Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

Abstract

Digital imaging allows the identification of genes controlling novel lesion traits. 16Abstract 19 Plant resistance to generalist pathogens with broad host ranges, such as Botrytis cinerea, is 20 typically quantitative and highly polygenic. Recent studies have begun to elucidate the 21 molecular genetic basis underpinning plant-pathogen interactions using commonly measured 22 traits including lesion size and/or pathogen biomass. Yet with the advent of digital imaging and 23 phenomics, there are a large number of additional resistance traits available to study 24 quantitative resistance. In this study, we used high-throughput digital imaging analysis to 25 investigate previously uncharacterized visual traits of plant-pathogen interactions related 26 disease resistance using the Arabidopsis thaliana/Botrytis cinerea pathosystem. Using a large 27 collection of 75 visual traits collected from every lesion, we focused on lesion color, lesion 28 shape, and lesion size, to test how these aspects of the interaction are genetically related. Using 29 genome wide association (GWA) mapping in A. thaliana, we show that lesion color and shape 30 are genetically separable traits associated with plant-disease resistance. Using defined mutants 31 in 23 candidate genes from the GWA mapping, we could identify and show that novel loci 32 associated with each different plant-pathogen interaction trait, which expands our 33 understanding of the functional mechanisms driving plant disease resistance. 34 35 36 99, US NSF grants IOS 1339125, MCB 1330337 and IOS1021861, and the USDA National 595 Institute of Food and Agriculture, Hatch project number CA-D-PLS-7033-H. 596 597 598

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

“…Previous work in the B. cinerea -A. thaliana pathosystem established connections between host polymorphisms and lesion growth, between gene expression and lesion size, and between transcriptomes of the host and pathogen , Zhang, Corwin et al 2017, Fordyce, Soltis et al 2018, Zhang, Corwin et al 2018). This study begins to establish the foundation to begin testing directional causal inferences from pathogen genome to transcriptome to disease phenotype by connecting genetic variation in the pathogen to expression changes in both the host's and pathogen's transcriptomes.…”

“…We used a previously described collection of B. cinerea genotypes that were isolated as single spores from natural infections of fruit and vegetable tissues collected in California and internationally (Atwell, Corwin et al 2015, Zhang, Corwin et al 2017, Fordyce, Soltis et al 2018, Zhang, Corwin et al 2018. We focused analysis on the A. thaliana accession Columbia-0 (Col-0), and all plants were grown as described in a previous study, with 4-fold replication of the full randomized complete block experimental design across two independent experiments (Zhang, Corwin et al 2017, Zhang, Corwin et al 2018.…”

“…In contrast to qualitative systems, quantitative plant-pathogen interactions exhibit a lack of large effect virulence/ resistance genes (Poland, Balint-Kurti et al 2009, Kou and Wang 2010, St. Clair 2010, Roux, Voisin et al 2014. Rather, the genetic basis of both organisms in these interactions is highly polygenic with genetic variation influencing loci that alter a diverse array of molecular mechanisms that extend well beyond perception events (Glazebrook 2005, Nomura, Melotto et al 2005, Goss and Bergelson 2006, Rowe and Kliebenstein 2008, Barrett, Kniskern et al 2009, Corwin, Copeland et al 2016, Bartoli and Roux 2017, Wu, Sakthikumar et al 2017, Fordyce, Soltis et al 2018, Soltis, Atwell et al 2019. It is, however, unclear how these polygenic molecular systems in different organisms interact to alter higherorder phenotypes such as virulence, or even more direct phenotypes like the transcriptome of both species.…”

“…It is, however, unclear how these polygenic molecular systems in different organisms interact to alter higherorder phenotypes such as virulence, or even more direct phenotypes like the transcriptome of both species. There is some conflicting evidence on the balance of the system, with some studies and traits suggesting that genetic variation in the pathogen dominates the system (Bartha, McLaren et al 2017, Wang, Roux et al 2018, while others suggest a balanced contribution of plant and pathogen genetics (Corwin, Copeland et al 2016, Fordyce, Soltis et al 2018, Soltis, Atwell et al 2019. Thus, there is a need to develop genomic approaches to understand how polygenic information is transmitted between the pathogen and the host to shift the genomic response of both organisms.…”