High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

Xianliang Zhu; Qijie Weng; David Bush; Changpin Zhou; Haiwen Zhao; Ping Wang; Fagen Li

doi:10.3389/fpls.2022.1099705

High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

Front Plant Sci. 2023 Jan 18:13:1099705. doi: 10.3389/fpls.2022.1099705. eCollection 2022.

Authors

Xianliang Zhu¹, Qijie Weng¹, David Bush², Changpin Zhou¹, Haiwen Zhao¹, Ping Wang¹, Fagen Li¹

Affiliations

¹ Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China.
² Commonwealth Scientific and Industrial Research Organisation (CRISO) Australian Tree Seed Centre, Canberra, ACT, Australia.

Abstract

Introduction: Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms.

Method: A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis.

Results: Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation.

Discussion: While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.

Keywords: Eucalyptus urophylla × tereticornis; candidate genes; genotyping by sequencing; multi-environment trials; stable QTL.

Grants and funding

This work was financially supported by the Fundamental Research Funds of Chinese Academy of Forestry (CAFYBB2021ZA001; CAFYBB2021SY001; CAFYBB2021QD001-3).