Table 1.
Plant material used for mapping and marker testing.
Fig 1.
Frequency distribution of disease severity.
Evaluation of resistance of the LP97-F2 population and control plants (A) and of Eagle-F1 and Eagle-F2 plants (B) to Pepper yellow leaf curl virus (PepYLCV) Indonesia strain performed 6 weeks after transfer of seedlings to the screen house. The disease severity index from 0 to 4 was used.
Fig 2.
Genome-wide distribution of SNPs and bins across pepper genomes.
The outermost box with scale represents the 12 pepper chromosomes. The green histogram represents the density of raw SNPs; the blue histogram indicates the SNPs that are polymorphic between LP97 and ECW30R that were used for bin construction; the red histogram indicates the bins of adjacent SNPs that were used for linkage-map construction.
Fig 3.
Collinearity between the genetic map and the physical map of pepper.
The outer circle represents the total number of chromosomes (chr = ID) on left side and linkage groups (chr = ID) on right side; markers located within linkage groups are linked to the parallel position on chromosomes by different colored lines in the inner circle.
Table 2.
Summary of the bins and genetic linkage map for the LP97-F2 population.
Fig 4.
A bin based linkage map showing the locations of QTLs for resistance to PepYLCV.
The genetic distance is shown in centimorgans (cM). LP97-F2 plants were evaluated for resistance to PepYLCV Indonesia strain in a screen house.
Table 3.
QTL analysis for resistance to PepYLCV Indonesia strain in the LP97-F2 population using composite interval mapping.
Table 4.
Candidate genes associated with PepYLCV resistance and their functions.
Fig 5.
Box plots of tightly linked bins to QTLs from chromosome P7 and P12 of LP97-F2.
A–C) LP97-F2 grouped based on the tightly linked bin to QTL peplcv-7 against PepYLCV Indonesia strain. D) LP97-F2 grouped based on the tightly linked bin to QTL peplcv-12 against PepYLCV Indonesia strain.
Fig 6.
A) Parental survey with marker Chr7-LCV-7 on P7. B) Parental survey with marker Chr12-LCV-12 on P12. C) Marker Chr7-LCV-7 on P7 validation using resistant hybrids. D) Marker Chr12-LCV-12 on P12 validation using resistant hybrids. E) Marker Chr7-LCV-7 on P7 validation using additional F2 segregating population Egale-F2. F) Marker Chr12-LCV-12 on P12 validation using additional F2 segregating population Eagle-F2. G) Single marker Chr7-LCV-7 on P7 genotype–phenotype association in Eagle-F2. H) Single marker Chr12-LCV-12 on P12 genotype–phenotype association in the Eagle-F2 population. (G & H) Green, blue and grey represents exact phenotype-genotype matched, when heterozygous counted as susceptible and unmatched, respectively.
Table 5.
Marker sequence information used for QTL validation and genotyping.