Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes.

Gloria De Mori,Alessandro Spadotto,Francesco Palmisano,Federica Savazzini,Rachele Falchi,Simone Scalabrin,Raffaele Testolin,Luca Dondini,Angelantonio Minafra,Daniele Bassi,Stefano Tartarini,Filippo Geuna

doi:10.3389/fpls.2019.01576

Abstract

Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which—the cultivar ‘Lito’ heterozygous for the resistance—has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A ‘Lito’ bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of ‘Lito’ was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar ‘Lito’ allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of ‘Lito’ is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.

Highlights

Sharka is one of the most prominent viral diseases affecting apricot and other stone fruit crops and is caused by a potyvirus (Plum Pox Virus, PPV) transmitted by aphid vectors
The increase in marker density allowed for the identification of 18 recombinants that were grafted onto GF305 and challenged with the PPV for 2 years
Despite the high degree of similarity found between peach, P. armeniaca, P. mume, and P. sibirica (Zuriaga et al, 2013), apricot and peach genomes were not strictly collinear in the region of the major determinant of resistance to PPV due to several indels and a sequence inversion

Summary

Introduction

Sharka is one of the most prominent viral diseases affecting apricot and other stone fruit crops and is caused by a potyvirus (Plum Pox Virus, PPV) transmitted by aphid vectors. Genetic sources of resistance to Sharka have been identified in several apricot cultivars as well as in wild apricots originating in Central Asia (Kegler et al, 1998; Zhebentyayeva et al, 2008; Decroocq et al, 2016). Analysis of these genotypes may suggest possible ways of overcoming the severe impact of Sharka on the apricot industry. Weaker QTLs were identified in linkage groups (LGs) 3, 4, and 7 and upstream of the main QTL of LG 1 (Lambert et al, 2007; Marandel et al, 2009), but their role in PPV resistance has not yet been well defined, probably due to the limited size of the populations used or due to the difficulties encountered in phenotyping (Mariette et al, 2016)

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Conclusion