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

Area of Science:

• Forestry and Genetics
• Bioinformatics
• Genomics

Background:

• Loblolly pine (Pinus taeda) is an economically important conifer with a complex genome.
• Existing genetic resources may not fully capture the genomic diversity of loblolly pine across its native range.

Purpose of the Study:

• To construct a high-density genotyping array for loblolly pine using an informatics approach.
• To develop a genome-wide resource for genetic studies and breeding applications in loblolly pine.

Main Methods:

• An informatics pipeline was developed to process heterogeneous, high-throughput sequence data from 2698 loblolly pine trees.
• Variant detection, filtering, and probe design were performed using improved genome assembly and annotation.
• A total of 423,695 variants were screened across a range-wide population.

Main Results:

• An Axiom genotyping array, named Pita50K, was successfully constructed, containing 46,439 high-confidence variants.
• Approximately 34% of the array variants are located in or near genic regions based on the annotated reference genome.
• The array integrates data from independent projects, covering loblolly pine sampled across its native range.

Conclusions:

• The Pita50K array is a valuable genome-wide resource for the forest tree breeding and genetics community.
• This resource addresses challenges posed by the large and repetitive loblolly pine genome.
• It facilitates advanced genetic research and breeding strategies for this economically significant conifer.