Genetic dissection of fruit maturity date in apricot (P. armeniaca L.) through a Single Primer Enrichment Technology (SPET) approach

Abstract

Background Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one. Results The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies. Conclusions Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics.

Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce

“…The sequenced dataset comprised an average of 4 million SNPs per sample, which has been indicated to be adequate for processing several thousands of probes (Scaglione et al, 2019). Compared to the 25K SPET panel reported in peach (Baccichet et al, 2022) and the 5K SPET panel described for tomato, eggplant, and oil palm (Barchi et al, 2019;Herrero et al, 2020), the 40K SPET assay designed in lettuce provides a higher number of…”

“…(Herrero et al, 2020), cultivated and wild species of tomato and eggplant (Solanum spp.) (Barchi et al, 2019), and peach (Prunus armeniaca L.) (Baccichet et al, 2022), showing the power of this method for genotyping germplasm collections and crossing populations. Applications included population structure analyses, phylogenetic investigations, high-density linkage map development, and association mapping analysis.…”

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study

“…Based on a single primer enrichment technology (SPET), ATG relies on the design of ∼40 bp long probes based on reference genomes or transcriptomes, enabling to target with high reproducibility specific genomic regions carrying genetic variants of interest. The method has so far mainly been used in human health (Scolnick et al ., 2015; Nairismägi et al ., 2016; Saber et al ., 2017) or plants of agronomic interest (Barchi et al ., 2019; Scaglione et al ., 2019; Baccichet et al ., 2022; Tripodi et al ., 2023) and its use on wildlife species for conservation purposes is only starting to develop (Gramazio et al ., 2020; Gavriliuc et al ., 2022).…”