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Genetic mapping of local adaptation along the altitudinal gradient in Abies sachalinensis

Abstract

Understanding the genetic bases of local adaptation in dominant conifer species is critical in predicting the impacts of rapid climate change on forest ecosystems. However, the genetic basis of adaptation is not yet fully understood due to the huge and complex genomes of conifers and the unavailability to date of suitable crossing material. In this study, we constructed a linkage map for Abies sachalinensis (2n = 24) and investigated quantitative trait loci (QTLs) associated with local adaptation along an altitudinal gradient. A segregating population of 239 seedlings was produced from a cross between two F1 hybrids (high-altitude × low-altitude genotypes). QTL mapping of phenological and growth traits was performed using a pseudo-testcross strategy with linkage maps based on 1251 single-nucleotide polymorphism (SNP) and three simple sequence repeat (SSR) markers. Two maps consisting of 12 linkage groups with an average marker interval of ca. 3 cM were constructed for each parent. The total lengths of the maps were 1861 and 1949 cM. A permutation test identified four significant QTLs and 11 additional suggestive QTLs, with high logarithm of odds (LOD) scores (> 3.0). This is the first highly saturated linkage map produced for Abies taxa. Our results suggest that spring bud phenology is controlled by several QTLs with moderate effects. The use of the mapping population created by crossing two hybrids (high × low altitude genotypes) and numerous SNP markers enabled us to investigate the genetic basis of adaptive traits in conifer species.

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Acknowledgements

The authors thank A. Kurahashi for establishing the hybrid (high-altitude × low-altitude genotypes) parents of the mapping population used in this study. We also thank Y. Takashima, N. Kimura, S. Fukuoka, Y. Ando, Y, Nakatsubo, Y, Sato, K. Uchishiba, K. Okamura, and A. Takazawa for technical assistance. We thank S. Sakaguchi and S. Yabe for making suggestions about the experimental approach. We thank two anonymous reviewers and the associated editor for helpful suggestions to the early version of the manuscript. This work was supported by grants from JSPS KAKENHI, Grant Numbers 25292081 and 16H02554.

Data Archiving Statement

The nucleotide sequence data obtained in this study are archived in the DDBJ.

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Correspondence to Susumu Goto.

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Communicated by F. Gugerli

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Fig. S1

The P1 and P2 Abies sachalinensis linkage maps used in this study. The linkage maps obtained consisted of 12 linkage groups. The total lengths of the linkage groups making up the P1 and the P2 map were 1861.4 and 1948.9 cM, respectively. The number of markers and the average distance between markers was 632 and 3.1 cM for the P1 map and 625 and 3.3 cM for the P2 map (Table 2). (PDF 31 kb)

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Goto, S., Kajiya-Kanegae, H., Ishizuka, W. et al. Genetic mapping of local adaptation along the altitudinal gradient in Abies sachalinensis . Tree Genetics & Genomes 13, 104 (2017). https://doi.org/10.1007/s11295-017-1191-3

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Keywords

  • Adaptive traits
  • Altitudinal gradient
  • Linkage map
  • Phenology
  • QTL
  • RAD-seq