Does the P Value Have a Future in Plant Pathology?

The P value (significance level) is possibly the mostly widely used, and also misused, quantity in data analysis. P has been heavily criticized on philosophical and theoretical grounds, especially from a Bayesian perspective. In contrast, a properly interpreted P has been strongly defended as a measure of evidence against the null hypothesis, H0. We discuss the meaning of P and null-hypothesis statistical testing, and present some key arguments concerning their use. P is the probability of observing data as extreme as, or more extreme than, the data actually observed, conditional on H0 being true. However, P is often mistakenly equated with the posterior probability that H0 is true conditional on the data, which can lead to exaggerated claims about the effect of a treatment, experimental factor or interaction. Fortunately, a lower bound for the posterior probability of H0 can be approximated using P and the prior probability that H0 is true. When one is completely uncertain about the truth of H0 before an experiment (i.e., when the prior probability of H0 is 0.5), the posterior probability of H0 is much higher than P, which means that one needs P values lower than typically accepted for statistical significance (e.g., P = 0.05) for strong evidence against H0. When properly interpreted, we support the continued use of P as one component of a data analysis that emphasizes data visualization and estimation of effect sizes (treatment effects).

First Report of Phakopsora pachyrhizi on Soybean in Costa Rica.

Phakopsora meibomiae (Arthur) Arthur has been reported to occur in several legume species in the tropical regions of Central and South America. In Costa Rica, this pathogen was initially reported as P. pachyrhizi Sydow (1); however, to our knowledge, P. pachyrhizi has not been detected in Costa Rica. In routine evaluations of a 0.2-ha field planted with soybean (Glycine max (L.) Merr var. CIGRAS 06) in La Garita, Alajuela, Costa Rica, symptoms similar to Asian soybean rust were observed in December 2012 and January 2013. Soybean plants were at growth stages R4 to R5 when these symptoms were observed, which included yellow spots on leaves with brown spots on the abaxial surface. Further evaluations at growth stage R5 to R6 indicated that the spots had coalesced, turned grayish-brown, and caused substantial defoliation. Microscopic examination of symptomatic leaves showed the presence of uredinia and urediniospores on the lower surface of the leaf. While initial symptoms were on the southern side of the field, a substantial area of the field was infected at the second evaluation. Infected leaves were submitted to the USDA-ARS Foreign Disease-Weed Science Research Unit under the appropriate USDA-Animal Plant Health Inspection Service permit for molecular characterization and identification. Urediniospores were collected by washing infected leaves with sterile water and then pelleted by centrifugation. DNA was extracted from urediniospore pellets and excised leaf pieces using a DNeasy Plant Mini Kit (Qiagen, Germantown, MD), and eight samples were amplified in real-time polymerase chain reaction (PCR) with P. pachyrhizi-specific primers Ppm1 and Ppa2 but not with the P. meibomiae-specific primers Ppm1 and Pme2 (2). Nucleotide sequence alignment of the internal transcribed spacer (ITS) regions 1 and 2 that were amplified by PCR using the primers Ppa1 and Ppa2 further confirmed the identification as P. pachyrhizi. To the best of our knowledge, this is the first known confirmation of soybean rust, caused by P. pachyrhizi in Costa Rica. CIGRAS-06 is the only soybean variety bred in the country as well as one of the very few varieties available for growers. Given that breeding for disease resistance is not a short-term option for P. pachyrhizi, alternative disease management strategies will have to be developed. References: (1) K. R. Bromfield. Soybean Rust, Monograph No. 11. APS Press, St. Paul, MN, 1984. (2) R. D. Frederick et al. Phytopathology 92:217, 2002.