Mapping QTL associated with resistance to Pseudomonas syringae pv. actinidiae in kiwifruit ( Actinidia chinensis var. chinensis )

• Published in: Frontiers in plant science Vol. 14; p. 1255506
• Main Authors: Flay, Casey, Symonds, V Vaughan, Storey, Roy, Davy, Marcus, Datson, Paul
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 26-03-2024
• Subjects: bulk segregant analysis; Plant Science; pool sequencing; QTLseqR; selection mapping; WGS; pool sequencing; QTLseqR; WGS; bulk segregant analysis; selection mapping
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2023.1255506

pv.
(Psa) is a bacterial pathogen of kiwifruit. This pathogen causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families of diploid
seedlings grown in the field show a range of susceptibilities to the disease with up to 100% of seedlings in some families succumbing to Psa. But the effect of selection for field resistance to Psa on the alleles that remain in surviving seedlings has not been assessed. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid
var.
parents to make 28 F
families. However, because of the diversity of these families, low numbers of surviving individuals, and a lack of samples from dead individuals, standard QTL mapping approaches were unlikely to yield good results. Instead, a modified bulk segregant analysis (BSA) overcame these drawbacks while reducing the costs of sampling and sample processing, and the complexity of data analysis. Because the method was modified, part one of this work was used to determine the signal strength required for a QTL to be detected with BSA. Once QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population that had multiple individuals removed due to Psa infection. Each family was assigned to one of eight bulks based on a single parent that contributed to the families. DNA was extracted in bulk by grinding sampled leaf discs together before DNA extraction. Each sample bulk was compared against a bulk made up of 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. The identification of these Psa resistance QTL will enable marker development to selectively breed for resistance to Psa in future kiwifruit breeding programs.