Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L)

Abstract

Background: Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected.

Results: Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469-55,190,112 bp in Dt_chr9. A regional association analysis-based fine-mapping strategy was developed to narrow down the confidence intervals of the above QTL. The estimated LD decay of the genome region of interest was much faster than those of the Dt_chr9 chromosome and the whole genome, suggesting the existence of a recombination hotspot. Thirty-seven haplotype blocks were detected. The confidence intervals of the three clustered QTL were narrowed down to a region of 937,906 bp involving QTL-i23734Gh and a region of 1,389,417 bp involving QTL- i10740Gh, respectively. Each region contained the strongest association signal. Comparative analysis redefined the confidence intervals of the other three QTLs, qDL52T2-c19, QTL-BNL4069, and QTL-JESPR0001. The broad-spectrum VW resistance QTL qVW-D9-1 was demonstrated to be closely linked with the three redefined QTL, QTL-i23734Gh, QTL- i10740Gh and QTL-JESPR0001. Twelve functional genes were detected to be located within the redefined confidence intervals of VW resistance QTL. The mRNA CotAD_60243, encoding E3 ubiquitin-protein ligase UPL2-like, responsible for plant innate immunity and broad-spectrum disease resistance, was found to be overlapped with the strongest association signal i10740Gh. Six mRNAs encoding putative disease-resistance proteins were within the redefined confidence interval of QTL-JESPR0001, suggesting a tandem arrangement of R genes.

Conclusions: Our results proved that the VW resistance effect related to three clustered VW resistance-related QTL was actually controled by two redefined major QTL and severlal minor loci. The broad-spectrum VW resistance QTL qVW-D9-1 may be closely linked with the two redefined major QTLs. The tandem arrangement of R genes were detected in the redefined confidence interval of QTL-JESPR0001. The candidate genes obtained should be helpful in identifying and characterizing defense genes related to VW resistance QTL.

Keywords: Cotton; QTL; Regional association analysis; SNP; Verticillium wilt.

Fig. 1

Histogram of the relative disease index of the 120 cotton lines identified in the field disease nursery (a) and in the greenhouse (b)

Fig. 2

Linkage disequilibrium (LD) decay plot of the genome region of interest of Dt_chr9in cotton. The LD,measured as R squared, between pairs of SNPs is plotted against the distance between the SNPs. For the genome region of interest, LD decayed within 33 kb

Fig. 3

Manhattan plots showing the regional association mapping ofverticillium wilt resistance using 2253 SNPs from the target genome regionon Dt_chr9in cotton(Gossypium hirsutum L.). The blue asterisks depict the results of the field disease nursery environment, and the red asterisks depict the results of the greenhouse environment

Fig. 4

The LD blocks around the strongest associated signals i23734Gh (a) and i10740Gh (b), which span the distance from 41,156,543 bp to 42,094,449 bp and from 47,330,154 bp to 48,719,571 bp, respectively