Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Abstract

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissuespecific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

Whole‐genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species

“…Of these, 20 372 (40.84%) are inside of 9002 gene models (the rest are in intergenic regions), and 156 are associated with the traits of interest (44 of them inside gene models, the remaining 112 intergenic). Of the 9002 gene models, 6147 (68.28%) are shared with those present in the PiSy50K array (Kastally et al., 2022), while 2855 (31.72%) are unique to our new array Psyl50K (Figure 4).…”

“…Moreover, 97.59% of Psyl50K's probes align to the assembly with more than 90% identity and 98.5% probe coverage. This represents an improvement in sequence fidelity compared to the other available SNP array for Scots pine (Kastally et al., 2022), in which 86.33% of the probes align to the genome assembly with the same parameters.…”

“…Breeding of Scots pine in Sweden started with the selection of plus trees in the 1940s and 1950s, and a further expansion of the breeding populations occurred in the 1980s (Haapanen et al., 2015). Until recently, conifer SNP arrays have been limited to a couple thousand SNPs, and are currently based on RNA sequencing, exome capture, or candidate gene sequencing (Chancerel et al., 2013; Graham et al., 2022; Howe et al., 2020; Kastally et al., 2022; Pavy et al., 2013; Perry et al., 2020; Plomion et al., 2016; reviewed in Ahmar et al., 2021; Grattapaglia, 2022). Markers in such SNP arrays thus only represent coding sequences, leaving out all the intergenic space, which constitutes the bigger part of the genome and is an integral part of population genetics studies.…”

“…Recently, the PiSy50K genotyping array was developed for Scots pine based on transcriptome sequencing, exome capture sequencing, and candidate genes (Kastally et al., 2022). Similarly, a SNP array for the genotyping of four European pine species, among them Scots pine, was developed from resequenced candidate genes and transcriptomic sequences (Perry et al., 2020).…”

Editorial: The past, present and future of The Plant Journal Resource Articles

“…Similarly, the resequencing of Brachipodium inbred lines to massively improve genome annotation of this important grass (Gordon et al., 2014), while the genome sequencing of Spirodela polyrhiza provided a model for a fast‐growing aquatic model monocot (Michael et al., 2017). TPJ Resource articles also reported genome assemblies of the important cereals; sorghum (McCormick et al., 2018), rye (Bauer et al., 2017), flax (You et al., 2018) and bread wheat (Montenegro et al., 2017; Zhu et al., 2021); tree species walnut (Martínez‐García et al., 2016), scots pine (Kastally et al., 2022), Jatropha (Wu et al., 2015), white spruce (Warren et al., 2015) and the stress tolerant forest species Casuarina equisetifolia (Ye et al., 2019); as well as the more minor crop species tomato (Aflitos et al., 2014), black raspberry (VanBuren et al., 2016), bottle gourde (Wu et al., 2017), Chinese liquorice (Mochida et al., 2017) and pomegranate (Qin et al., 2017). These studies span a wide range of genome sizes, technologies and computational approaches with more recent papers including optical mapping approaches as a complement to sequencing approaches (You et al., 2018) Zhu et al., 2021).…”