Allele Discovery of Economic Pine Traits (ADEPT 2)

Genotyping of single nucleotide polymorphisms (SNPs) discovered via resequencing in loblolly pine is currently underway. We are using Illumina's Infinium platform, which is approximately seven to 15 times higher throughput than the GoldenGate assay. A 7,600 SNP chip was developed from the resequencing data, which represents approximately 6,500 genes within the loblolly pine genome.

Genotyping of SNPs is proceeding through two steps:

Genotyping within two linkage mapping pedigrees

Goal: To map as many resequenced amplicons to approximate positions in the loblolly pine genome, so as to be able to understand linkage relationships among them and aid in downstream population genetic inferences.

Status: A total of 185 progeny from two loblolly pine linkage mapping pedigrees have been genotyped with the 7,600 SNP Infinium SNP chip. Conversion rate (i.e. the number of SNPs producing genotype calls conducive to downstream analysis) varied by pedigree, but demonstrated a success rate of approximately 75% . Inclusion of three positive controls illustrated that the genotype calls were very reliable and reproducible. This translated into a total of 2,711 SNPs that were segregating within at least one of the pedigrees. Those SNPs represent 2,425 genes potentially able to be mapped within the loblolly pine genome.

Summary of data quantity and quality for the application of the Infinium 7,600 SNP chip to two loblolly pine pedigrees (qtl and base).

Pedigree Progeny Polymorphic SNPs Unique SNPs BI^a MI^b PI^c Genes Unique Genes Missing Data^d Repeatability^e (%) Clusterability^f (%)

qtl

91 1908 1415 368 783 757 1749 1265 3.69± 5.82 (0.00-56.98) 99.49 94.14

base

94 1789 1296 358 710 731 1644 1160 3.78± 5.56 (0.00-58.51) --- ---

Total 185 2711 --- --- --- --- 2425 --- --- --- ---

^aBI = both informative (heterozygous in both parents)
^bMI = maternally informative (heterozygous in maternal parent)
^cPI = paternally informative (heterozygous in paternal parent)
^dMissing data were calculated as:
^eRepeatability was calculated based on three replicated samples within the qtl pedigree as:
^fClusterability was calculated with the same data as repeatability in the following manner:
^gTotals are given as unique counts.

Genotyping within three association populations

Goal: Association of genotype to phenotype for five categories of phenotypic traits (wood properties, disease resistance, drought tolerance, gene expression and metabolomic profiles).

Status: Genotyping of 1,000 loblolly pine samples using the 7,600 Infiniun SNP chip is currently underway at the UC Davis Genome Center. Those samples represent two of the three association populations (Weyerhaeuser and NC State). Those data should be fully delivered by August, 2008. The third association population consisting of another 1,000 samples is currently being processed to obtain DNA for genotyping.