A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze

Abstract

High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellitebased assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to pro-vide~29,000 informative SNPs across~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.

Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome

“…The loblolly pine reference genome and transcriptome assemblies helped to eliminate probes that overlapped estimated intron boundaries and also provided an estimate of multiple‐hit alignments. Other recent approaches in Axiom array development for species with limited genome resources used RNA‐seq (Mishima et al, 2018 ) or a combination of RNA and restriction site–associated DNA sequencing (RAD‐seq) (Silva et al, 2020 ) to both generate EST contigs and identify SNPs and coding regions for probe design. These arrays had moderate conversion rates (<50%).…”

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

“…Given the need for molecular tools that support genomic studies of species of interest in forestry, different SNP arrays that are transferable between taxa of the same genus, such as Populus , Eucalyptus , Quercus , Picea , Araucaria , Pinus and Pseudotsuga have been developed [ 87 , 88 , 89 , 90 , 91 , 92 , 93 ] ( Table 1 ). For example, a 50 K Axiom array, developed from the genome of Picea abies (L.) H.…”

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

“…Among forest tree species, SNP arrays are already available for: Juglans regia (walnut; Marrano et al, 2019), Picea abies (Norway spruce; Bernhardsson et al, 2020), Pinus taeda (loblolly pine; Caballero et al, 2021), Pseudotsuga menziesii (Douglas fir; Howe et al, 2020), four European pine species (Perry et al, 2020), eight tropical pines (Jackson et al, 2022) and several eucalypt species . They have been used, for instance, to build linkage maps Grattapaglia, 2015, Pavy et al, 2017), develop genomic selection (GS) models (Tan et al, 2017), in GWAS (Bernard et al, 2020), for candidate gene selection (Zaborowska et al, 2021) and to help conservation guidelines by informing on fine genetic structure (Silva et al, 2020) Here, we present the Axiom PiSy50k (ThermoFisher Scientific, https://www.thermofisher.com), a new SNP genotyping array for Scots pine. We describe the SNP sources, discovery panels and selection processes used during the array design.…”