Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.)

Abstract

Background: An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome.

Results: Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004.

Conclusions: We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for the arcelin gene, linked genes and other members of the APA family are essential for breaking linkage drag while maintaining high levels of bruchid resistance in common bean.

Figure 1

Schematic diagram of the APA locus showing the placement of arcelin and flanking genes in relationship to SSR markers evaluated for linkage disequilibrium. Gene annotation for BAC 71F18 based on Kami et al. (2006) and microsatellite markers inidcated in bold.

Figure 2

Relative size of bruchid-resistant wild and cultivated beans used in the study. Wild bean contain the Arc1 and Arc5 alleles, respectively, and the cultivated beans are two RAZ lines containing arcelin-based bruchid resistance introgressed into a cultivated background.

Figure 3

Population structure of Andean and Mesoamerican, bruchid-susceptible and resistant beans used in the study. Two levels of subdivision, K = 2 and K = 3, are considered for the 105 common bean genotypes from the cultivated Andean and Mesoamerican genepools and from the wild sources of resistance to bruchids.

Figure 4

Allele pair linkage disequilibrium matrices for each linkage group across the entire common bean genome for the full group of genotypes and for the Andean and Mesoamerican group genotypes. Linkage groups are indicated as B1 through B11 based on map order from Blair et al. (2003). Darker squares indicate higher linkage disequilibrium in terms of correlation coefficient (r²) as indicated in the legend. B04, the linkage group with the APA locus is highlighted. Genepools are abbreviated as Mesoamerican (Meso), Andean (Andean) and both together (All).