Association mapping of quantitative resistance to charcoal root rot in mulberry germplasm.

Outbreaks of root rot disease in the productive South Indian sericulture belt have threatened the sustainability of the industry. Macrophomina phaseolina (Tassi) Goid. causing charcoal rot is the predominant pathogen to which all productive mulberry cultivars are susceptible. The present study was undertaken to identify molecular markers associated with charcoal rot resistance in mulberry. A mapping panel comprising 214 diverse entries from the Indian germplasm collection was assessed for charcoal rot resistance by artificial inoculation. Resistance to the pathogen was observed in 20 entries, and 51 were found to be moderately resistant. A total of 773 alleles generated across 105 SSR loci and 20,384 AFLP markers generated using 32 EcoRI-NN and MseI-CNN primer combinations were used in genetic analysis. The panel was weakly structured with two subpopulations. However, most entries were found to be admixtures. Survival of cuttings and number of roots per sapling were associated with root rot resistance. Association mapping was performed using different linear mixed models. Five AFLP markers explaining 9.6-12.7% of the total phenotypic variance were found to be significantly (p < 0.05) associated with root rot resistance. Significant associations were also detected in four AFLP markers for survival of cuttings, and these markers explained 10.7-14.2% of the total phenotypic variance. These markers should be validated using mapping populations derived from contrasting biparental combinations by linkage analysis for use in marker-assisted gene pyramiding for durable resistance. The resistant genotypes identified in this study will substantially contribute to genetic improvement of mulberry for charcoal rot resistance and can be integrated into conventional breeding programmes.

STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface.

BACKGROUND: Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer population structure using multi-locus genotype data. However, a tool with graphical-user interface is currently not available to visualize STRUCTURE bar plots. RESULTS: We introduce STRUCTURE PLOT, a program for drawing STRUCTURE bar plots. The program generates publication ready, aesthetic STRUCTURE bar plots by using individual Q matrix from STRUCTURE or CLUMPP output. The program is very simple to use and includes variety of options like sorting bar by original order or by K, and selection of colors from R colors or RColorBrewer palette. Individual or population labels can be printed below or above the plot in any angle. Size of the graph and label can be defined, and option is provided to save plot in variety of picture formats in user defined resolution. CONCLUSION: The program is implemented as a web application for online users and also as a standalone shiny application. Web application is compatible to majority of leading web browsers and standalone version can be launched using a simple R command. The program can be freely accessed at http://btismysore.in/strplot.