Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars

Understanding the sequence diversity of rice blast resistance genes is important for breeding new resistant rice cultivars against the rice blast fungusMagnaporthe oryzae. In this study, we selected 24 rice cultivars with different genetic back-grounds to study the alelic diversity of rice blast resistance genesPiz-t, Pitaand Pik. For Piz-t, a total of 17 alelic types were found within the 24 cultivars. Blast inoculations showed that most of the mutations can affect the function of the resistance gene. For Pita, except for the difference at the 918th amino acid, a majority of the 21 mutations were detected among the cultivars. Inoculations with blast isolates carryingAvr-Pita revealed that cultivars with mutations in other sites except for the 918th amino acid did not affect the function of thePita gene. ForPik, a total of six alelic types were found within the 24 cultivars, but ifve of them lost the function of the resistance gene. In addition, we found thatPiz-t, Pita and Pik were expressed constitutively in the 24 rice cultivars and the expression level was not related to resistance. Our results have provided the sequence diversity information of the resistance genesPiz-t, Pita and Pik among the popular rice cultivars grown in the northeast region of China. Keywords：resistance gene, avirulence gene, aleles, function, genetic evolution zae（M. oryzae）, is one of the most destructive diseases in rice production worldwide. Over the years, comprehensive studies on rice blast resistance have been conducted （Silue et al. 1992）. The resistance in newly cultivated rice cultivars to M. oryzae can be lost quickly due to the high level of instability in the genome of the fungus （Bonmanet al. 1992）. Previous studies show that cultivars with durable and broad-spectrum resistance againstM. oryzae carry multiple major resistance （R） and minor resistance genes （Liuet al. 2014）. An effective way to control rice blast disease is, therefore, to breed rice cultivars with multiple R and QTL genes. To date, over 83 rice blast R genes have been identiifed, and are distributed on 11 rice chromosomes except Received 22 May, 2015 Accepted 26 October, 2015 WANG Yan, E-mail： 8806wy@163.com; Correspondence LIU Zhi-heng, Tel： ＋86-24-23738857, E-mail： lzhh1954@163.com; ZHENG Wen-jing, Tel： ＋86-24-31021081, E-mail： zwj27@126. com ＊These authors contributed equaly to this study. ？ 2016, CAAS. Al rights reserved. Published by Elsevier Ltd. doi： 10.1016/S2095-3119（15）61207-2 1. Introduction Rice blast disease, caused by the fungusMagnaporthe ory-

Improving <i>in Silico</i>Prediction of Epitope Vaccine Candidates by Union and Intersection of Single Predictors

The in silico prediction of peptide binding affinities to MHC proteins is a very important first step in the process of epi-tope-based vaccine design and development. Five MHC class II binding prediction servers were combined in different ways and the resulting performance of these combinations was evaluated using a test set, which consisted of 4540 known HLA-DRB1 binders. The five servers were: NetMHCIIpan, NetMHCII, ProPred, RANKPEP, and EpiTOP. The top 5% of the ranked predictions from each server were combined using union and intersection operators. The outputs were evaluated in terms of sensitivity and positive predictive value (PPV). The union operator showed high sensitivity (65-79%) and low PPVs (6-8%), while intersection outputs had low sensitivities (4-41%) yet significantly higher PPVs (14-31%). Thus there is a defining trade-off between sensitivity and PPV for each combination. The union of outputs from different servers brings more “noise” than “signal” to the resulting set of predicted binders. Conversely, selecting only commonly predicted binders increases the probability that an identified binder is a true binder.