A greenhouse-based high-throughput phenotyping platform for identification and genetic dissection of resistance to Aphanomyces root rot in field pea

Aphanomyces root rot (ARR) is a devastating disease in field pea (Pisum sativum L.) that can cause up to 100% crop failure. Assessment of ARR resistance can be a rigorous, costly, time-demanding activity that is relatively low-throughput and prone to human errors. These limits the ability to effectively and efficiently phenotype the disease symptoms arising from ARR infection, which remains a perennial bottleneck to the successful evaluation and incorporation of disease resistance into new cultivars. In this study, we developed a greenhouse-based high throughput phenotyping (HTP) platform that moves along the rails above the greenhouse benches and captures the visual symptoms caused by Aphanomyces euteiches in field pea. We pilot tested this platform alongside with conventional visual scoring in five experimental trials under greenhouse conditions, assaying over 12,600 single plants. Precision estimated through broad-sense heritability (H2) was consistently higher for the HTP-indices (H2 Exg =0.86) than the traditional visual scores (H2 DSI=0.59), potentially increasing the power of genetic mapping. We genetically dissected variation for ARR resistance using the HTP-indices, and identified a total of 260 associated single nucleotide polymorphism (SNP) through genome-wide association (GWA) mapping. The number of associated SNP for HTP-indices was consistently higher with some SNP overlapped to the associated SNP identified using the visual scores. We identified numerous small-effect QTLs, with the most significant SNP explaining about 5 to 9% of the phenotypic variance per index, and identified previously mapped genes known to be involved in the biological pathways that trigger immunity against ARR, including Psat5g280480, Psat5g282800, Psat5g282880, and Psat2g167800. We also identified a few novel QTLs with small-effect sizes that may be worthy of validation in the future. The newly identified QTLs and underlying genes, along with genotypes with promising resistance identified in this study, can be useful for improving a long-term, durable resistance to ARR.