Genome‐wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca)

Abstract

SummaryIn fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot.This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification.The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study.This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

“…The program mlrho was also used to estimate the global sequencing error rate and the nucleotide diversity for each individual separately (see Haubold, Pfaffelhuber, & Lynch, 2010 for the definitions of estimates; Lynch, 2008). The minimum (-m) and maximum (-M) length of reads were fixed at 1 and 100, respectively, with a step (-S) of one (Mariette et al, 2016).…”

“…How to cite this article: Verdu, C. F., Guichoux, E., Quevauvillers, S., De Thier, O., Laizet, Y., Delcamp, A., Gévaudant, F., Monty, A., Porté, A. J., Lejeune, P., Lassois, L. and Mariette, S. (2016), Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecology and Evolution, 6: 7323-7333. doi: 10.1002/ece3.2466…”

Application of Genomic Technologies to the Breeding of Trees

“…In apricot, the implementation of GWASs for Plum Pox virus (PPV) resistance utilizing NGS platforms to genotype a broad spectrum of the available apricot breeding germplasm verified a previously described single family QTL and specific candidate genes. Thus, demonstrating the utility of the combined approaches of both single family QTL and GWAS studies (Mariette et al, 2016). …”

“…AM has been successfully applied in mapping genes involved in several traits in different plant species (maize, sunflower, lettuce, potato, tomato, wheat, etc. ), but only a few studies have been carried out in fruit tree crops, such as peach (Font i Forcada et al, 2013; Micheletti et al, 2015), apple (Cevik et al, 2010), pear (Oraguzie et al, 2010), almond (Font i Forcada et al, 2015a,b), and apricot (Mariette et al, 2016). In almond, these studies have been able to detect the genomic regions where candidate genes involved in the accumulation of important compounds for fruit quality such as tocopherol and phytosterol are located, using the peach reference genome.…”

Recessive Resistance to Plant Viruses: Potential Resistance Genes Beyond Translation Initiation Factors

“…Simultaneously, genomics-based crop breeding using NGS technologies is expected to overcome the challenge of feeding an increasing world population. As suggested by Varshney et al (2014), NGS technologies, which have rarely been applied to antiviral breeding using natural variants (Zuriaga et al, 2013; Mariette et al, 2016), would be quite useful for identifying loci in naturally resistant variants and also for breeding to introduce resistant loci into specific cultivars. Several studies have identified loci of interest from Arabidopsis mutants using whole-genome sequencing of pooled mutant F2 populations (Schneeberger et al, 2009; Austin et al, 2011; Uchida et al, 2011).…”