The mixed linear model has been widely used in genome-wide association studies (GWAS), but its application to multi-locus GWAS analysis has not been explored and assessed. Here, we implemented a fast multi-locus random-SNP-effect EMMA (FASTmrEMMA) model for GWAS. The model is built on random single nucleotide polymorphism (SNP) effects and a new algorithm. This algorithm whitens the covariance matrix of the polygenic matrix K and environmental noise, and specifies the number of nonzero eigenvalues as one. The model first chooses all putative quantitative trait nucleotides (QTNs) with ≤ 0.005 P-values and then includes them in a multi-locus model for true QTN detection. Owing to the multi-locus feature, the Bonferroni correction is replaced by a less stringent selection criterion. Results from analyses of both simulated and real data showed that FASTmrEMMA is more powerful in QTN detection and model fit, has less bias in QTN effect estimation and requires a less running time than existing single- and multi-locus methods, such as empirical Bayes, settlement of mixed linear model under progressively exclusive relationship (SUPER), efficient mixed model association (EMMA), compressed MLM (CMLM) and enriched CMLM (ECMLM). FASTmrEMMA provides an alternative for multi-locus GWAS.

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Resistance of Xanthomonas oryzae pv. oryzae (Xoo), which causes rice bacterial leaf blight, to bismerthiazol has been detected in China since the 1990s. Interestingly, the strains resistant to bismerthiazol on rice plants were more sensitive to bismerthiazol than wild-type (WT) strains in vitro. Here, qPCR was applied to detect the fold expression of ATP-dependent proteases, ClpP and its subunits, which cope with stresses including bactericides in bismerthiazol-resistant strains and their parental susceptible WT strain (ZJ173). Results showed that the expression of ClpP and its subunits were all higher in bismerthiazol-resistant strains than that in ZJ173. They were up-regulated during early growth phase and down-regulated during middle growth phase in ZJ173 treated with bismerthiazol but did not change in the resistant strains. ClpP and its subunits were overexpressed in Xoo in this study, the higher expression of these genes increased sensitivity in vitro and enhanced resistance in vivo to bismerthiazol. Inhibition of bismerthiazol to exopolysaccharide production, biofilm, and motility was also reduced in ClpP and its subunit’s overexpression mutants of Xoo. The deletion mutants of ClpP and its subunits in ZJ173 abated pathogenicity, biofilm production, swimming ability, exopolysaccharide production, and growth in low-nutrient environments. Moreover, ClpP and its subunits may act downstream of the histidine utilization pathway, which could be inhibited by bismerthiazol in Xoo. Taken together, our results indicated that ClpP and its subunits of Xoo influenced the resistance to bismerthiazol.