Exome Genotyping and Association Genetics of Environmental Adaptation and Stress Mitigation Traits in a Clonally Tested Loblolly Pine (Pinus taeda L.) Population

Loblolly pine, Pinus taeda L., is the most widely planted and commercially important tree species in the southeastern U.S. To increase the number of known single nucleotide polymorphisms (SNPs) and functional markers available for research and tree breeding, we used genotyping by sequencing for targeted exome regions. The exons were captured in 375 trees using NimbleGen probes and then sequenced using the Illumina HiSeq 2500 platform. Hybridization oligonucleotide probes were designed for 199,723 exons (≈49Mb) partitioned from the loblolly pine genome annotation v2 (PineRefSeq). The bioinformatics analyses demonstrated 90.2% of the targeted exons were covered by the probes. The capture efficiency analyses showed that an average of 67.2% of the captured bases were in the target regions and more than 70% of the target bases had at least 10X sequencing depth. A total of 972,720 SNPs were acquired after filtering. Among them, 52.8% were located in coding regions and 5.3% were located in 5’ or 3’ untranslated regions. Mean heterozygosity (0.32±0.01) and nucleotide diversity (0.27±0.13, on a per site basis) were high within this population. The zygotic linkage disequilibrium (LD) coefficient (r²) decayed to half within 55 bp, to r²=0.1 within 192 bp, and r²=0.05 within 451 bp. The fastStructure analysis using unlinked SNPs demonstrated two distinct clusters representing west and east parts of the loblolly pine area. We will describe association tests that are being conducted to discover markers and genome regions associated with phenotypic traits including height, specific leaf area and carbon isotope discrimination.