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Title: Genetic analysis of resistance to Pythium ultimum a major component of replant disease in apple rootstocks

item Fazio, Gennaro
item MAZZOLA, MARK - Retired ARS Employee
item Zhu, Yanmin

Submitted to: Journal of the American Pomological Society
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/28/2022
Publication Date: 1/1/2023
Citation: Fazio, G., Mazzola, M., Zhu, Y. 2023. Genetic analysis of resistance to Pythium ultimum a major component of replant disease in apple rootstocks. Journal of the American Pomological Society. 77(1)28-37.

Interpretive Summary: Natural genetic resistance to components of the apple replant disease (ARD) complex syndrome is available in apple rootstocks developed by the Geneva apple rootstock breeding program. This very desirable genetic resistance is mostly derived from a wild apple species, Malus robusta, a common parent in Geneva apple rootstocks. This research was performed to discover the genetic factors associated with the resistance to Pythium ultimum one of the major components of the ARD syndrome. The experiments involved inoculating breeding lines derived from Malus robusta and measuring their resistance to Pythium ultimum, then using the resistance score to discover genetic markers associated with it. The results of the genetic analysis showed that this trait is more complex than initially thought of and that it responds to the combination of at least 5 genetic factors residing on different chromosomes of the apple genome. This information is being used to develop genetic markers to select rootstocks with improved resistance to apple replant disease.

Technical Abstract: Apple rootstocks from the Geneva® breeding program have demonstrated the ability to tolerate apple replant disease in experimental and commercial plantings in North and South America, Europe and Africa. Apple replant disease (ARD) is biological in nature and composed by several bacterial, fungal and animal actors that when combined can stunt or even kill young roots. A major contributor to the ARD syndrome is the necrotrophic soilborne oomycete Pythium ultimum, which can individually overwhelm young roots causing them to decline. Genetic resistance to ARD and its components has been incorporated into apple rootstocks from a wild apple species Malus x robusta ‘Robusta 5’. This research was aimed at increasing our understanding of the genetic complexity of the resistance to P. ultimum in progeny of ‘Robusta 5’. In a replicated experiment we phenotyped 48 individual progeny (breeding lines) belonging to a larger population derived from a cross between replant susceptible apple rootstock ‘Ottawa 3’ and resistant ‘Robusta 5’. We also leveraged existing genomic infrastructure in the form of high density genetic maps composed of microsatellite and single nucleotide polymorphic markers segregating in the same cross which, when combined with the genotypic means of the 48 progeny in Quantitative Trait Locus (QTL) analysis yielded candidate genomic locations on chromosomes 2, 5, 13, 16 and 17 that seem to have had an effect on the susceptibility of those breeding lines to P. ultimum infection. The allelic effects of the loci were measured using a generalized linear model and their combinatorial interactions were studied. Of all the resistance allelic effects examined all but one were derived from ‘Robusta 5’ The ultimate goal of this work is to develop genetic markers that can aid in the selection of P. ultimum resistant rootstocks because the process of root phenotyping is extremely labor intensive and difficult. However, the multi-locus nature of this resistance trait may necessitate that only loci with larger effects (on chromosome 5, 17 and 13) be targeted for further development.