A flexible multi‐species genome‐wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species

Abstract

SummaryWe used whole genome resequencing of pooled individuals to develop a high-density single-nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.59 each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome-wide distributed chip content.Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome-wide coverage with 1 SNP/12-20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome.Given the EUChip60K multi-species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against 'gold standard' genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias.The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

“…The characterization of natural genetic perturbations segregating in phenotypically wild-type individuals offers an attractive alternative tool to study properties that emerge from permissible genetic variation (11,13). With the availability of high-throughput genotyping and high-resolution linkage maps in Populus (14,15) and Eucalyptus (16)(17)(18)(19), genetic approaches such as quantitative trait locus (QTL) (14,20,21) and LD-based association mapping (22)(23)(24)(25) are becoming feasible to…”

Genetic divergence among Psidium accessions based on single nucleotide polymorphisms developed for Eucalyptus

“…The chip EUChip60K is composed of 60,904 SNPs, of which 51,204 were polymorphic in 14 species of Eucalyptus (Silva-Junior et al, 2015). Thus, the amplification of Eucaliptus SNPs to Psidium was nearly 7%, and the effective transferability, by validation criteria in another Psidium sample, almost 2%.…”

“…DNA samples of accessions were genotyped with 60,904 SNPs of the EUChip60K chip, developed by Silva-Junior et al (2015). The genotyping services were performed by GeneSeek (Lincoln, NE, USA).…”

Genomic and transcriptomic approaches toward plant selection

“…A multi-species 60K SNP chip has developed for Eucalyptus from 12 species that is an outstanding tool to address population genomics questions and empower genomic selection, GWAS and complex trait variant studies in Eucalyptus (Silva-Junior et al, 2015). In a study on oil palm, Kwong et al have reported a study outputting an array of 200K SNPs for two oil palm species (Elaeis guineensis and E.oleifera) with more than 170K successful probe (Kwong et al, 2016).…”