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QTL detection for growth and form traits in three full-sib pedigrees of Pinus elliottii var. elliottii × P. caribaea var. hondurensis hybrids

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Abstract

Quantitative trait locus (QTL) analysis was conducted on three full-sib Pinus elliottii var. elliottii × P. caribaea var. hondurensis (PEE × PCH) hybrid families to identify genomic regions affecting two growth traits, height (Ht) and DBH at age 5, and seven morphological (“form”) traits. The QTL detection population consisted of family A containing 122 progeny, which was related to the validation population family B (n = 66) via a common PEE parent, but unrelated to the second validation population, family C (n = 107). Using a double pseudo-testcross QTL mapping approach, quantitative trait loci (QTLs) had been identified in the detection population for Ht, DBH, and three form traits. One QTL for Ht05 was validated in the shared common PEE lineage. For two other form traits, QTLs were validated by identifying QTLs that co-located to the same genomic regions in both validation populations. Two QTL, for another form trait and DBH05 were not identified in the original detection population but occurred in both validation populations. The QTL positions detected in this study provide a resource to identify form-trait loci using the Pinus genome or expressed sequence tag (EST) sequences, which may be useful for future association studies.

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Acknowledgments

This study was financially supported by the National Natural Science Foundation of China (30671706). The authors thank Longshan Forest Farm in Lechang City and the Suixi Institute of Forestry in Suixi City, Guangdong Province, China for assistance in the sample collection. We also thank Khongsak Pinyopusarerk of CSIRO, Australia for the valuable comments and English editing.

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    Authors and Affiliations

    1. Guangdong Provincial Key Laboratory of Bio-control for the Forest Disease and Pest, Guangdong Academy of Forestry, Guangzhou, 510520, People’s Republic of China

      Huixiao Yang, Bin Xu & Fencheng Zhao

    2. Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry, South China Agricultural University, Guangzhou, 510642, People’s Republic of China

      Huixiao Yang, Tianyi Liu, Chunxin Liu & Shaowei Huang

    3. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, People’s Republic of China

      Shaowei Huang

    Authors
    1. Huixiao Yang
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    2. Tianyi Liu
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    3. Bin Xu
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    4. Chunxin Liu
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    Corresponding author

    Correspondence to Shaowei Huang.

    Additional information

    Communicated by R. Burdon

    This article is part of Topical Collection on Complex Traits

    Huixiao Yang and Tianyi Liu contributed equally to this work.

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    Figure S1

    Frequency distribution of phenotypic traits from a pooled sample of all three populations. STR, stem straightness (values are on a scale of 1–5); CW, crown width (m); WG, length of whorl growth (m); BRN, branch number; BRA, branch angle (1–6); WN, whorl number; NL, needle length (cm), only for population A. (DOCX 25 kb)

    Figure S2

    Genomic DNA concentration and quality of the polymerase chain reaction (PCR) amplification. (DOCX 67 kb)

    Table S1

    PCR amplification system for the SRAP, SSR, EST, and ISSR markers. (DOCX 19 kb)

    Table S2

    QTL detection using the Kruskal-Wallis test and interval mapping for form traits. (DOCX 27 kb)

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    Yang, H., Liu, T., Xu, B. et al. QTL detection for growth and form traits in three full-sib pedigrees of Pinus elliottii var. elliottii × P. caribaea var. hondurensis hybrids. Tree Genetics & Genomes 11, 130 (2015). https://doi.org/10.1007/s11295-015-0954-y

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    • DOI: https://doi.org/10.1007/s11295-015-0954-y

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