Detecting the genetic basis of local adaptation in loblolly pine (Pinus taeda L.) using whole exome-wide genotyping and an integrative landscape genomics analysis approach.

Mengmeng Lu,Carol A Loopstra,Konstantin V Krutovsky

doi:10.1002/ece3.5225

Mengmeng Lu, Carol A Loopstra + Show 1 more

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https://doi.org/10.1002/ece3.5225

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Abstract

In the Southern United States, the widely distributed loblolly pine contributes greatly to lumber and pulp production, as well as providing many important ecosystem services. Climate change may affect the productivity and range of loblolly pine. Nevertheless, we have insufficient knowledge of the adaptive potential and the genetics underlying the adaptability of loblolly pine. To address this, we tested the association of 2.8 million whole exome‐based single nucleotide polymorphisms (SNPs) with climate and geographic variables, including temperature, precipitation, latitude, longitude, and elevation data. Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 SNPs associated with 56 climate and geographic variables. Longitude, maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine. Functions of candidate genes related to terpenoid synthesis, pathogen defense, transcription factors, and abiotic stress response. We provided evidence that environment‐associated SNPs also composed the genetic structure of adaptive phenotypic traits including height, diameter, metabolite levels, and gene transcript abundance. Our study promotes understanding of the genetic basis of local adaptation in loblolly pine and provides promising tools for selecting genotypes adapted to local environments in a changing climate.

Highlights

Pine comprises 80% of the planted forestland and over one half of the standing volume in the Southern U.S (Wear, Huggett, Li, Perryman, & Liu, 2013)
Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 single nucleotide polymorphisms (SNPs) associated with 56 climate and geographic variables
Maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine

Summary

Introduction

Pine comprises 80% of the planted forestland and over one half of the standing volume in the Southern U.S (Wear, Huggett, Li, Perryman, & Liu, 2013). The natural habitat of loblolly pine ranges from East Texas to central Florida and north to Southern New Jersey, demonstrating adaptability to various types of soil and growing conditions. The seed transfer guidelines for southern pines emphasize three key points: 1) low temperature to the north and low rainfall to the west limit the distribution of southern pines; 2) the annual average minimum temperature is the most important climate variable related to growth and survival; 3) for loblolly pine, seeds from east of the Mississippi River should not be used in the west because of the higher danger of losses due to droughts (Schmidtling, 2003). Traditional seed selection guidelines may need to be adjusted to select for robust genotypes adapted to a changing climate scenario. An altered temperature and precipitation pattern threatens forests with droughts, fires and pathogen outbreaks, eventually leading to damage to the quality and yield of wood produced (Allen et al, 2010)

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