High‐density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

Abstract

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

“…High-density SNP arrays (12 and 9 thousand SNPs) have recently been developed for maritime pine [23, 24]. Given the size of the maritime pine genome (25.8 Gb/C, [25], these arrays cover only a limited proportion of the relevant variation underlying phenotypes.…”

Application of selected molecular markers in studies on forest trees

“…Data obtained by this method have wideranging applications: mapping genomes, identifying seeds with their origins, comparing natural and bred populations, investigating genetic diversity with respect to phenotypic diversity, concluding on historical processes, demographic events as well as selection and adaptation. Notwithstanding such impressive data size, in confrontation with the size of coniferous genome -24.5G in maritime pine Pinus pinaster (Chagne et al 2002) -it should be noted that the obtained SNP number (Plomion et al 2016) only coincides with a small fraction of potential genetic diversity. In spite of the need for attaining more and more data, it has been found, however, that a few thousand of appropriately selected SNPs is as much as necessary to draw a reliable conclusion about polygenic patterns of adaptation process (Berg and Coop 2014).…”

“…Next-generation sequencing (NGS) technique in fact allows for analyzing an unlimited number of single nucleotide polymorphisms. By use of the Illumina platform, it was possible to create a genotyping chip containing 7252 SNP, the largest of the so far prepared ones for Pinus pinaster (Plomion et al 2016). Analyses with the use of thirdgeneration sequencing technology have been successfully performed also for other coniferous species (Pavy et al 2008;Eckert et al 2009;Chancerel et al 2013;Liu et al 2014).…”

Ecological and association genetics in two Mediterranean pine species

“…Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, et al 2016.…”

“…) and differential expression under biotic and abiotic stress in maritime pine (Plomion et al 2016). After removing SNPs with uncertain scoring (visual inspection using GenomeStudio), we kept 6,100 SNPs for further analysis in the studied populations.…”