Abstract
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.
Highlights
The natural range of slash pine (Pinus elliottii Engelm. var. elliottii) is the most restricted of all major southern pines; it only extends from southern South Carolina to central Florida and westward to southeastern Louisiana
Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 single nucleotide polymorphisms (SNPs) significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits
Slash pine is an important source of original timber and resin production on commercial forest plantations
Summary
The natural range of slash pine (Pinus elliottii Engelm. var. elliottii) is the most restricted of all major southern pines; it only extends from southern South Carolina to central Florida and westward to southeastern Louisiana. Elliottii) is the most restricted of all major southern pines; it only extends from southern South Carolina to central Florida and westward to southeastern Louisiana. Slash pine planting is nearing 3 million ha in China, where breeding programs began more than 40 years ago and there are large breeding populations consisting of several hundred selections. For advanced genetic improvement of slash pine, marker-assisted breeding (MAB), genomic selection (GS) and gene editing would accelerate the breeding progress. A transcriptome-referenced association study (TRAS, called transcriptome wide association study (TWAS)), with a genome-wide association study (GWAS-like) approach was recently carried out as part of the improvement program for slash pine breeding populations in China [6]
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