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

Abstract

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.

Fig 1

Infected roots–external view (A), traverse section (B) and longitudinal section (C).

Fig 2. Correlation among various phenotypic traits observed in the mapping panel.

RR, root rot; HR, healthy root; LW, leaf wilting; PM, plant mortality; S, survival of cuttings; RW-F, fresh root weight per sapling; RW-D, dry root weight per sapling; NR, number of roots per sapling; RV, root volume; LRL, longest root length per sapling; LY, leaf yield per plant.

Fig 3. Linear relationship between the leaf wilting and root rot traits.

Fig 4. NJ dendrogram of the mapping panel.

The Structure-defined subpopulation Q1 is coloured red, and Q2 is coloured blue.

Fig 5. Variation in ΔK values across different subpopulation numbers.

Fig 6. Proportion of subpopulation membership of the 214 diverse mulberry accessions inferred by Structure.

Fig 7. Population stratification in the mapping panel deciphered by PCA.

Inset: Eigenvalues of the principal components. The Structure-defined subpopulation Q1 is coloured red, and Q2 is coloured blue.

Fig 8

Distribution of expected and observed p-values of different statistical models used in marker–trait association analysis of charcoal rot resistance (A) and survival of cuttings (B).

Fig 9

Adventitious shoot (A, B) and root (B, C) regeneration in mulberry infected with M. phaseolina.