Ppe.XapF: High throughput KASP assays to identify fruit response to Xanthomonas arboricola pv. pruni (Xap) in peach

Abstract

Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. We developed simple, accurate, and efficient DNA assays (Ppe.XapF) based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit that allows breeders to cull seedlings at the greenhouse stage. The objective of this research was to validate newly developed DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Our study confirms that with only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, individuals carrying susceptible alleles can be identified. Use of these efficient and accurate Ppe.XapF KASP tests resulted in 44% reduction in seedling planting rate in the Clemson University peach breeding program.

Mapping the genomic landscape of peach and almond with PrunusMap

“…To benchmark PrunusMap, we analyzed relevant markers documented in the literature. For instance, (Fleming et al, 2022) reported two quantitative trait loci (QTLs) linked to fruit resistance to bacterial spot infection (“Xap.PpOC-1.2” and “Xap.PpOC-1.6”), sitting on chromosomes 1 and 6. Eleven SNPs in close proximity to these QTLs were used to design KASP markers, resulting in 44% reduction in seedling planting (Fleming et al, 2022).…”

Ppe.RPT/SSC-1: From QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach

“…DNA samples for these individuals were obtained using a rapid crude DNA extraction protocol described by Noh et al 43 . The template spreadsheet designed by Fleming et al 23 was employed to automatically assign genotypes. Statistical differences between classes were evaluated using one-way ANOVA, followed by the Tukey test for multiple comparisons in SPSS.…”

“…In peach, rapid and accurate DNA tests for predicting bacterial spot severity in fruit and chilling requirement were recently developed 23,24 . Additional tests for peach skin blush 25 , fruit pubescence 26 , subacid trait 27 and esh color 28 are also available.…”

Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach

“…In peach, rapid and accurate DNA tests for predicting bacterial spot severity in fruit and chilling requirement were recently developed 23 , 24 . Additional tests for peach skin blush 25 , fruit pubescence 26 , subacid 27 and flesh color 28 are also available.…”