Mapping QTL associated with resistance to Pseudomonas syringae pv. actinidiae (Psa) in kiwifruit (Actinidia chinensis var. chinensis).
The samples in this submission were created to analyse, the effect of Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid A. chinensis var. chinensis parents to make 28 F1 families. However, because of a pervasive Psa infection many F1 seedlings were removed from the population. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of this population. Part one of this work was used to determine the signal strength required to detect QTL with a modified bulk segregant analysis (BSA). This was achieved by using male and female F1 individuals from a mix of families from the incomplete-factorial-cross population that had parent P8 as the father. Female parents of these families included samples P10, P14, P15, and P17. The shift in allele frequency at the sex locus on chromosome 25 was tested between the nine bulks of DNA named 1-9 in the paper (table 1) corresponding to sample names J16, I5, H14, G13, F12, C3, B2, E11, and A1 respectively. The nine bulks contained about 10, 20, 25, 40, 50, 55, 68.4, 78.9 or 89.5 percent male contribution to the bulk containing 19 - 20 individuals. Once the QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population. Each family was assigned to one of eight bulks named P1, P2, P3, P4, P9, P10, P11, and P12, based on a single parent that contributed to the families. Each sample bulk was compared against a bulk made up of the available WGS data from the parents contributing to the sample bulk. The deviation in allele frequency from the expected allele frequency within surviving populations using the modified BSA method was able to identify 11 QTLs for Psa that were present in at least two analyses.