Genetic diversity and population structure in the narrow endemic Chinese walnut Juglans hopeiensis Hu: implications for conservation

Abstract

The conservation of narrow endemic species relies on accurate information regarding their population structure. Juglans hopeiensis Hu (Ma walnut), found only in Hebei province, Beijing, and Tianjin, China, is a threatened tree species valued commercially for its nut and wood. Sequences of two maternally inherited mitochondrial markers and two maternally inherited chloroplast intergenic spacers, three nuclear DNA sequences, and allele sizes from 11 microsatellites were obtained from 108 individuals of J. hopeiensis, Juglans regia, and Juglans mandshurica. Haplotype networks were constructed using NETWORK. Genetic diversity, population differentiation, and analysis of molecular variance (AMOVA) were used to determine genetic structure. MEGA was used to construct phylogenetic trees. Genetic diversity of J. hopeiensis was moderate based on nuclear DNA, but low based on uniparentally inherited mitochondrial DNA and chloroplast DNA. Haplotype networks showed that J. hopeiensis haplotypes were different than haplotypes found in J. regia and J. mandshurica. Allelic variants in nuclear genes that were shared among J. hopeiensis populations were not found in J. regia or J. mandshurica. Sampled populations of J. hopeiensis showed clear genetic structure. The maximum parsimony (MP) tree showed J. hopeiensis to be distinct from J. mandshurica but threatened by hybridization with J. regia and J. mandshurica. J. hopeiensis populations are strongly differentiated from sympatric Juglans species, but they are threatened by small population sizes and hybridization.

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Acknowledgements

The authors wish to thank Shuhai Yin and Yong Wang for sample collection. This work was supported by the National Natural Science Foundation of China (41471038; 31200500; J1210063), the Training Programs of Innovation for graduates (YZZ15062), and Changjiang Scholars and Innovative Research Team in University (IRT1174). Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the US Department of Agriculture and does not imply its approval to the exclusion of other products or vendors that also may be suitable.

Data archiving statement

The haplotype sequences were deposited in GenBank under accession numbers KY660646–KY660676 and KY652952–KY652972.

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Correspondence to Keith Woeste or Peng Zhao.

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Communicated by A. M. Dandekar

Electronic supplementary material

Fig. S1

Nucleotide sequence variation of (a) mtDNA(3-9 and nad5). (b) cpDNA (trnS-G and trnL-F). (c) 15R-8. (d) ITS. (e) Jr5680. Hap=haplotype. The yellow color indicates that “G”, green color indicates that “T”, red color indicates that “A”, blue color indicates that “C” which is different with the consensus sequence, respectively. (PDF 1109 kb)

Fig. S2

Maximum parsimony (MP) trees for all 17 populations of J. regia, J. hopeiensis, and J. mandshurica based on (a) mtDNA (3-9 and nad5), (b) cpDNA (trnS-G and trnL-F), and (c) nrDNA (ITS, 15R-8, and Jr5680) sequences. (PDF 404 kb)

Fig. S3

Mismatch distribution analysis for mtDNA(nad5 and 3-9) (a), cpDNA(trnL-F and trn S-G) (b), and nrDNA (ITS, 15R-8, and Jr5680) (c). (PDF 449 kb)

Fig. S4

Principal coordinate analyses (PCoA) of 108 individuals based on 11 microsatellite loci. Green Circle: Cluster I (J. regia), Red Circle: Cluster II (J. mandshurica), Purple Circle: Cluster III (J. hopeiensis). (GIF 24 kb)

Fig. S5

Isolation by distance (IBD) analysis of J. hopeiensis populations. The plot was generated using the allele data and geographic information from IBD. (PDF 262 kb)

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Hu, Y., Dang, M., Feng, X. et al. Genetic diversity and population structure in the narrow endemic Chinese walnut Juglans hopeiensis Hu: implications for conservation. Tree Genetics & Genomes 13, 91 (2017). https://doi.org/10.1007/s11295-017-1172-6

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Keywords

  • Chinese walnut
  • Hybridization
  • Conservation
  • Genetic differentiation
  • Microsatellites
  • Juglans regia
  • Juglans mandshurica