Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar

Xia, Wenxiu; Xiao, Zheng’ang; Cao, Pei; Zhang, Yan; Du, Kebing; Wang, Nian

doi:10.1007/s00425-018-2958-y

Original Article
Published: 07 August 2018

Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar

Wenxiu Xia¹^na1,
Zheng’ang Xiao¹^na1,
Pei Cao¹,
Yan Zhang¹,
Kebing Du¹ &
Nian Wang ORCID: orcid.org/0000-0001-9185-4199^1,2

Planta volume 248, pages 1173–1185 (2018)Cite this article

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Abstract

Main conclusion

High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar.

Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics. Here, we generated a high-quality and dense genetic map for an F1 poplar population using high-throughput NGS-based genotyping. A total of 92,097 high-quality SNP markers were developed by stringent filtering and identification. In total, 889 and 1650 SNPs formed the female and male genetic maps, respectively. To test the application of the genetic maps, QTL mapping of leaf shape was conducted for this F1 population. A total of nine parameters were scored for leaf shape variation in three different environments. Combining genetic maps and measurements of the nine leaf shape parameters, we mapped a total of 42 significant QTLs. The highest LOD score of all QTLs was 9.2, and that QTL explained the most (15.13%) trait variation. A total of nine QTLs could be detected in at least two environments, and they were located in two genomic regions. Within these two QTL regions, some candidate genes for regulating leaf shape were predicted through functional annotation. The successful mapping of leaf shape QTLs demonstrated the utility of our genetic maps. According to the performance of this study, we were able to provide high-quality and dense genetic maps and dissect the leaf shape variation in poplar.

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Abbreviations

CI:: Confidence interval
GBS:: Genotyping by sequencing
GWAS:: Genome-wide association
LPI:: Leaf plastochron index
LOD:: Logarithm of odds
NGS:: Next generation sequencing
QTL:: Quantity trait locus

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Acknowledgements

Financial support for this work was provided by the National Natural Science Foundation of China (NSFC Accession No. 31670651 and No. 31570665) and Fundamental Research Funds for the Central Universities (No. 520902-0900202801). The authors are grateful to American Journal Experts (AJE) for improving the English in this paper.

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Wenxiu Xia and Zheng’ang Xiao contributed equally.

Affiliations

College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
Wenxiu Xia, Zheng’ang Xiao, Pei Cao, Yan Zhang, Kebing Du & Nian Wang
Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
Nian Wang

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Wenxiu Xia
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Zheng’ang Xiao
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Pei Cao
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Yan Zhang
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Kebing Du
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Nian Wang
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Correspondence to Kebing Du or Nian Wang.

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Xia, W., Xiao, Z., Cao, P. et al. Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar. Planta 248, 1173–1185 (2018). https://doi.org/10.1007/s00425-018-2958-y

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Received: 06 June 2018
Accepted: 17 July 2018
Published: 07 August 2018
Issue Date: November 2018
DOI: https://doi.org/10.1007/s00425-018-2958-y

Keywords

Poplars
Genetic maps
QTL mapping
Leaf shape variation