. E., Subedy, A., Denby, K. J., & Kliebenstein, D. J. (2015). Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.00996

Bagavathiannan, M. V., Graham, S., Ma, Z., Barney, J. N., Coutts, S. R., Caicedo, A. L., … Beckie, H. (2019). Considering weed management as a social dilemma bridges individual and collective interests. Nature Plants, 5(4), 343–351. https://doi.org/10.1038/s41477-019-0395-y

Coker, T. L. R., Rozsypálek, J., Edwards, A., Harwood, T. P., Butfoy, L., & Buggs, R. J. A. (2018). Estimating mortality rates of European ash (Fraxinus excelsior) under the ash dieback (Hymenoscyphus fraxineus) epidemic. PLANTS, PEOPLE, PLANET, 1(1), 48–58. https://doi.org/10.1002/ppp3.11

Crocker, E., Condon, B., Almsaeed, A., Jarret, B., Nelson, C. D., Abbott, A. G., … Staton, M. (2019). TreeSnap: A citizen science app connecting tree enthusiasts and forest scientists. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.41

Graziosi, I., Tembo, M., Kuate, J., & Muchugi, A. (2019). Pests and diseases of trees in Africa: A growing continental emergency. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.31

Hammond, W. M., Yu, K., Wilson, L. A., Will, R. E., Anderegg, W. R. L., & Adams, H. D. (2019). Dead or dying? Quantifying the point of no return from hydraulic failure in drought‐induced tree mortality. New Phytologist. https://doi.org/10.1111/nph.15922

Harper, A. L., McKinney, L. V., Nielsen, L. R., Havlickova, L., Li, Y., Trick, M., … Bancroft, I. (2016). Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics. Scientific Reports, 6(1). https://doi.org/10.1038/srep19335

Hoyos, V., Plaza, G., & Caicedo, A. L. (2019). Characterization of the phenotypic variability in Colombian weedy rice (Oryza spp.). Weed Science, 67(4), 441–452. https://doi.org/10.1017/wsc.2019.18

Huang, Z., Young, N. D., Reagon, M., Hyma, K. E., Olsen, K. M., Jia, Y., & Caicedo, A. L. (2017). All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza. Molecular Ecology, 26(12), 3151–3167. https://doi.org/10.1111/mec.14120

Huang, Z., Kelly, S., Matsuo, R., Li, L.-F., Li, Y., Olsen, K. M., … Caicedo, A. L. (2018). The Role of Standing Variation in the Evolution of Weedines Traits in South Asian Weedy Rice (Oryza spp.). G3: Genes|Genomes|Genetics, 8(11), 3679–3690. https://doi.org/10.1534/g3.118.200605

Ingle, R. A., Stoker, C., Stone, W., Adams, N., Smith, R., Grant, M., … Denby, K. J. (2015). Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogenBotrytis cinerea. The Plant Journal, 84(5), 937–948. https://doi.org/10.1111/tpj.13050

Larsen, B., Gardner, K., Pedersen, C., Ørgaard, M., Migicovsky, Z., Myles, S., & Toldam-Andersen, T. B. (2018). Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing. PLOS ONE, 13(8), e0201889. https://doi.org/10.1371/journal.pone.0201889

Li, L.-F., Li, Y.-L., Jia, Y., Caicedo, A. L., & Olsen, K. M. (2017). Signatures of adaptation in the weedy rice genome. Nature Genetics, 49(5), 811–814. https://doi.org/10.1038/ng.3825

Migicovsky, Z., Li, M., Chitwood, D. H., & Myles, S. (2018). Morphometrics Reveals Complex and Heritable Apple Leaf Shapes. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.02185

Peace, C. P., Bianco, L., Troggio, M., van de Weg, E., Howard, N. P., Cornille, A., … Vanderzande, S. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6(1). https://doi.org/10.1038/s41438-019-0141-7

Plumb, W. J., Coker, T. L. R., Stocks, J. J., Woodcock, P., Quine, C. P., Nemesio‐Gorriz, M., … Buggs, R. J. A. (2019). The viability of a breeding programme for ash in the British Isles in the face of ash dieback. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.10060

Rodriguez‐Zaccaro, F. D., & Groover, A. (2019). Wood and water: How trees modify wood development to cope with drought. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.29

Sambles, C. M., Salmon, D. L., Florance, H., Howard, T. P., Smirnoff, N., Nielsen, L. R., … Grant, M. (2017). Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease. Scientific Data, 4(1). https://doi.org/10.1038/sdata.2017.190

Singh, V., Singh, S., Black, H., Boyett, V., Basu, S., Gealy, D., … Burgos, N. R. (2017). Introgression of Clearfield™ rice crop traits into weedy red rice outcrosses. Field Crops Research, 207, 13–23. https://doi.org/10.1016/j.fcr.2017.03.004

Sniezko, R. A., Johnson, J. S., & Savin, D. P. (2019). Assessing the durability, stability, and usability of genetic resistance to a non‐native fungal pathogen in two pine species. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.49

Stocks, J. J., Buggs, R. J. A., & Lee, S. J. (2017). A first assessment of Fraxinus excelsior (common ash) susceptibility to Hymenoscyphus fraxineus (ash dieback) throughout the British Isles. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-16706-6

Stocks, J. J., Metheringham, C. L., Plumb, W., Lee, S. J., Kelly, L. J., Nichols, R. A., & Buggs, R. J. A. (2019). Genomic basis of European ash tree resistance to ash dieback fungus. https://doi.org/10.1101/626234

Sollars, E. S. A., & Buggs, R. J. A. (2018). Genome-wide epigenetic variation among ash trees differing in susceptibility to a fungal disease. BMC Genomics, 19(1). https://doi.org/10.1186/s12864-018-4874-8

Vigueira, C. C., Qi, X., Song, B., Li, L., Caicedo, A. L., Jia, Y., & Olsen, K. M. (2018). Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications, 12(1), 93–104. https://doi.org/10.1111/eva.12581

Westbrook, J. W., Holliday, J. A., Newhouse, A. E., & Powell, W. A. (2019). A plan to diversify a transgenic blight‐tolerant American chestnut population using citizen science. PLANTS, PEOPLE, PLANET. https://doi.org/10.1002/ppp3.10061

Woodcock, P., Cottrell, J. E., Buggs, R. J. A., & Quine, C. P. (2017). Mitigating pest and pathogen impacts using resistant trees: a framework and overview to inform development and deployment in Europe and North America. Forestry: An International Journal of Forest Research, 91(1), 1–16. https://doi.org/10.1093/forestry/cpx031

Yeats, T. H., Migicovsky, Z., Watts, S., Song, J., Forney, C. F., Burgher-MacLellan, K., … Myles, S. (2019). Allelic diversity of NAC18.1 is a major determinant of fruit firmness and harvest date in apple (Malus domestica). https://doi.org/10.1101/708040