Ppe.CR.1 DNA test for predicting chilling requirement in peach

Abstract

Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1-1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in determining expected CR genotype (compared to SNP array) and predicting phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1-1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1-1 and -4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy.

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

“…The complexity of RPT and SSC traits due to their polygenic nature and environmental influence 37 made development of breeding tools for MAS difficult. However, quantitative traits were recently targeted in peach for DNA test development resulting in tools such as the Ppe.CR.1 designed for predicting chilling requirement 24 . RPT and SSC display similar patterns to chilling requirements, where multiple genes control the phenotype and the major QTL explained more than 30% of the phenotypic variation.…”

“…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.…”

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

“…The Ppe.RPT/SSC-1 was designed using a recently reported KASP approach for fruit response to Xanthomonas arboricola pv. pruni 23 and chilling requirement 24 prediction in peach. In combination with crude DNA extraction 41 , this technology provides an inexpensive, trustworthy, and user-friendly tool for accurately predicting SNP genotypes 29,46 .…”

“…Additionally, the Ppe.RPT/SSC-1 assay developed for SNP discrimination successfully predicted the genotypes previously obtained from the 9K SNP array with disagreement in only four accessions. From those, two accessions ('Fantasia' and 'Saturn') also demonstrated discrepancies between the SNP array and KASP genotypes when Ppe.CR.1 for prediction of chilling requirement was validated 24 . This result supports the hypothesis that the discrepancies could be due to the incorrectly called array genotypes or different DNA sources used in the array (genotyping carried out by the RosBREED project 22 ) and KASP genotyping.…”

“…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.…”